SGD Publications

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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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. Full-Text PDF | PMID: 9847146
  26. 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
  27. 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
  28. 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
  29. Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. Full-Text PDF | PMID: 9297238
  30. 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
  31. 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
  32. Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. Full-Text PDF | PMID: 7660459
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