SGD Publications

This is a list of publications written by or in collaboration with members of the SGD staff.

1. Engel SR, Wong ED, Nash RS, Aleksander S, Alexander M, Douglass E, Karra K, Miyasato SR, Simison M, Skrzypek MS, Weng S, Cherry JM (2022) New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics. 2022 Apr 4; 220(4):iyab224. doi: 10.1093/genetics/iyab224. Full-Text PDF | PMID:34897464
2. Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM, the SGD Project (2019) Incorporation of a unified protein abundance dataset into the Saccharomyces Genome Database. Database (Oxford). 2020 Jan 1; 2020. doi: 10.1093/database/baaa008. Full-Text PDF | PMID: 32128557
3. Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, Genome Resources TAO (2020) Automated generation of gene summaries at the Alliance of Genome Resources. Database (Oxford). 2020 Jan 1;2020:baaa037. doi: 10.1093/database/baaa037. Full-Text PDF | PMID: 32559296
4. Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15; pii: gkz892. doi: 10.1093/nar/gkz892. Full-Text PDF | PMID: 31612944
5. Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM, the SGD Project (2019) Integration of macromolecular complex data into the Saccharomyces Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008. Full-Text PDF | PMID: 30715277
6. Meldal BHM, Bye-A-Jee H, Gajdoš L, Hammerová Z, Horácková A, Melicher F, Perfetto L, Pokorný D, Lopez MR, Türková A, Wong ED, Xie Z, Casanova EB, Del-Toro N, Koch M, Porras P, Hermjakob H, Orchard S (2019) Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. Nucleic Acids Res. 2019 Jan 8;47(D1):D550-D558. doi: 10.1093/nar/gky1001. Full-Text PDF | PMID:30357405]
7. Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2018) Model organism data evolving in support of translational medicine. Lab Anim (NY). Sep 17; 2018. doi: 10.1038/s41684-018-0150-4. Full-Text PDF | PMID: 30224793
8. Lang OW, Nash RS, Hellerstedt ST, Engel SR, the SGD Project (2018) An Introduction to the Saccharomyces Genome Database (SGD). Methods Mol Biol. 2018 May 15; 1757:21-30. Full-Text PDF | PMID: 29761454
9. Engel SR, Skrzypek MS, Hellerstedt ST, Wong ED, Nash RS, Weng S, Binkley G, Sheppard TK, Karra K, Cherry JM (2018) Updated regulation curation model at the Saccharomyces Genome Database. Database (Oxford). 2018 Jan 1; 2018. doi: 10.1093/database/bay007. Full-Text PDF | PMID: 29140510
10. Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) Saccharomyces genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. doi: 10.1093/nar/gkx1112. Full-Text PDF | PMID: 29140510
11. Wong ED (2017) Exploring Protein Function Using the Saccharomyces Genome Database. Methods Mol Biol. 2017 Apr 28; 1611:169-182. doi: 10.1007/978-1-4939-7015-5_13. Full-Text PDF | PMID: 28365719
12. MacPherson KA, Starr B, Wong ED, Dalusag KS, Hellerstedt ST, Lang OW, Nash RS, Skrzypek MS, Engel SR, Cherry JM (2017) Outreach and online training services at the Saccharomyces Genome Database. 2017 Jan 1; pii: bax002. doi: 10.1093/database/bax002. Full-Text PDF | PMID: 28365719
13. Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the Saccharomyces Genome Database. 2017 Mar 11; pii: bax011. doi: 10.1093/database/bax011. Full-Text PDF | PMID: 28365727
14. Engel SR, MacPherson KA (2016) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2016 Nov. doi: 10.1002/cpet.4. Full-Text PDF
15. 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 Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. Full-Text PDF | PMID: 27252399
16. 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. Full-Text PDF | PMID: 26989152
17. 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. Full-Text PDF | PMID: 26578556
18. 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. Full-Text PDF | PMID: 26631132
19. 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. Full-Text PDF | PMID: 26631126
20. 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. Full-Text PDF | PMID: 26631125
21. 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. Full-Text PDF | PMID: 26631124
22. 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. Full-Text PDF | PMID: 26631123
23. Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. Full-Text PDF | PMID: 25997651
24. 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. Full-Text PDF | PMID: 25781462
25. 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. Full-Text PDF | PMID: 25313161
26. 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 Full-Text PDF | PMID: 25052702
27. 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. Full-Text PDF | PMID: 24265222
28. 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. Full-Text PDF | PMID: 24374639
29. 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. Full-Text PDF | PMID: 23842463
30. 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. Full-Text PDF | PMID: 23487186
31. 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. Full-Text PDF | PMID: 23396302
32. 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. Full-Text PDF | PMID: 22110037
33. 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. Full-Text PDF | PMID: 22434830
34. 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. Full-Text PDF | PMID: 22434826
35. 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. Full-Text PDF | PMID: 22434836
36. 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. Full-Text PDF | PMID: 21411447
37. 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. Full-Text PDF | PMID: 19906697
38. 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. Full-Text PDF | PMID: 20157474
39. 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. Full-Text PDF | PMID: 19577472
40. Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. Full-Text PDF
41. 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. Full-Text PDF | PMID: 17982175
42. 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. Full-Text PDF | PMID: 17001629
43. 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. Full-Text PDF | PMID: 17142221
44. 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. Full-Text PDF | PMID: 16381907
45. 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. Full-Text PDF | PMID: 15608219
46. 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. Full-Text PDF | PMID: 15153302
47. 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. Full-Text PDF | PMID: 14681421
48. 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. Full-Text PDF | PMID: 12519985
49. 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. Full-Text PDF | PMID: 12073322
50. 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. Full-Text PDF | PMID: 11752257
51. 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. Full-Text PDF | PMID: 11125055
52. 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. Full-Text PDF | PMID: 10592186
53. 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. Full-Text PDF | PMID: 9847146
54. 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. Full-Text PDF | PMID: 9851918
55. 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. Full-Text PDF | PMID: 9885151
56. 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. Full-Text PDF | PMID: 9399804
57. Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. Full-Text PDF | PMID: 9297238
58. 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. Full-Text PDF | PMID: 9159100
59. 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. Full-Text PDF | PMID: 9169866
60. Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. Full-Text PDF | PMID: 7660459