https://wiki.yeastgenome.org/api.php?action=feedcontributions&feedformat=atom&user=OwlangSGD-Wiki - User contributions [en]2026-06-15T16:24:00ZUser contributionsMediaWiki 1.31.14https://wiki.yeastgenome.org/index.php?title=File:Engel_2016_UsingModelOrganisms.pdf&diff=399620File:Engel 2016 UsingModelOrganisms.pdf2016-12-12T18:26:02Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399619SGD Publications2016-12-12T18:25:41Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. [[media:Engel_2016_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the <em>Saccharomyces</em> genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399618SGD Publications2016-12-12T18:05:47Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the <em>Saccharomyces</em> genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Webinar_Series&diff=399574SGD Webinar Series2016-08-29T23:00:01Z<p>Owlang: /* Upcoming Webinars */</p>
<hr />
<div>[[File:SGD-webinars.png|center|350px]]<br />
'''About the SGD Webinar Series:''' <br><br />
<br />
The SGD Webinar Series is a series of interactive webcasts aimed at demonstrating the SGD website and the value of yeast as a model organism. Information about previous and upcoming webinars can be found on this page or at the SGD newsfeed (http://www.yeastgenome.org/blog). Video recordings of previous webinars are always uploaded at the SGD YouTube channel (https://www.youtube.com/SaccharomycesGenomeDatabase) <br><br />
<br />
=Upcoming Webinars=<br />
<br />
[[File:sgd_webinar_5_preview.jpg|border|400px]]<br />
===Coming Soon: Exploring Expression Datasets & Coexpressed Genes with SPELL===<br />
'''<big>September 7, 2016 – 9:30 AM PDT</big>'''<br />
<br />
Ever wonder what that "SPELL" expression tool at SGD does and how you would use it for your research? Have questions about what kind of datasets get added to SPELL and where we get them? This short webinar will provide an overview of how to locate informative expression datasets and coexpressed genes with the SPELL tool that SGD hosts.<br />
<br />
To reserve your spot, please register for this event '''[http://bit.ly/SGDwebinar5 here]'''.<br />
<br />
=Previous Webinars=<br />
[[File:SGD-webinars-youtube-1.png|300px||link=https://www.youtube.com/watch?v=57VPZYdttzY]]<br />
===April 6, 2016 – SGD: A Catalyst for Biological Research===<br />
Function is just one of many important angles to consider a gene and its product. Other concepts like regulation, genetic/physical interactions, phenotypes, are critical to understanding how a gene fits into the overall biology of the cell. By quickly connecting users to high-quality annotations, different types of data, and useful tools to explore the yeast genome, SGD acts as a catalyst for biological research and has become an indispensable resource for many scientists. This short webinar provides an overview of the different ways you can find information about your favorite genes in SGD.<br />
<br />
<br />
[[File:SGD-webinars-youtube-2.png|300px||link=https://www.youtube.com/watch?v=-Qefg1gm7ho]]<br />
===May 4, 2016 – Predicting Chemotherapy Targets in YeastMine===<br />
If you’re not already using YeastMine to answer all your questions about ''S. cerevisiae'' genes and gene products… you should be! SGD's YeastMine is a powerful search tool that can retrieve, compare, and analyze data on thousands of genes at a time, greatly reducing the time needed to answer practical research questions. Through YeastMine, questions such as "What proportion of plasma membrane proteins are essential?" or "How many different gene products physically interact with the mitochondrial ribosome?" can be answered within minutes. This short webinar provides a brief tutorial on how to run queries and save gene lists in YeastMine, and demonstrates a research scenario where yeast-human homology data is used to predict potential chemotherapy targets.<br />
:For reference, the list of human tumor suppressors that was analyzed during the webinar is provided here: [[File:TSGene-LOFdataset.xlsx]]<br />
<br />
<br />
[[File:sgd-webinars-3-youtube2.png|300px||link=https://www.youtube.com/watch?v=VuruioRRlqw]]<br />
===June 1, 2016 – Exploring Your Favorite Genes with SGD's Genome Browser===<br />
SGD's JBrowse is a quick and easy way to browse through the information-rich yeast genome. Using JBrowse, you can visualize spatial relationships between genes, locate SGD annotations throughout the yeast genome, and compare chromosomal features to hundreds of experimental data sets. This short webinar demonstrates how to navigate the genome with JBrowse, locate your favorite genes or chromosomal features, and visualize experimental data with data tracks. Whether you're an experienced GBrowse user looking to try JBrowse for the first time or someone new to genome browsing as a whole, this webinar is sure to help you get started.<br />
<br />
<br />
[[File:sgd-webinars-4-youtube.jpg|300px||link=https://www.youtube.com/watch?v=hVO3BpbCEzk]]<br />
===August 3, 2016 – Comparing Yeast Strains with SGD's Sequence Variant Viewer===<br />
SGD's Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used ''S. cerevisiae'' strains. This brief webinar demonstrates how to use Variant Viewer to compare nucleotide and amino acid sequences of different ''S. cerevisiae'' genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_August_2016&diff=399573SGD Newsletter, August 20162016-08-29T19:13:27Z<p>Owlang: </p>
<hr />
<div><br />
[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the August 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==SGD's new Faceted Search Tool==<br />
[[File:faceted_search_youtube.jpg|link=https://www.youtube.com/watch?v=hw4LZJJSHMw|300px]][[File:newsletter2016_newsearch.png|thumb|200px|Explore all the data available at SGD using the facets of our new search!]]<br />
<br>You may have noticed that SGD has a new look, but the recent changes have not been limited to a website makeover. Introducing SGD's new '''Faceted Search''' that allows you to refine your search results by categories! Our developers have been hard at work creating a new search that will not only help you easily find what you are looking for, but also will also allow you to explore more of what SGD has to offer.<br />
<br />
If you aren't sure where to start, click the "Try this?" button on the [http://www.yeastgenome.org homepage] for a random query like [http://www.yeastgenome.org/search?q=polymerase "polymerase"]. From there, you can play around with the various facets to explore all the different types of pages that have to do with "polymerase", like GO term pages, gene pages, reference pages, contig pages, and more!<br />
<br />
For more help, check out our [https://www.youtube.com/watch?v=hw4LZJJSHMw video tutorial] or [http://www.yeastgenome.org/cgi-bin/suggestion contact us]. We'd love to hear from you!<br />
<br><br />
<br />
==Updated Genome Browser (JBrowse)==<br />
[[File:JBrowse.png|300px|]]<br />
<br>Since the last newletter, we have upgraded to JBrowse for our genome browser which improves on the speed of the browser's response and features a search option for data tracks based on author, pmid, topic of the publication and more! To learn about the various features for navigation, searching for data tracks, and uploading data tracks, check out our help videos that can be found through our [https://www.youtube.com/SaccharomycesGenomeDatabase Youtube channel's] [https://www.youtube.com/playlist?list=PL0VHJdmmIuj88wZKi9FsnlBkriSUZlYYt playlist on JBrowse]!<br />
<br />
*[https://www.youtube.com/watch?v=NNA_egurX0A SGD Help: Navigating JBrowse] <br />
*[https://www.youtube.com/watch?v=mH6kwbqiLiQ SGD Help: Downloading Sequences in JBrowse]<br />
*[https://www.youtube.com/watch?v=VWBN75bJpbc SGD Help: Working with Data Tracks in JBrowse]<br />
*[https://www.youtube.com/watch?v=OVh1c1xS25s SGD Help: Downloading and Uploading JBrowse Data Tracks]<br />
*[https://www.youtube.com/watch?v=HUI-of9IYXo SGD Help: Uploading Gene Lists to JBrowse]<br />
<br />
Keep an eye out for updates on JBrowse as we are looking to regularly add '''new data tracks'''. If you have a publication in mind whose data you would like to see incorporated into our genome browser, please [http://www.yeastgenome.org/cgi-bin/suggestion send us a message] so we can add it to JBrowse!<br />
<br><br />
<br />
==Three New YeastMine Templates!==<br />
[[File:newsletter2016_newYMtemplate_utr.png|600px|Check out our new YeastMine template for retrieving the UTRs (untranslated regions) of a list of genes]]<br />
<br>We have been getting a lot of user feedback requesting UTR information at SGD recently so in response to your input, SGD has put together a new '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=global Gene-->UTR]''' template under the 'Expression' templates in [http://yeastmine.yeastgenome.org/ YeastMine]! The UTRs are based off transcripts from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] dataset and the results display information on other datasets that confirm these results.<br />
<br />
We've also added two new templates for protein half-life information based on the data from a study by [http://www.yeastgenome.org/reference/S000178561/overview Christiano et al 2014]. You can retrieve the half-life information on a list of genes using the '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Protein_Half_Life&scope=all Gene-->Protein Half-life]''' template or get a list of genes that have a half-life within a given range by using the '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinHalfLife_Range&scope=all Retrieve-->Proteins with half-life in a given range]''' template. Both of these templates can be found in the "Templates" section of YeastMine under the "Protein" category.<br />
<br />
Thank you to all who wrote in and be sure to check out the new templates!<br />
<br><br />
<br />
==Upcoming SGD Webinar: September 7==<br />
[[File:SGDwebinars-redbud.png|175px]][[File:sgd_webinar_5_preview.jpg|thumb|300px|The SPELL tool stands for "Serial Pattern of Expression Levels Locator" which helps you search expression datasets at SGD]]<br />
===Exploring Expression Datasets & Coexpressed Genes with SPELL===<br />
The next SGD webinar in our Webinar Series is scheduled for ''' September 7th, 2016, 9:30 AM PDT.''' Ever wonder what that "SPELL" expression tool at SGD does and how you would use it for your research? Have questions about what kind of datasets get added to SPELL and where we get them? This short webinar will provide an overview of how to locate informative expression datasets and coexpressed genes with the SPELL tool that SGD hosts.<br />
:<br />
Space for this webinar is limited. To reserve your spot, please register for this event '''[http://bit.ly/SGDwebinar5 here]'''.<br />
<br />
To read about and register for SGD's latest webinars, or to browse the videos and materials of past webinars, visit our SGD Webinars page here: [http://wiki.yeastgenome.org/index.php/SGD_Webinar_Series SGD Webinars]<br />
<br><br />
<br />
==The ALLIANCE of Genome Resources==<br />
[[File:alliance_logo.png|300px]]<br />
<br>Recently, SGD has teamed up with [http://www.wormbase.org/#012-34-5 WormBase], [http://flybase.org/ FlyBase], [https://zfin.org/ ZFIN], [http://www.informatics.jax.org/ MGI], [http://rgd.mcw.edu/ RGD], and the [http://geneontology.org/ Gene Ontology Consortium] to establish the '''Alliance of Genome Resources'''. One of the goals for the Alliance is to provide users (you!) with an integrated approach of accessing the data from all of the Model Organism Databases. This will also provide us with an opportunity to join forces in our tool development efforts to better serve user demand. Read more about the Alliance in the "Genes to Genomes" [http://genestogenomes.org/model-organism-databases-join-forces-announcing-the-alliance-of-genome-resources/ blog post] by the Genetics Society of America.<br />
<br />
''We are still looking for feedback'' on input for development and on future directions. Please help us by filling out a short [http://www.yeastgenome.org/alliance-of-genome-resources-survey survey] for the Alliance.<br />
<br />
We’d like to thank everyone that signed the [http://www.genetics-gsa.org/MODSupport/ letter] to Dr. Francis Collins, Director, NIH. Over 11,000 signatures were collected. The letter and signatures was presented to Dr. Collins just before the TAGC meeting. He responded to the letter during his [http://genestogenomes.org/policy-points-collins-reports-model-organism-funding-at-tagc16/ keynote address] at TAGC.<br />
<br />
For more updates and announcements on the Alliance, check out the Alliance [https://www.facebook.com/alliancegenome/ Facebook page], or check out our twitter page [https://twitter.com/alliancegenome @alliancegenome].<br />
<br><br />
<br />
==Research Spotlight (Blog Posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
*'''[http://www.yeastgenome.org/keep-only-what-you-need Keep Only What You Need]''' At points throughout the Lord of the Rings trilogy, it was necessary for characters to drop all unnecessary baggage for survival. Similarly, yeast keep very few introns, which says something about the introns that stick around, as [http://www.yeastgenome.org/reference/S000183960/overview Hooks and coworkers] investigate...<br />
*'''[http://www.yeastgenome.org/chocolate-and-coffee-too Chocolate and Coffee Too]''' In addition to bread and booze, we can thank yeast for their role in processing cacao and coffee. [http://www.cell.com/current-biology/pdf/S0960-9822(16)30064-1.pdf Ludlow and coworkers] take a look at the long ignored cacao and coffee strains of yeast and find that they differ greatly from the well-studied wine strains.<br />
*'''[http://www.yeastgenome.org/cant-get-there-like-that Can't Get There Like That]''' A new methodology by [http://www.yeastgenome.org/reference/S000183177/overview Rich and coworkers] shows that duplication is the only way to boost the expression of SUL1, as opposed to taking the “route” of mutation to the promoter region, under sulfate-limiting conditions.<br />
*'''[http://www.yeastgenome.org/sometimes-simple-is-better Sometimes Simple is Better]''' In a recent study, [http://www.yeastgenome.org/reference/S000182601/overview Fernandez-Murray and coworkers] investigate yeast for the answers to a human condition called congenital sideroblastic anemia caused by a mutation in the human homolog of HEM25.<br />
*'''[http://www.yeastgenome.org/friends-with-benefits Friends with Benefits]''' Yet another study by [http://www.yeastgenome.org/reference/S000184329/overview Petty and coworkers] demonstrates the Awesome Power of Yeast Genetics (APOYG) using mutants for the gene GCN5, a cancer related gene that is essential in most eukaryotes, but not yeast!<br><br />
<br />
==New SGD Help Videos==<br />
SGD is actively expanding its library of short video tutorials to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:<br />
<br />
*[https://www.youtube.com/watch?v=AoVfmaZmTK4 YeastMine Scenario: Finding Uncharacterized Subunits of the MTR]<br />
*[https://www.youtube.com/watch?v=NNA_egurX0A SGD Help: Navigating JBrowse] <br />
*[https://www.youtube.com/watch?v=mH6kwbqiLiQ SGD Help: Downloading Sequences in JBrowse]<br />
*[https://www.youtube.com/watch?v=VWBN75bJpbc SGD Help: Working with Data Tracks in JBrowse]<br />
*[https://www.youtube.com/watch?v=OVh1c1xS25s SGD Help: Downloading and Uploading JBrowse Data Tracks]<br />
*[https://www.youtube.com/watch?v=HUI-of9IYXo SGD Help: Uploading Gene Lists to JBrowse]<br />
*[https://www.youtube.com/watch?v=PnYD1D2ZjWU SGD Help: Exploring Expression Datasets with SPELL]<br />
*[https://www.youtube.com/watch?v=hw4LZJJSHMw SGD Help: Introduction to SGD's Faceted Search]<br />
<br />
Videos are accessible via SGD's [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel. If you have a great idea for a video, or would like to see a particular topic covered, feel free to [http://www.yeastgenome.org/cgi-bin/suggestion contact us!]<br />
<br><br />
<br />
==SGD at ''The Allied Genetics Conference'' (TAGC) 2016 in Orlando FL==<br />
[[File:TAGC.png|300px]]<br />
<br><br>In July 2016, members of the SGD staff attended the [http://www.genetics2016.org The Allied Genetics Conference] in Orlando, FL that was organized by the Genetics Society of America. We held a workshop, hosted an exhibit booth, and several of our members presented posters on current SGD projects:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/5/51/Biocuration2015posterBig.pdf Homology Curation at SGD: budding yeast as a model for eukaryotic biology]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Gail Binkley<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/c/cf/TAGC-FindingDataPoster.pdf ''Saccharomyces'' Genome Database: How to find what you are looking for]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Olivia Lang<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/c/c7/TAGC_variantviewer_poster.pdf The ''Saccharomyces'' Genome Database Variant Viewer]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Sage Hellerstedt<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/9/9c/TAGC-PTM-poster.pdf Integrating Post-Translational Modification Data into the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|-<br />
|}<br />
<br />
A big thank you to all of you who stopped by! We are always interested in answering questions and meeting the researchers and users that make up our community. We really appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our both, please feel free to share any comments or suggestions by [http://www.yeastgenome.org/cgi-bin/suggestion contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23tagc16 #TAGC16] on [https://twitter.com/yeastgenome Twitter].<br />
<br><br />
<br />
==SGD swag: out and about==<br />
<br />
''Do you have pictures to share of SGD swag out and about? Send them to SGD curators for possible inclusion in a future newsletter!''<br />
<br />
{|<br />
| [[File:newsletter2016_thelon_river2.jpeg|300px|thumb|left|Brenda Andrews represents SGD with her superbud hat in Northwest Territories Canada on the Thelon River]]<br />
| [[File:newsletter2016_chlcourse_platerace2.jpeg|300px|thumb|The Yeast Genetics and Genomics class competed with other Cold Spring Harbor courses in a plate race]]<br />
|-<br />
| [[File:OrlandoHats.jpg|300px|thumb|Showing off that superbud swag at TAGC16 in Orlando! These yeast champs must have completed the crossword puzzle!]]<br />
|[[File:newsletter2016_superbudwsturgeonv2.jpg|300px|thumb|Karl Kuchler in Lillooett, British Columbia Canada on the Fraser River with a huge white sturgeon. Why, that's a nice hat you're wearing, Karl!]]<br />
|}<br />
<br />
==Recent Publications from SGD Staff==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.75]]<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [http://www.ncbi.nlm.nih.gov/pubmed/26989152 PMID: 26989152]<br><br />
#Song G, Balakrishnan R, Binkley G, Costanzo M, Dalusag K, Demeter J, Engel SR, Hellerstedt S, Karra K, Hitz B, Nash R, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the <em>Saccharomyces</em> genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [http://www.ncbi.nlm.nih.gov/pubmed/27252399 PMID: 27252399]<br><br />
<br><br />
==What else have we been up to lately?==<br />
In addition to The Allied Genetics Conference mentioned above, you may have seen SGD representatives at the following meetings:<br />
<br><br />
*Senior Biocuration Scientist Stacia Engel and PI Mike Cherry attended the [http://www.sib.swiss/events/biocuration2016/ Biocuration 2016] meeting in Geneva Switzerland in April.<br />
*Senior Biocuration Scientists Edith Wong and Rob Nash attended the [http://bigdata.stanford.edu/ Big Data in Biomedicine] meeting at Stanford in May.<br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=16 Yeast Genetics and Genomics] course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br><br />
==Upcoming Meetings==<br />
*[http://icy2016.com/ ICY 2016: 14th International Congress on Yeasts]<br />
:Awaji Yumebutai International Conference Center, Hyogo, Japan<br />
:September 11-15, 2016<br />
:Abstract submission and early registration deadline: June 10, 2016<br />
<br />
*[http://www.embl.de/training/events/2016/EAE16-01/index.html Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]<br />
:EMBL Heidelberg, Germany<br />
:October 19 - 23, 2016<br />
:Abstract deadline: July 24, 2016<br />
:Registration deadline: August 17, 2016<br />
<br />
*[http://www.yeastlipidconference.com/next-ylc-2017.html 13th Yeast Lipid Conference]<br />
:AgroParisTech Claude Bernard campus, Paris, France<br />
:May 17-19, 2017</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_August_2016&diff=399571SGD Newsletter, August 20162016-08-26T17:03:15Z<p>Owlang: </p>
<hr />
<div><br />
[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the August 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==SGD's new Faceted Search Tool==<br />
[[File:faceted_search_youtube.jpg|link=https://www.youtube.com/watch?v=hw4LZJJSHMw|300px]][[File:newsletter2016_newsearch.png|thumb|200px|Explore all the data available at SGD using the facets of our new search!]]<br />
<br>You may have noticed that SGD has a new look, but the recent changes have not been limited to a website makeover. Introducing SGD's new '''Faceted Search''' that allows you to refine your search results by categories! Our developers have been hard at work creating a new search that will not only help you easily find what you are looking for, but also will also allow you to explore more of what SGD has to offer.<br />
<br />
If you aren't sure where to start, click the "Try this?" button on the [http://www.yeastgenome.org homepage] for a random query like [http://www.yeastgenome.org/search?q=polymerase "polymerase"]. From there, you can play around with the various facets to explore all the different types of pages that have to do with "polymerase", like GO term pages, gene pages, reference pages, contig pages, and more!<br />
<br />
For more help, check out our [https://www.youtube.com/watch?v=hw4LZJJSHMw video tutorial] or [http://www.yeastgenome.org/cgi-bin/suggestion contact us]. We'd love to hear from you!<br />
<br><br />
<br />
==Updated Genome Browser (JBrowse)==<br />
[[File:JBrowse.png|300px|]]<br />
<br>Since the last newletter, we have upgraded to JBrowse for our genome browser which improves on the speed of the browser's response and features a search option for data tracks based on author, pmid, topic of the publication and more! To learn about the various features for navigation, searching for data tracks, and uploading data tracks, check out our help videos that can be found through our [https://www.youtube.com/SaccharomycesGenomeDatabase Youtube channel's] [https://www.youtube.com/playlist?list=PL0VHJdmmIuj88wZKi9FsnlBkriSUZlYYt playlist on JBrowse]!<br />
<br />
*[https://www.youtube.com/watch?v=NNA_egurX0A SGD Help: Navigating JBrowse] <br />
*[https://www.youtube.com/watch?v=mH6kwbqiLiQ SGD Help: Downloading Sequences in JBrowse]<br />
*[https://www.youtube.com/watch?v=VWBN75bJpbc SGD Help: Working with Data Tracks in JBrowse]<br />
*[https://www.youtube.com/watch?v=OVh1c1xS25s SGD Help: Downloading and Uploading JBrowse Data Tracks]<br />
*[https://www.youtube.com/watch?v=HUI-of9IYXo SGD Help: Uploading Gene Lists to JBrowse]<br />
<br />
Keep an eye out for updates on JBrowse as we are looking to regularly add '''new data tracks'''. If you have a publication in mind whose data you would like to see incorporated into our genome browser, please [http://www.yeastgenome.org/cgi-bin/suggestion send us a message] so we can add it to JBrowse!<br />
<br><br />
<br />
==Three New YeastMine Templates!==<br />
[[File:newsletter2016_newYMtemplate_utr.png|600px|Check out our new YeastMine template for retrieving the UTRs (untranslated regions) of a list of genes]]<br />
<br>We have been getting a lot of user feedback requesting UTR information at SGD recently so in response to your input, SGD has put together a new '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=global Gene-->UTR]''' template under the 'Expression' templates in [http://yeastmine.yeastgenome.org/ YeastMine]! The UTRs are based off transcripts from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] dataset and the results display information on other datasets that confirm these results.<br />
<br />
We've also added two new templates for protein half-life information based on the data from a study by [http://www.yeastgenome.org/reference/S000178561/overview Christiano et al 2014]. You can retrieve the half-life information on a list of genes using the '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Protein_Half_Life&scope=all Gene-->Protein Half-life]''' template or get a list of genes that have a half-life within a given range by using the '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinHalfLife_Range&scope=all Retrieve-->Proteins with half-life in a given range]''' template. Both of these templates can be found in the "Templates" section of YeastMine under the "Protein" category.<br />
<br />
Thank you to all who wrote in and be sure to check out the new templates!<br />
<br><br />
<br />
==Upcoming SGD Webinar: September 7==<br />
[[File:SGDwebinars-redbud.png|175px]][[File:sgd_webinar_5_preview.jpg|thumb|300px|The SPELL tool stands for "Serial Pattern of Expression Levels Locator" which helps you search expression datasets at SGD]]<br />
===Exploring Expression Datasets & Coexpressed Genes with SPELL===<br />
The next SGD webinar in our Webinar Series is scheduled for ''' September 7th, 2016, 9:30 AM PDT.''' Ever wonder what that "SPELL" expression tool at SGD does and how you would use it for your research? Have questions about what kind of datasets get added to SPELL and where we get them? This short webinar will provide an overview of how to locate informative expression datasets and coexpressed genes with the SPELL tool that SGD hosts.<br />
:<br />
Space for this webinar is limited. To reserve your spot, please register for this event '''[http://bit.ly/SGDwebinar5 here]'''.<br />
<br />
To read about and register for SGD's latest webinars, or to browse the videos and materials of past webinars, visit our SGD Webinars page here: [http://wiki.yeastgenome.org/index.php/SGD_Webinar_Series SGD Webinars]<br />
<br><br />
<br />
==The ALLIANCE of Genome Resources==<br />
[[File:alliance_logo.png|300px]]<br />
<br>Recently, SGD has teamed up with [http://www.wormbase.org/#012-34-5 WormBase], [http://flybase.org/ FlyBase], [https://zfin.org/ ZFIN], [http://www.informatics.jax.org/ MGI], [http://rgd.mcw.edu/ RGD], and the [http://geneontology.org/ Gene Ontology Consortium] to establish the '''Alliance of Genome Resources'''. One of the goals for the Alliance is to provide users (you!) with an integrated approach of accessing the data from all of the Model Organism Databases. This will also provide us with an opportunity to join forces in our tool development efforts to better serve user demand. Read more about the Alliance in the "Genes to Genomes" [http://genestogenomes.org/model-organism-databases-join-forces-announcing-the-alliance-of-genome-resources/ blog post] by the Genetics Society of America.<br />
<br />
''We are still looking for feedback'' on input for development and on future directions. Please help us by filling out a short [http://www.yeastgenome.org/alliance-of-genome-resources-survey survey] for the Alliance.<br />
<br />
We’d like to thank everyone that signed the [http://www.genetics-gsa.org/MODSupport/ letter] to Dr. Francis Collins, Director, NIH. Over 11,000 signatures were collected. The letter and signatures was presented to Dr. Collins just before the TAGC meeting. He responded to the letter during his [http://genestogenomes.org/policy-points-collins-reports-model-organism-funding-at-tagc16/ keynote address] at TAGC.<br />
<br />
For more updates and announcements on the Alliance, check out the Alliance [https://www.facebook.com/alliancegenome/ Facebook page], or check out our twitter page [https://twitter.com/alliancegenome @alliancegenome].<br />
<br><br />
<br />
==Research Spotlight (Blog Posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
*'''[http://www.yeastgenome.org/keep-only-what-you-need Keep Only What You Need]''' At points throughout the Lord of the Rings trilogy, it was necessary for characters to drop all unnecessary baggage for survival. Similarly, yeast keep very few introns, which says something about the introns that stick around, as [http://www.yeastgenome.org/reference/S000183960/overview Hooks and coworkers] investigate...<br />
*'''[http://www.yeastgenome.org/chocolate-and-coffee-too Chocolate and Coffee Too]''' In addition to bread and booze, we can thank yeast for their role in processing cacao and coffee. [http://www.cell.com/current-biology/pdf/S0960-9822(16)30064-1.pdf Ludlow and coworkers] take a look at the long ignored cacao and coffee strains of yeast and find that they differ greatly from the well-studied wine strains.<br />
*'''[http://www.yeastgenome.org/cant-get-there-like-that Can't Get There Like That]''' A new methodology by [http://www.yeastgenome.org/reference/S000183177/overview Rich and coworkers] shows that duplication is the only way to boost the expression of SUL1, as opposed to taking the “route” of mutation to the promoter region, under sulfate-limiting conditions.<br />
*'''[http://www.yeastgenome.org/sometimes-simple-is-better Sometimes Simple is Better]''' In a recent study, [http://www.yeastgenome.org/reference/S000182601/overview Fernandez-Murray and coworkers] investigate yeast for the answers to a human condition called congenital sideroblastic anemia caused by a mutation in the human homolog of HEM25.<br />
*'''[http://www.yeastgenome.org/friends-with-benefits Friends with Benefits]''' Yet another study by [http://www.yeastgenome.org/reference/S000184329/overview Petty and coworkers] demonstrates the Awesome Power of Yeast Genetics (APOYG) using mutants for the gene GCN5, a cancer related gene that is essential in most eukaryotes, but not yeast!<br><br />
<br />
==New SGD Help Videos==<br />
SGD is actively expanding its library of short video tutorials to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:<br />
<br />
*[https://www.youtube.com/watch?v=AoVfmaZmTK4 YeastMine Scenario: Finding Uncharacterized Subunits of the MTR]<br />
*[https://www.youtube.com/watch?v=NNA_egurX0A SGD Help: Navigating JBrowse] <br />
*[https://www.youtube.com/watch?v=mH6kwbqiLiQ SGD Help: Downloading Sequences in JBrowse]<br />
*[https://www.youtube.com/watch?v=VWBN75bJpbc SGD Help: Working with Data Tracks in JBrowse]<br />
*[https://www.youtube.com/watch?v=OVh1c1xS25s SGD Help: Downloading and Uploading JBrowse Data Tracks]<br />
*[https://www.youtube.com/watch?v=HUI-of9IYXo SGD Help: Uploading Gene Lists to JBrowse]<br />
*[https://www.youtube.com/watch?v=PnYD1D2ZjWU SGD Help: Exploring Expression Datasets with SPELL]<br />
*[https://www.youtube.com/watch?v=hw4LZJJSHMw SGD Help: Introduction to SGD's Faceted Search]<br />
<br />
Videos are accessible via SGD's [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel. If you have a great idea for a video, or would like to see a particular topic covered, feel free to [http://www.yeastgenome.org/cgi-bin/suggestion contact us!]<br />
<br><br />
<br />
==SGD at ''The Allied Genetics Conference'' (TAGC) 2016 in Orlando FL==<br />
[[File:TAGC.png|300px]]<br />
<br><br>In July 2016, members of the SGD staff attended the [http://www.genetics2016.org The Allied Genetics Conference] in Orlando, FL that was organized by the Genetics Society of America. We held a workshop, hosted an exhibit booth, and several of our members presented posters on current SGD projects:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/5/51/Biocuration2015posterBig.pdf Homology Curation at SGD: budding yeast as a model for eukaryotic biology]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Gail Binkley<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/c/cf/TAGC-FindingDataPoster.pdf ''Saccharomyces'' Genome Database: How to find what you are looking for]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Olivia Lang<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/c/c7/TAGC_variantviewer_poster.pdf The ''Saccharomyces'' Genome Database Variant Viewer]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Sage Hellerstedt<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/9/9c/TAGC-PTM-poster.pdf Integrating Post-Translational Modification Data into the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|-<br />
|}<br />
<br />
A big thank you to all of you who stopped by! We are always interested in answering questions and meeting the researchers and users that make up our community. We really appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our both, please feel free to share any comments or suggestions by [http://www.yeastgenome.org/cgi-bin/suggestion contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23tagc16 #TAGC16] on [https://twitter.com/yeastgenome Twitter].<br />
<br><br />
<br />
==SGD swag: out and about==<br />
<br />
''Do you have pictures to share of SGD swag out and about? Send them to SGD curators for possible inclusion in a future newsletter!''<br />
<br />
{|<br />
| [[File:newsletter2016_thelon_river2.jpeg|300px|thumb|left|Brenda Andrews represents SGD with her superbud hat in Northwest Territories Canada on the Thelon River]]<br />
| [[File:newsletter2016_chlcourse_platerace2.jpeg|300px|thumb|The Yeast Genetics and Genomics class competed with other Cold Spring Harbor courses in a plate race]]<br />
|-<br />
| [[File:OrlandoHats.jpg|300px|thumb|Showing off that superbud swag at TAGC16 in Orlando! These yeast champs must have completed the crossword puzzle!]]<br />
|[[File:newsletter2016_superbudwsturgeonv2.jpg|300px|thumb|Karl Kuchler in Lillooett, British Columbia Canada on the Fraser River with a huge white sturgeon. Why, that's a nice hat you're wearing, Karl!]]<br />
|}<br />
<br />
==Recent Publications from SGD Staff==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.75]]<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [http://www.ncbi.nlm.nih.gov/pubmed/26989152 PMID: 26989152]<br><br />
#Song G, Balakrishnan R, Binkley G, Costanzo M, Dalusag K, Demeter J, Engel SR, Hellerstedt S, Karra K, Hitz B, Nash R, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the <em>Saccharomyces</em> genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [http://www.ncbi.nlm.nih.gov/pubmed/27252399 PMID: 27252399]<br><br />
<br><br />
==What else have we been up to lately?==<br />
In addition to The Allied Genetics Conference mentioned above, you may have seen SGD representatives at the following meetings:<br />
<br><br />
*Senior Biocuration Scientist Stacia Engel and PI Mike Cherry attended the [http://www.sib.swiss/events/biocuration2016/ Biocuration 2016] meeting in Geneva Switzerland in April.<br />
*Senior Biocuration Scientists Edith Wong and Rob Nash, and Assistant Biocuration Scientist Olivia Lang attended the [http://bigdata.stanford.edu/ Big Data in Biomedicine] meeting at Stanford in May.<br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=16 Yeast Genetics and Genomics] course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br><br />
==Upcoming Meetings==<br />
*[http://icy2016.com/ ICY 2016: 14th International Congress on Yeasts]<br />
:Awaji Yumebutai International Conference Center, Hyogo, Japan<br />
:September 11-15, 2016<br />
:Abstract submission and early registration deadline: June 10, 2016<br />
<br />
*[http://www.embl.de/training/events/2016/EAE16-01/index.html Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]<br />
:EMBL Heidelberg, Germany<br />
:October 19 - 23, 2016<br />
:Abstract deadline: July 24, 2016<br />
:Registration deadline: August 17, 2016<br />
<br />
*[http://www.yeastlipidconference.com/next-ylc-2017.html 13th Yeast Lipid Conference]<br />
:AgroParisTech Claude Bernard campus, Paris, France<br />
:May 17-19, 2017</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:alliance_logo.png&diff=399570File:alliance logo.png2016-08-26T16:41:10Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:newsletter2016_newYMtemplate_utr.png&diff=399569File:newsletter2016 newYMtemplate utr.png2016-08-26T16:40:50Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:newsletter2016_chlcourse_platerace2.jpeg&diff=399568File:newsletter2016 chlcourse platerace2.jpeg2016-08-26T16:40:17Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:newsletter2016_superbudwsturgeonv2.jpg&diff=399567File:newsletter2016 superbudwsturgeonv2.jpg2016-08-26T16:39:57Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:OrlandoHats.jpg&diff=399566File:OrlandoHats.jpg2016-08-26T16:39:24Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:newsletter2016_thelon_river2.jpeg&diff=399565File:newsletter2016 thelon river2.jpeg2016-08-26T16:39:13Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:newsletter2016_newsearch.png&diff=399564File:newsletter2016 newsearch.png2016-08-26T16:36:33Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:faceted_search_youtube.jpg&diff=399563File:faceted search youtube.jpg2016-08-26T16:36:10Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Newsletter,_August_2016&diff=399562SGD Newsletter, August 20162016-08-26T16:34:34Z<p>Owlang: Created page with " Category:Newsletter '''About this newsletter:''' <br> This is the August 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new f..."</p>
<hr />
<div><br />
[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the August 2016 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
<br />
==SGD's new Faceted Search Tool==<br />
[[File:faceted_search_youtube.jpg|link=https://www.youtube.com/watch?v=hw4LZJJSHMw|300px]][[File:newsletter2016_newsearch.png|thumb|200px|Explore all the data available at SGD using the facets of our new search!]]<br />
<br>You may have noticed that SGD has a new look, but the recent changes have not been limited to a website makeover. Introducing SGD's new '''Faceted Search''' that allows you to refine your search results by categories! Our developers have been hard at work creating a new search that will not only help you easily find what you are looking for, but also will also allow you to explore more of what SGD has to offer.<br />
<br />
If you aren't sure where to start, click the "Try this?" button on the [http://www.yeastgenome.org homepage] for a random query like [http://www.yeastgenome.org/search?q=polymerase "polymerase"]. From there, you can play around with the various facets to explore all the different types of pages that have to do with "polymerase", like GO term pages, gene pages, reference pages, contig pages, and more!<br />
<br />
For more help, check out our [https://www.youtube.com/watch?v=hw4LZJJSHMw video tutorial] or [http://www.yeastgenome.org/cgi-bin/suggestion contact us]. We'd love to hear from you!<br />
<br><br />
<br />
==Updated Genome Browser (JBrowse)==<br />
[[File:JBrowse.png|300px|]]<br />
<br>Since the last newletter, we have upgraded to JBrowse for our genome browser which improves on the speed of the browser's response and features a search option for data tracks based on author, pmid, topic of the publication and more! To learn about the various features for navigation, searching for data tracks, and uploading data tracks, check out our help videos that can be found through our [https://www.youtube.com/SaccharomycesGenomeDatabase Youtube channel's] [https://www.youtube.com/playlist?list=PL0VHJdmmIuj88wZKi9FsnlBkriSUZlYYt playlist on JBrowse]!<br />
<br />
*[https://www.youtube.com/watch?v=NNA_egurX0A SGD Help: Navigating JBrowse] <br />
*[https://www.youtube.com/watch?v=mH6kwbqiLiQ SGD Help: Downloading Sequences in JBrowse]<br />
*[https://www.youtube.com/watch?v=VWBN75bJpbc SGD Help: Working with Data Tracks in JBrowse]<br />
*[https://www.youtube.com/watch?v=OVh1c1xS25s SGD Help: Downloading and Uploading JBrowse Data Tracks]<br />
*[https://www.youtube.com/watch?v=HUI-of9IYXo SGD Help: Uploading Gene Lists to JBrowse]<br />
<br />
Keep an eye out for updates on JBrowse as we are looking to regularly add '''new data tracks'''. If you have a publication in mind whose data you would like to see incorporated into our genome browser, please [http://www.yeastgenome.org/cgi-bin/suggestion send us a message] so we can add it to JBrowse!<br />
<br><br />
<br />
==Three New YeastMine Templates!==<br />
[[File:newsletter2016_newYMtemplate_utr.png|600px|Check out our new YeastMine template for retrieving the UTRs (untranslated regions) of a list of genes]]<br />
<br>We have been getting a lot of user feedback requesting UTR information at SGD recently so in response to your input, SGD has put together a new '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_UTRs&scope=global Gene-->UTR]''' template under the 'Expression' templates in [http://yeastmine.yeastgenome.org/ YeastMine]! The UTRs are based off transcripts from the [http://www.yeastgenome.org/reference/S000153368/overview Pelachano et al 2013] dataset and the results display information on other datasets that confirm these results.<br />
<br />
We've also added two new templates for protein half-life information based on the data from a study by [http://www.yeastgenome.org/reference/S000178561/overview Christiano et al 2014]. You can retrieve the half-life information on a list of genes using the '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Protein_Half_Life&scope=all Gene-->Protein Half-life]''' template or get a list of genes that have a half-life within a given range by using the '''[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinHalfLife_Range&scope=all Retrieve-->Proteins with half-life in a given range]''' template. Both of these templates can be found in the "Templates" section of YeastMine under the "Protein" category.<br />
<br />
Thank you to all who wrote in and be sure to check out the new templates!<br />
<br><br />
<br />
==Upcoming SGD Webinar: September 7==<br />
[[File:SGDwebinars-redbud.png|175px]][[File:sgd_webinar_5_preview.jpg|thumb|300px|The SPELL tool stands for "Serial Pattern of Expression Levels Locator" which helps you search expression datasets at SGD]]<br />
===Exploring Expression Datasets & Coexpressed Genes with SPELL===<br />
The next SGD webinar in our Webinar Series is scheduled for ''' September 7th, 2016, 9:30 AM PDT.''' Ever wonder what that "SPELL" expression tool at SGD does and how you would use it for your research? Have questions about what kind of datasets get added to SPELL and where we get them? This short webinar will provide an overview of how to locate informative expression datasets and coexpressed genes with the SPELL tool that SGD hosts.<br />
:<br />
Space for this webinar is limited. To reserve your spot, please register for this event '''[http://bit.ly/SGDwebinar5 here]'''.<br />
<br />
To read about and register for SGD's latest webinars, or to browse the videos and materials of past webinars, visit our SGD Webinars page here: [http://wiki.yeastgenome.org/index.php/SGD_Webinar_Series SGD Webinars]<br />
<br><br />
<br />
==The ALLIANCE of Genome Resources==<br />
[[File:alliance_logo.png|300px]]<br />
<br>Recently, SGD has teamed up with [http://www.wormbase.org/#012-34-5 WormBase], [http://flybase.org/ FlyBase], [https://zfin.org/ ZFIN], [http://www.informatics.jax.org/ MGI], [http://rgd.mcw.edu/ RGD], and the [http://geneontology.org/ Gene Ontology Consortium] to establish the '''Alliance of Genome Resources'''. One of the goals for the Alliance is to provide users (you!) with an integrated approach of accessing the data from all of the Model Organism Databases. This will also provide us with an opportunity to join forces in our tool development efforts to better serve user demand. Read more about the Alliance in the "Genes to Genomes" [http://genestogenomes.org/model-organism-databases-join-forces-announcing-the-alliance-of-genome-resources/ blog post] by the Genetics Society of America.<br />
<br />
''We are still looking for feedback'' on input for development and on future directions. Please help us by filling out a short [http://www.yeastgenome.org/alliance-of-genome-resources-survey survey] for the Alliance.<br />
<br />
We’d like to thank everyone that signed the [http://www.genetics-gsa.org/MODSupport/ letter] to Dr. Francis Collins, Director, NIH. Over 11,000 signatures were collected. The letter and signatures was presented to Dr. Collins just before the TAGC meeting. He responded to the letter during his [http://genestogenomes.org/policy-points-collins-reports-model-organism-funding-at-tagc16/ keynote address] at TAGC.<br />
<br />
For more updates and announcements on the Alliance, check out the Alliance [https://www.facebook.com/alliancegenome/ Facebook page], or check out our twitter page [https://twitter.com/alliancegenome @alliancegenome].<br />
<br><br />
<br />
==Research Spotlight (Blog Posts)==<br />
In case you missed them, here are some of the most popular Research Spotlights posted on our blog lately:<br />
*'''[http://www.yeastgenome.org/keep-only-what-you-need Keep Only What You Need]''' At points throughout the Lord of the Rings trilogy, it was necessary for characters to drop all unnecessary baggage for survival. Similarly, yeast keep very few introns, which says something about the introns that stick around, as [http://www.yeastgenome.org/reference/S000183960/overview Hooks and coworkers] investigate...<br />
*'''[http://www.yeastgenome.org/chocolate-and-coffee-too Chocolate and Coffee Too]''' In addition to bread and booze, we can thank yeast for their role in processing cacao and coffee. [http://www.cell.com/current-biology/pdf/S0960-9822(16)30064-1.pdf Ludlow and coworkers] take a look at the long ignored cacao and coffee strains of yeast and find that they differ greatly from the well-studied wine strains.<br />
*'''[http://www.yeastgenome.org/cant-get-there-like-that Can't Get There Like That]''' A new methodology by [http://www.yeastgenome.org/reference/S000183177/overview Rich and coworkers] shows that duplication is the only way to boost the expression of SUL1, as opposed to taking the “route” of mutation to the promoter region, under sulfate-limiting conditions.<br />
*'''[http://www.yeastgenome.org/sometimes-simple-is-better Sometimes Simple is Better]''' In a recent study, [http://www.yeastgenome.org/reference/S000182601/overview Fernandez-Murray and coworkers] investigate yeast for the answers to a human condition called congenital sideroblastic anemia caused by a mutation in the human homolog of HEM25.<br />
*'''[http://www.yeastgenome.org/friends-with-benefits Friends with Benefits]''' Yet another study by [http://www.yeastgenome.org/reference/S000184329/overview Petty and coworkers] demonstrates the Awesome Power of Yeast Genetics (APOYG) using mutants for the gene GCN5, a cancer related gene that is essential in most eukaryotes, but not yeast!<br><br />
<br />
==New SGD Help Videos==<br />
SGD is actively expanding its library of short video tutorials to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:<br />
<br />
*[https://www.youtube.com/watch?v=AoVfmaZmTK4 YeastMine Scenario: Finding Uncharacterized Subunits of the MTR]<br />
*[https://www.youtube.com/watch?v=NNA_egurX0A SGD Help: Navigating JBrowse] <br />
*[https://www.youtube.com/watch?v=mH6kwbqiLiQ SGD Help: Downloading Sequences in JBrowse]<br />
*[https://www.youtube.com/watch?v=VWBN75bJpbc SGD Help: Working with Data Tracks in JBrowse]<br />
*[https://www.youtube.com/watch?v=OVh1c1xS25s SGD Help: Downloading and Uploading JBrowse Data Tracks]<br />
*[https://www.youtube.com/watch?v=HUI-of9IYXo SGD Help: Uploading Gene Lists to JBrowse]<br />
*[https://www.youtube.com/watch?v=PnYD1D2ZjWU SGD Help: Exploring Expression Datasets with SPELL]<br />
*[https://www.youtube.com/watch?v=hw4LZJJSHMw SGD Help: Introduction to SGD's Faceted Search]<br />
<br />
Videos are accessible via SGD's [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel. If you have a great idea for a video, or would like to see a particular topic covered, feel free to [http://www.yeastgenome.org/cgi-bin/suggestion contact us!]<br />
<br><br />
<br />
==SGD at ''The Allied Genetics Conference'' (TAGC) 2016 in Orlando FL==<br />
[[File:TAGC.png|300px]]<br />
<br><br>In July 2016, members of the SGD staff attended the [http://www.genetics2016.org The Allied Genetics Conference] in Orlando, FL that was organized by the Genetics Society of America. We held a workshop, hosted an exhibit booth, and several of our members presented posters on current SGD projects:<br />
<br />
{| width="50%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Presenter <br />
| style="text-align:center;"|Poster Title <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Stacia Engel<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/5/51/Biocuration2015posterBig.pdf Homology Curation at SGD: budding yeast as a model for eukaryotic biology]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Gail Binkley<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/c/cf/TAGC-FindingDataPoster.pdf ''Saccharomyces'' Genome Database: How to find what you are looking for]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Olivia Lang<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/c/c7/TAGC_variantviewer_poster.pdf The ''Saccharomyces'' Genome Database Variant Viewer]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Sage Hellerstedt<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/9/9c/TAGC-PTM-poster.pdf Integrating Post-Translational Modification Data into the ''Saccharomyces'' Genome Database]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Kevin MacPherson<br />
| style="text-align:center;"|[http://wiki.yeastgenome.org/images/4/4b/TAGC_outreach_poster.pdf ''Saccharomyces'' Genome Database: Outreach and online training services]<br />
|-<br />
|}<br />
<br />
A big thank you to all of you who stopped by! We are always interested in answering questions and meeting the researchers and users that make up our community. We really appreciate hearing your thoughts and all the suggestions you shared with us. For those of you who couldn't make it or didn't get a chance to stop by our both, please feel free to share any comments or suggestions by [http://www.yeastgenome.org/cgi-bin/suggestion contacting us]!<br />
<br />
If you would like to see tweets from the conference, search [https://twitter.com/search?q=%23tagc16 #TAGC16] on [https://twitter.com/yeastgenome Twitter].<br />
<br><br />
<br />
==SGD swag: out and about==<br />
<br />
''Do you have pictures to share of SGD swag out and about? Send them to SGD curators for possible inclusion in a future newsletter!''<br />
<br />
{|<br />
| [[File:newsletter2016_thelon_river2.jpeg|300px|thumb|left|Brenda Andrews represents SGD with her superbud hat in Northwest Territories Canada on the Thelon River]]<br />
| [[File:newsletter2016_chlcourse_platerace2.jpeg|300px|thumb|The Yeast Genetics and Genomics class competed with other Cold Spring Harbor courses in a plate race]]<br />
|-<br />
| [[File:OrlandoHats.jpg|350px|thumb|Showing off that superbud swag at TAGC16 in Orlando]]<br />
|[[File:newsletter2016_superbudwsturgeonv2.jpg|300px|thumb|Karl Kuchler in Lillooett, British Columbia Canada on the Fraser River with a huge white sturgeon. Why, that's a nice hat you're wearing, Karl!]]<br />
|}<br />
<br />
==Recent Publications from SGD Staff==<br />
[[File:SuperYeast.jpg|thumb|left|upright=.75]]<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [http://www.ncbi.nlm.nih.gov/pubmed/26989152 PMID: 26989152]<br><br />
#Song G, Balakrishnan R, Binkley G, Costanzo M, Dalusag K, Demeter J, Engel SR, Hellerstedt S, Karra K, Hitz B, Nash R, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the <em>Saccharomyces</em> genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [http://www.ncbi.nlm.nih.gov/pubmed/27252399 PMID: 27252399]<br><br />
<br><br />
==What else have we been up to lately?==<br />
In addition to The Allied Genetics Conference mentioned above, you may have seen SGD representatives at the following meetings:<br />
<br><br />
*Senior Biocuration Scientist Stacia Engel and PI Mike Cherry attended the [http://www.sib.swiss/events/biocuration2016/ Biocuration 2016] meeting in Geneva Switzerland in April.<br />
*Senior Biocuration Scientists Edith Wong and Rob Nash, and Assistant Biocuration Scientist Olivia Lang attended the [http://bigdata.stanford.edu/ Big Data in Biomedicine] meeting at Stanford in May.<br />
*Senior Biocuration Scientist Rob Nash presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=16 Yeast Genetics and Genomics] course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website.<br><br />
==Upcoming Meetings==<br />
*[http://icy2016.com/ ICY 2016: 14th International Congress on Yeasts]<br />
:Awaji Yumebutai International Conference Center, Hyogo, Japan<br />
:September 11-15, 2016<br />
:Abstract submission and early registration deadline: June 10, 2016<br />
<br />
*[http://www.embl.de/training/events/2016/EAE16-01/index.html Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems]<br />
:EMBL Heidelberg, Germany<br />
:October 19 - 23, 2016<br />
:Abstract deadline: July 24, 2016<br />
:Registration deadline: August 17, 2016<br />
<br />
*[http://www.yeastlipidconference.com/next-ylc-2017.html 13th Yeast Lipid Conference]<br />
:AgroParisTech Claude Bernard campus, Paris, France<br />
:May 17-19, 2017</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Song_2016_PMID_27252399.pdf&diff=399534File:Song 2016 PMID 27252399.pdf2016-06-08T23:50:06Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399533SGD Publications2016-06-08T23:49:31Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Weng S, Wong E, Cherry JM (2016) Integration of new alternative reference strain genome sequences into the <em>Saccharomyces</em> genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [[media:Song_2016_PMID_27252399.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/27252399 '''PMID: 27252399''']<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399489SGD Publications2016-03-22T20:01:36Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2016_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399488SGD Publications2016-03-22T20:01:13Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399487SGD Publications2016-03-22T20:00:34Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2016_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399486SGD Publications2016-03-22T20:00:02Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2016) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2016 Jan 4. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399485SGD Publications2016-03-22T19:33:39Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the ''Saccharomyces cerevisiae'' reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The ''Saccharomyces'' Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The ''Saccharomyces'' Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the ''Saccharomyces'' Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) ''Saccharomyces'' Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of ''Saccharomyces cerevisiae'': Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple ''Saccharomyces cerevisiae'' strains at the ''Saccharomyces'' Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the ''Saccharomyces'' Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) ''Saccharomyces'' Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for ''S. cerevisiae'' data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) ''Saccharomyces'' Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the ''Saccharomyces'' Genome Database Project. (2009) New mutant phenotype data curation system in the ''Saccharomyces'' Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the ''Saccharomyces cerevisiae'' genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the ''Saccharomyces'' Genome Database (SGD) presenting an overview of the ''Saccharomyces cerevisiae'' genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the ''Saccharomyces'' Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides tools to identify and analyze sequences from ''Saccharomyces cerevisiae'' and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. ''Saccharomyces'' Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the ''Saccharomyces'' genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the ''Saccharomyces'' Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: ''Saccharomyces'' Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of ''Saccharomyces cerevisiae''. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. ''Saccharomyces cerevisiae''. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399484SGD Publications2016-03-22T19:29:32Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the <i>Saccharomyces cerevisiae</i> reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of ''Saccharomyces cerevisiae''. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Cherry_2016_PMID_26631123.pdf&diff=399483File:Cherry 2016 PMID 26631123.pdf2016-03-22T19:28:44Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Cherry_2016_PMID_26631124.pdf&diff=399482File:Cherry 2016 PMID 26631124.pdf2016-03-22T19:28:35Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Cherry_2016_PMID_26631125.pdf&diff=399481File:Cherry 2016 PMID 26631125.pdf2016-03-22T19:28:24Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Cherry_2016_PMID_26631126.pdf&diff=399480File:Cherry 2016 PMID 26631126.pdf2016-03-22T19:28:13Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399479SGD Publications2016-03-22T19:27:41Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the <i>Saccharomyces cerevisiae</i> reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020. [[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906. [[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399478SGD Publications2016-03-22T19:27:24Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the <i>Saccharomyces cerevisiae</i> reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020.<br />
[[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. [[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922. [[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906.<br />
[[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Cherry_2016_PMID_26631132.pdf&diff=399477File:Cherry 2016 PMID 26631132.pdf2016-03-22T19:27:06Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Engel_2016_PMID_26989152.pdf&diff=399476File:Engel 2016 PMID 26989152.pdf2016-03-22T19:26:48Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399475SGD Publications2016-03-22T19:25:36Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the <i>Saccharomyces cerevisiae</i> reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020.<br />
[[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. <br />
[[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922.<br />
[[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906.<br />
[[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The <i>Saccharomyces</i> Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399474SGD Publications2016-03-22T19:24:53Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the <em>Saccharomyces cerevisiae</em> reference genome panel. 2016 Mar 17; pii: baw020. doi: 10.1093/database/baw020.<br />
[[media:Engel_2016_PMID_26989152.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26989152 '''PMID: 26989152''']<br />
#Cherry JM (2015) The <em>Saccharomyces</em> Genome Database: A Tool for Discovery. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.top083840. doi: 10.1101/pdb.top083840. <br />
[[media:Cherry_2016_PMID_26631132.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631132 '''PMID: 26631132''']<br />
#Cherry JM (2015) The <em>Saccharomyces</em> Genome Database: Exploring Genome Features and Their Annotations. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088922. doi: 10.1101/pdb.prot088922.<br />
[[media:Cherry_2016_PMID_26631126.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631126 '''PMID: 26631126''']<br />
#Cherry JM (2015) The <em>Saccharomyces</em> Genome Database: Gene Product Annotation of Function, Process, and Component. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088914. doi: 10.1101/pdb.prot088914. [[media:Cherry_2016_PMID_26631125.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631125 '''PMID: 26631125''']<br />
#Cherry JM (2015) The <em>Saccharomyces</em> Genome Database: Advanced Searching Methods and Data Mining. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088906. doi: 10.1101/pdb.prot088906.<br />
[[media:Cherry_2016_PMID_26631124.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631124 '''PMID: 26631124''']<br />
#Cherry JM (2015) The <em>Saccharomyces</em> Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes. Cold Spring Harb Protoc. 2015 Dec 2; 2015(12):pdb.prot088898. doi: 10.1101/pdb.prot088898. [[media:Cherry_2016_PMID_26631123.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26631123 '''PMID: 26631123''']<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399434SGD Publications2016-01-05T23:43:37Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015) The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399433SGD Publications2016-01-05T23:28:52Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399432SGD Publications2016-01-05T23:24:29Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR(2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Engel_2009_UsingModelOrganisms.pdf&diff=399431File:Engel 2009 UsingModelOrganisms.pdf2016-01-05T23:24:04Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399430SGD Publications2016-01-05T23:23:35Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Engel SR(2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [[media:Engel_2009_UsingModelOrganisms.pdf| '''Full-Text PDF''']]<br />
<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399429SGD Publications2016-01-05T23:03:32Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Skrzypek_2015_PMID_25997651.pdf&diff=399428File:Skrzypek 2015 PMID 25997651.pdf2016-01-05T23:00:56Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399427SGD Publications2016-01-05T22:59:53Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#1. Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [[media:Skrzypek_2015_PMID_25997651.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=File:Sheppard_2015_PMID_26578556.pdf&diff=399426File:Sheppard 2015 PMID 26578556.pdf2016-01-05T22:57:40Z<p>Owlang: </p>
<hr />
<div></div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399425SGD Publications2016-01-05T22:57:01Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#1. Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399424SGD Publications2016-01-05T22:54:53Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#1. Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.<br />
<br />
[[media:Sheppard_2015_PMID_26578556.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlanghttps://wiki.yeastgenome.org/index.php?title=SGD_Publications&diff=399423SGD Publications2016-01-05T22:53:05Z<p>Owlang: </p>
<hr />
<div>This is a list of publications written by or in collaboration with members of the SGD staff.<br />
<br />
#1. Shepard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM (2015 The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 2015 Nov 17. pii: gkv1250.<br />
<br />
[[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/26578556 '''PMID: 26578556''']<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [[media:Song_2015_PMID_25781462.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']<br />
#Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43(Database issue):D479-84. doi: 10.1093/nar/gku975. [[media:Nucl._Acids_Res.-2015-Meldal-D479-84.pdf | '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25313161 '''PMID: 25313161''']<br />
#Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) doi: 10.1093/database/bau075 [[media:Database-2014-Chibucos-database-bau075.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/25052702 '''PMID: 25052702''']<br />
#Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM (2014) Saccharomyces Genome Database provides new regulation data. Nucleic Acids Res. 2014 Jan 1;42(1):D717-25. doi: 10.1093/nar/gkt1158. [[media:Costanzo_2013_PMID_24265222.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24265222 '''PMID: 24265222''']<br />
#Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM (2013) The reference genome sequence of Saccharomyces cerevisiae: Then and now. Database (Oxford) G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [[media:EngelSR_2013_PMID_24374639.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=24374639 '''PMID: 24374639''']<br />
#Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) doi: 10.1093/database/bat054. [[media:Database-2013-Balakrishnan-database-bat054.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/23842463 '''PMID: 23842463''']<br />
#Engel SR, Cherry JM (2013) The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford) doi: 10.1093/database/bat012. [[media:Engel_2013_PMID_23487186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23487186 '''PMID: 23487186''']<br />
#Wong ED, Karra K, Hitz BC, Hong EL, Cherry JM (2013) The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database (Oxford) doi: 10.1093/database/bat004. [[media:Wong_2013_PMID_23396302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=23396302 '''PMID: 23396302''']<br />
#Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan;40(Database issue):D700-5. [[media:Cherry_2012_PMID_22110037.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22110037 '''PMID: 22110037''']<br />
#Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM (2012) YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit. Database (Oxford) doi: 10.1093/database/bar062. [[media:Balakrishnan_2012_PMID_22434830.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434830 '''PMID: 22434830''']<br />
#Chan ET, Cherry JM (2012) Considerations for creating and annotating the budding yeast Genome Map at SGD: A progress report. Database (Oxford) doi: 10.1093/database/bar057. [[media:Chan_2012_PMID_22434826.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434826 '''PMID: 22434826''']<br />
#Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL (2012) CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database (Oxford) doi: 10.1093/database/bas001. [[media:Park_2012_PMID_22434836.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=22434836 '''PMID: 22434836''']<br />
#Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL (2011) Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) doi: 10.1093/database/bar004. [[media:Costanzo_2011_PMID_21411447.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=21411447 '''PMID: 21411447''']<br />
#Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. [[media:Engel_2009_PMID_19906697.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19906697 '''PMID: 19906697''']<br />
#Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [[media:Costanzo_2009_PMID_20157474.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=20157474 '''PMID: 20157474''']<br />
#Christie KR, Hong EL, Cherry JM. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009 Jul;17(7):286-94. [[media:Christie_2009_PMID_19577472.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=19577472 '''PMID: 19577472''']<br />
#Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. [[media:Hong_2008_PMID_17982175.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17982175 '''PMID: 17982175''']<br />
#Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Michael Cherry J (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12):857-65. [[media:Fisk_2006_PMID_17001629.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17001629 '''PMID: 17001629''']<br />
#Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [[media:Nash_2007_PMID_17142221.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=17142221 '''PMID: 17142221''']<br />
#Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM (2006) Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res 34(Database issue):D442-5. [[media:Hirschman_2006_PMID_16381907.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=16381907 '''PMID: 16381907''']<br />
#Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005 Jan 1; 33 Database Issue:D374-7. [[media:Balakrishnan_2005_PMID_15608219.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15608219 '''PMID: 15608219''']<br />
#Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004 Mar; 5(1):9-22. [[media:Dwight_2004_PMID_15153302.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=15153302 '''PMID: 15153302''']<br />
#Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004 Jan 1; 32 Database issue:D311-4. [[media:Christie_2004_PMID_14681421.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=14681421 '''PMID: 14681421''']<br />
#Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):216-8. [[media:Weng_2003_PMID_12519985.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12519985 '''PMID: 12519985''']<br />
#Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database. Methods Enzymol. 2002 350:329-46. [[media:Issel-Tarver_2002_PMID_12073322.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=12073322 '''PMID: 12073322''']<br />
#Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002 Jan 1; 30(1):69-72. [[media:Dwight_2002_PMID_11752257.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11752257 '''PMID: 11752257''']<br />
#Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001 Jan 1;29(1):80-1. [[media:Ball_2001_PMID_11125055.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=11125055 '''PMID: 11125055''']<br />
#Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM. Nucleic Acids Res 2000 28(1):77-80. Integrating functional genomic information into the saccharomyces genome database. [[media:Ball_2000_PMID_10592186.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=10592186 '''PMID: 10592186''']<br />
#Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock M, Weng S, Zhu Y, Cherry JM, Botstein D. Nucleic Acids Res 1999 27(1):74-8. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. [[media:Chervitz_1999_PMID_9847146.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9847146 '''PMID: 9847146''']<br />
#Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D. Science 1998 282(5396):2022-8. Comparison of the complete protein sets of worm and yeast: orthology and divergence. [[media:Chervitz_1998_PMID_9851918.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9851918 '''PMID: 9851918''']<br />
#Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D. Yeast 1998 Dec;14(16):1453-69. Expanding yeast knowledge online. [[media:Dolinski_1998_PMID_9885151.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9885151 '''PMID: 9885151''']<br />
#Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D. Nucleic Acids Res 1998 26(1):73-80. SGD: Saccharomyces Genome Database. [[media:Cherry_1998_PMID_9399804.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9399804 '''PMID: 9399804''']<br />
#Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [[media:Botstein_1997_PMID_9297238.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9297238 '''PMID: 9297238''']<br />
#Botstein D, Cherry JM. Proc Natl Acad Sci U S A 1997 94(11):5506-5507. Molecular linguistics: extracting information from gene and protein sequences. [[media:Botstein_1997_PMID_9159100.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9159100 '''PMID: 9159100''']<br />
#Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D. Nature 1997 387(6632 Suppl):67-73. Genetic and physical maps of Saccharomyces cerevisiae. [[media:Cherry_1997_PMID_9169866.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=9169866 '''PMID: 9169866''']<br />
#Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [[media:Cherry_1995_PMID_7660459.pdf| '''Full-Text PDF''']] | [http://www.ncbi.nlm.nih.gov/pubmed/?term=7660459 '''PMID: 7660459''']</div>Owlang