SGD Publications

Wong ED, Miyasato SR, Aleksander S, Karra K, Nash RS, Skrzypek MS, Weng S, Engel SR, Cherry JM (2023) Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources. Genetics. 2023 May 4;224(1):iyac191. doi: 10.1093/genetics/iyac191. PMID:36607068

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 220(4):iyab224.  doi: 10.1093/genetics/iyab224. [PMID:34897464]

Gene Ontology Consortium (2021) The Gene Ontology resource: enriching a GOld mine.  Nucleic Acids Res. 2021 Jan 8; doi: 10.1093/nar/gkaa1113. [PMID: 33290552]

Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM, Mungall CJ (2020) Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. Open Biol. 2020 Sep 10; doi: 10.1098/rsob.200149. [PMID: 32875947]

Alliance of Genome Resources Consortium (2020) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 2020 Jan 8; doi: 10.1093/nar/gkz813. [PMID: 31552413]

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; doi: 10.1093/database/baaa037. [PMID: 32559296]

Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM; SGD Project (2020) Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. Database (Oxford). 2020 Jan 1; doi: 10.1093/database/baaa008. [PMID: 32128557]

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. [PMID: 31612944]

Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium (2019) Annotation of gene product function from high-throughput studies using the Gene Ontology. Database (Oxford). 2019 Jan 1; doi: 10.1093/database/baz007. [PMID: 30715275]

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. [PMID: 30715277]

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. [PMID: 30224793]

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. [PMID: 29761454]

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. [PMID: 29688362]

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. [PMID: 29140510]

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. [PMID: 28451979]

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. [PMID: 28365719]

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. [PMID: 28365727]

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 Saccharomyces genome database. 2016 Jun 1; pii: baw074. doi: 10.1093/database/baw074. [PMID: 27252399]

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. [PMID: 26989152]

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. [PMID: 26578556]

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. [PMID: 26631132]

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. [PMID:26631126]

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. [PMID: 26631125]

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. [PMID: 26631124]

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. [PMID: 26631123]

Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. [PMID: 25997651]

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. [PMID: 25781462]

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. [PMID: 25313161]

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 [PMID: 25052702]

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. [PMID: 24265222]

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. [PMID: 24374639]

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. [PMID: 23842463]

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. [PMID: 23487186]

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. [PMID: 23396302]

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. [PMID: 22110037]

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. [PMID: 22434830]

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. [PMID: 22434826]

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. [PMID: 22434836]

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. [PMID: 21411447]

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. [PMID: 19906697]

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. [PMID: 20157474]

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. [PMID: 19577472]

Engel SR (2009) Using Model Organism Databases (MODs). Current Protocols Essential Laboratory Techniques. 2009 Jun. doi: 10.1002/9780470089941.et1104s01. [SGDID: S000184022]

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. [PMID: 17982175]

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. [PMID: 17001629]

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. [PMID: 17142221]

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. [PMID: 16381907]

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. [PMID: 15608219]

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. [PMID: 15153302]

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. [PMID: 14681421]

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. [PMID: 12519985]

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.[PMID: 12073322]

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. [PMID: 11752257]

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. [PMID: 11125055]

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. [PMID: 10592186]

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. [PMID: 9847146]

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. [PMID: 9851918]

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. [PMID: 9885151]

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. [PMID: 9399804]

Botstein D, Chervitz SA, Cherry JM. Science 1997 277(5330):1259-1260. Yeast as a model organism. [PMID: 9297238]

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. [PMID: 9159100]

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. [PMID: 9169866]

Cherry, JM. Trends Genet 1995 11-12. Genetic nomenclature guide. Saccharomyces cerevisiae. [PMID: 7660459]