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Publications

Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature 583(7818):744-751. doi:10.1038/s41586-020-2093-3PubMed PMID: 32728240; PubMed Central PMCID: PMC7398618
Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Perspectives on ENCODE. Nature 583(7818):693-698. doi:10.1038/s41586-020-2449-8 PubMed PMID: 32728248.
Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583(7818):699-710. doi:10.1038/s41586-020-2493-4
Luo Y, Hitz BC, Gabdank I, Hilton JA, Kagda MS, Lam B, Myers Z, Sud P, Jou J, Lin K, Baymuradov UK, Graham K, Litton C, Miyasato SR, Strattan JS, Jolanki O, Lee JW, Tanaka FY, Adenekan P, O'Neill E, Cherry JM. (2020) New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 48:D882-D889. doi: 10.1093/nar/gkz1062 PMID: 31713622
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. (2020) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 48:D743-D748. doi: 10.1093/nar/gkz892 PMID: 31612944
Alliance of Genome Resources Consortium. (2020) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 48:D650-D658. doi: 10.1093/nar/gkz813 PMID: 31552413
PMCID: PMC6943066
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). doi: 10.1093/database/baaa008 PMID: 32128557
Jou J, Gabdank I, Luo Y, Lin K, Sud P, Myers Z, Hilton JA, Kagda MS, Lam B, O'Neill E, Adenekan P, Graham K, Baymuradov UK, R Miyasato S, Strattan JS, Jolanki O, Lee JW, Litton C, Y Tanaka F, Hitz BC, Cherry JM. (2019) The ENCODE Portal as an Epigenomics Resource. Curr Protoc Bioinformatics. 68:e89. doi: 10.1002/cpbi.89 PMID: 31751002
Alliance of Genome Resources Consortium. (2019) The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. Genetics. 213:1189-1196. doi: 10.1534/genetics.119.302523 PMID: 31796553
PMCID: PMC6893393
Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J. (2019) Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies. PLoS One. 14:e0221858. doi: 10.1371/journal.pone.0221858 PMID: 31454399
PMCID: PMC6711525
The Gene Ontology Consortium. (2019) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 47:D330-D338. doi: 10.1093/nar/gky1055 PMID: 30395331
PMCID: PMC6323945
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. 47:D550-D558. doi: 10.1093/nar/gky1001 PMID: 30357405
PMCID: PMC6323931
Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BH, Perfetto L, Orchard SE, Engel SR, Cherry JM (2019) Integration of macromolecular complex data into the Saccharomyces Genome Database. Database (Oxford). doi:10.1093/database/baz008 PMID: 30715277
PMCID: PMC6360207
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 Animal (NY) doi:10.1038/s41684-018-0150-4 PMID: 30224793
PMCID: PMC6322546
Gabdank I, Chan ET, Davidson JM, Hilton JA, Davis CA, Baymuradov UK, Narayanan A, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Hitz BC, Sloan CA, Cherry JM. (2018) Prevention of data duplication for high throughput sequencing repositories. Database (Oxford). doi:10.1093/database/bay008 PMID: 29688363
PMCID: PMC5829560
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). doi:10.1093/database/bay007 PMID: 29688362
PMCID: PMC5829562
Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR and JM Cherry. (2018) Saccharomyces Genome Database informs human biology. Nucleic Acids Res. (Database Issue) doi:10.1093/nar/gkx1112.PMID: 29140510
PMCID: PMC5753351
Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK, Narayanan AK, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY and JM Cherry. (2018) The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res. (Database Issue) doi:10.1093/nar/gkx1081; PMCID: PMC5753278
Strande NT, Riggs ER, Buchanan AH, Ceyhan-Birsoy O, DiStefano MT, Dwight SS, Goldstein JL, Ghosh R, Seifert BA, Sneddon TP, Wright MW, Milko LV, Cherry JM, Giovanni MA, Murray MF, O'Daniel JM, Ramos EM, Santani AB, Scott AF, Plon SE, Rehm HL, Martin CL, Berg JS (2017) Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the Clinical Genome Resource. American Journal of Human Genetics doi:10.1016/j.ajhg.2017.04.015PMID:28552198; PMCID: PMC5473734
Wong ED (2017) Exploring Protein Function Using the Saccharomyces Genome Database. Methods Mol. Biol. 1611169-182. PMID:28451979; doi: 10.1007/978-1-4939-7015-5_13
Hitz B, Rowe LD, Podduturi N, Glick D, Baymuradov U, Malladi V, Chan E, Davidson J, Gabdank I, Narayanan A, Onate K, Hilton J, Ho M, Lee B, Miyasato S, Dreszer T, Sloan C, Strattan JS, Tanaka F, Hong EL, Cherry JM (2017) SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PLoS One doi: 10.1371/journal.pone.0175310. PloS One; PMCID: PMC5389787
Kramer MH, Farre JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T (2017) Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol. Cell. 65(4):761-774.e5. doi: 10.1016/j.molcel.2016.12.024. PMID:28132844; PMCID: PMC5439305
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. Database (Oxford). doi: 10.1093/database/bax011. PMID:28365727; PMCID: PMC5467551
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. Database (Oxford). doi: 10.1093/database/bax002. PMID:28365719; PMCID: PMC5467555
Overby CL, Heale B, Aronson S, Cherry JM, Dwight S, Milosavljevic A, Nelson T, Niehaus A, Weaver MA, Ramos EM, Williams MS (2016) Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup. Clin Pharmacol Ther. Feb;99(2):157-60. doi: 10.1002/cpt.270. PMID: 26418054 PMC4724305
Reid CD, Karra K, Chang J, Piskol R, Li Q, Li JB, Cherry JM, Baker JC (2016) XenMine: A genomic interaction tool for the Xenopus community. Dev. Biol. doi: 10.1016/j.ydbio.2016.02.034. PMID:27157655; doi: 10.1016/j.ydbio.2016.02.034
Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel SR, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov KM, Sheppard TK, Skrzypek MS, Weng S, Wong E, Cherry JM (2016). Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. Database (Oxford). doi:10.1093/database/baw074. PMID:27252399; PMCID: PMC4888754
Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM (2016) Principles of metadata organization at the ENCODE data coordination center. Database (Oxford). doi: 10.1093/database/baw001. PMID:26980513; PMCID: PMC4792520
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM (2016) ENCODE data at the ENCODE portal. Nucleic Acids Res. 44(D1):D726-32. doi: 10.1093/nar/gkv1160. PMID:26527727; PMCID: PMC4702836
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. 43(Database Issue):D698-702. doi: 10.1093/nar/gkv1250. PMID:26578556; PMCID: PMC4702884
Engel SR, Weng S, Binkley G, Paskov K, Song G, Cherry JM (2016) From one to many: expanding the Saccharomyces cerevisiae reference genome panel. Database (Oxford). doi: 10.1093/database/baw020 . PMID:26989152; PMCID: PMC4795930
Gene Ontology Consortium. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res. 43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. PMID:25428369; PMCID: PMC4383973
Skrzypek MS, Nash RS. (2015) Biocuration at the Saccharomyces genome database. Genesis 53:450-457 PMID:25997651; PMCID: PMC4545726
Song G, Dickins BJ, Demeter J, Engel S, Gallagher J, Choe K, Dunn B, Snyder M, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PLoS One. 10(3):e0120671. doi: 10.1371/journal.pone.0120671. . 10.1371/journal.pone.0120671PMID: 25781462
PMCID: PMC4363492
Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL (2015) Ontology application and use at the ENCODE DCC. Database (Oxford). doi: 10.1093/database/bav010. . 10.1093/database/bav010PMID: 25776021
PMCID: PMC4360730
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 (2014) The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (Bethesda). 4(3):389-98. doi: 10.1534/g3.113.008995. . PMID:24374639; PMCID: PMC3962479
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. 42(Database issue):D717-25. doi: 10.1093/nar/gkt1158. . PMID:24265222; PMCID: PMC3965049
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; PMCID: PMC4105709
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C (2014) DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration. Database (Oxford). doi: 10.1093/database/bat077. PMID:24319113; PMCID: PMC3706743
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; PMCID: PMC3706743
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. (2013) Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database (Oxford). 2013 Aug 27;2013(0):bat062. doi: 10.1093/database/bat062. PMID:23981286; PMCID: PMC3753819
Sullivan J, Karra K, Moxon SA, Vallejos A, Motenko H, Wong JD, Aleksic J, Balakrishnan R, Binkley G, Harris T, Hitz B, Jayaraman P, Lyne R, Neuhauser S, Pich C, Smith RN, Trinh Q, Cherry JM, Richardson J, Stein L, Twigger S, Westerfield M, Worthey E, Micklem G (2013) InterMOD: integrated data and tools for the unification of model organism research. Sci Rep. doi: 10.1038/srep01802. PMID:23652793; PMCID: PMC3647165
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 PMCID:PMC3567487
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 PMCID:PMC3595989
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T (2013) A gene ontology inferred from molecular networks. Nat. Biotechnol. 31:38-45. PMID:23242164; PMCID: PMC3654867
Boyle A, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Research. 22:1790-1797. PMID: 22955989 PMCID:PMC3431494
Klionsky DJ, Bruford EA, Cherry JM, Hodgkin J, Laulederkind SJ, Singer AG (2012) In the beginning there was babble… Autophagy. 8(8) 1165-1167. PMID:22836666; PMCID: PMC3625114
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 PMCID:PMC3308152
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 PMCID:PMC3308148
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 PMCID:PMC3308158
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Constanzo 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. 40(Database issue):D700-705. PMID: 22110037 PMCID:PMC3245034
Rangarajan A, Schedl T, Yook K, Chan J, Haenel S, Otis L, Faelten S, Depellegrin-Connelly T, Isaacson R, Skrzypek MS, Marygold SJ, Stefancsik R, Cherry JM, Sternberg PW, Müller HM (2011) Toward an interactive article: integrating journals and biological databases. BMC Bioinformatics. 2011: 12 175. PMID:21595960; PMCID: PMC3213741
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C and the BioDBCore Working Group. (2011) Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. PMID:21097465; PMCID: PMC3013734
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) Mar 15:2011:bar004. . PMID:21411447; PMCID: PMC2790299
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, Kolinski K, Botstein D, Cherry JM (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. (Database issue) D433-6 doi: 10.1093/nar/gkp917 . PMID:19906697; PMCID: PMC2808950
Gaudet P, Chisholm R, Berardini T, Dimmer E, Engel SR, Fey P, Hill DP, Howe D, Hu JC, Huntley R, Khodiyar VK, Kishore R, Li D, Lovering RC, McCarthy F, Ni L, Petri V, Siegele DA, Tweedie S, Van Auken K, Wood V, Basu S, Carbon S, Dolan M, Mungall CJ, Dolinski K, Thomas P, Ashburner M, Blake JA, Cherry JM, Lewis SE (2009) The Gene Ontology’s Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput. Biol. v.5(7): e1000431 . PMID:195784317; PMCID: PMC2699109
Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel S, 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 (Oxford) doi: 10.1093/database/bap001. PMID: 20157474 PMCID:PMC2790299
Christie KR, Hong EL, Cherry JM (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 17:286-294. PMID: 19577472 PMICD:PMC3057094
Tian W, Zhang LV, Tasan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP (2008) Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae function. Genome Biol. 9 Suppl 1:S7. Epub. PMID: 18613951 PMCID:PMC2447541
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., 36:D577-D581. PMID: 17982175 PMCID:PMC2238894
Crangle CE, Cherry JM, Hong EL, Zbyslaw A (2007) Mining experimental evidence of molecular function claims from the literature. Bioinformatics, 23:3232-3240. PMID:17942445; PMCID: PMC3041023
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:D468-D471. PMID:17142221; PMCID: PMC1669759
Fisk DG, Sethuraman A, Dolinski K, Balakrishnan R, Binkley G, Christie KR, Schwartz K, Costanzo MC, Dong Q, Dwight SS, Engel SR, Hirschman JE, Hong EL, Lane C, Nash R, Schroeder M, Theesfeld CL, Weng S, Botstein D, Cherry JM (2006) Saccharomyces cerevisiae S288C Genome Annotation: a Working Hypothesis. Yeast, 23:857-865. PMID:17001629; PMCID: PMC3040122
Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao C-C, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, delToro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology, 4:e286. PMID:16933976; PMCID: PMC1557398
Stover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, Nash R, Sethuraman A, Weng S, Cherry JM (2006) Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. Nucleic Acids Res. 34:D500-D503 . PMID:16381920; PMCID: PMC1347417
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:D442-D445. PMID:163819070; PMCID: PMC1347479
Gene Ontology Consortium (Harris MA, Clark JI, Ireland A, Lomax J, Ashburner M, Collins R, Eilbeck K, Lewis S, Mungall C, Richter J, Rubin GM, Shu SQ, Blake JA, Bult C, Diehl A, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, et al.) (2006) The Gene Ontology (GO) Project in 2006. Nucleic Acids Res. 34:D322-D326. . PMID:16381878; PMCID: PMC1347384
Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY (2005) PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res. 33:W262-266. PMID:15980466; PMCID: PMC1160129
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 (2005) Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 33:D374-D377. PMID:15608219; PMCID: PMC539977
Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H (2005) Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation. Proc Natl Acad Sci U S A. 102:1998-2003. PMID:15684073; PMCID: PMC548531
Boyle EL, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G (2004) GO::TermFinder -- Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20:3710-3715. PMID: 15297299PMCID:PMC3037731
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 DB, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane CD, Schroeder M, Weng S, Botstein D, Cherry JM (2004) Saccharomyces Genome Database: Underlying Principles and Organization. Briefings in Bioinfo. 5:9-22. PMID:15153302; PMCID: PMC3037832
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 (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 32:D311-D314. PMID:14681421; PMCID: PMC308767
Gene Ontology Consortium (Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, et al.) (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32:D258-D261. PMID:14681407; PMCID: PMC308770
Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA (2003) SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31:219-223. PMID:12519986; PMCID: PMC165461
Weng S, Dong S, 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 (2003) Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 31:216-218. PMID:12519985; PMCID: PMC165501
Wang W, Cherry JM, Botstein D, Li H (2002) A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 99:16893-16898. PMID:12482955; PMCID: PMC139240
Gutiérrez RA, Ewing RM, Cherry JM, Green PJ (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc. Natl. Acad. Sci. U.S.A. 99:11513-11518. PMID:12167669; PMCID: PMC123287
Issel-Tarver L, Ball CA, Christie KR, Dolinski K, Dwight SS, Fisk DG, Harris MA, Sethuraman A, Botstein D, Cherry JM (2002) The Saccharomyces Genome Database. Methods Enzymol. 350:329-346. PMID:12073322; doi: 10.1016/s0076-6879(02)50972-1
Finkelstein D, Ewing R, Gollub J, Sterky F, Cherry JM, Somerville S (2002) Microarray data quality analysis: lessons from the AFGC project. Plant Mol. Biol. 48:119-131. PMID:11860205; doi: 10.1023/a:1013765922672
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 (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30:69-72. PMID:11752257; PMCID: PMC99086
Ewing RM, Cherry JM (2001) Visualization of expression clusters using Sammon's non-linear mapping. Bioinfomatics 17:658-659. PMID:11448886; doi: 10.1093/bioinformatics/17.7.658
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2001) Creating the Gene Ontology Resource: Design and Implementation. Genome Res. 11:1425-1433. PMID:11483584; PMCID: PMC311077
Ball CA, Cherry JM (2001) Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms. Curr. Opinion in Chem. Biol. 5:86-89. PMID:11166654; PMCID: PMC3040119
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Heng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM (2001) The Stanford Microarray Database. Nucleic Acids Res. 29:152-155. PMID:11125075; PMCID: PMC29818
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 (2001) Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 29:80-81. PMID:11125075; PMCID: PMC29796
The Gene Ontology Consortium. (2000) Gene Ontology: tool for the unification of biology. Nature Genetics 25:25-29. PMID:10802651; PMCID: PMC3037419
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer S, Li PW, Galle RF, George RA, Hoskins RA, Lewis S, Richards S, Ashburner M, Henderson SN, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers Y-HC, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Nelson CR, Miklos GLG, Ferrando JFA, Agbayani A, An H-J, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Burtis KC, Busam D, Butler H, Cadieu E, Cherry JM, et al. (2000) The Genome Sequence of Drosophila melanogaster. Science 287:2185-2195. PMID:10731132; doi: 10.1126/science.287.5461.2185
Rubin GM, Yandell MD, Wortman JR, Miklos GLG, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, et al. (2000) Comparative Genomics of The Eukaryotes. Science 287:2204-2215. PMID:10731134; PMCID: PMC2754258
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 S, Botstein D, Cherry JM (2000) Integrating functional genomic information into the Saccharomyces Genome Database. Nucleic Acids Res. 28:77-80. PMID:10592186; PMCID: PMC102447
Rhee SY, Weng S, Bongard-Pierce DK, Garcia-Hernandez M, Malekian A, Flanders DJ, Cherry JM (1999) Unified Display of Arabidopsis thaliana Physical Maps from AtDB, the A. thaliana Database. Nucleic Acids Res. 27:79-84. PMID:9847147; PMCID: PMC148102
Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekain A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D (1999) Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 27:74-78. PMID:9847146; PMCID: PMC148101
Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D (1998) Expanding Yeast Knowledge Online. Yeast 14:1453-1469. PMID:9885151; PMCID: PMC3037831
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 (1998) Comparing the Complete Protein Sets of Worm and Yeast: Orthology and Divergence. Science 282:2022-2028. PMID:9851918; PMCID: PMC3057080
Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M (1998) Arabidopsis thaliana: A Model Plant for Genome Analysis. Science 282:662-682. PMID:9784120; doi: 10.1126/science.282.5389.662
Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D (1998) SGD - Saccharomyces Genome Database. Nucleic Acids Res. 26:73-79. PMID:9399804 PMCID:PMC147204
Flanders DJ, Weng S, Petel FX, Cherry JM (1998) AtDB, the Arabidopsis thaliana Database, and graphical-web-display of progress by the Arabidopsis Genome Initiative. Nucleic Acids Res. 26:80-84. PMID: 9399805/PCMID:PMC147237
Bevan M, Ecker J, Federspiel N, Davis R, McCombie D, Martienssen R, Chen E, Waterson B, Wilson R, Rounsley S, Venter C, Tabata S, Salanoubat M, Quetier F, Cherry JM, Meinke D (1997) Objective: The Complete Sequence of a Plant Genome. Plant Cell 9: 476-478. PMID:12237361; PMCID: PMC156932
Botstein D, Chervitz SA, Cherry JM (1997) Yeast as a model organism. Science 277:1259-1260. PMID:9297238 PMCID:PMC3039837
Botstein D, Cherry JM (1997) Molecular Linguistics: Extracting Information from Gene and Protein Sequences. Proc. Natl. Acad. Sci. USA 94: 5506-5507. PMID: 9159100 PMCID:PMC34160
Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, ... Cherry JM, et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature 387(Suppl.): 75-78. PMID:9169867
Bussey H, Storms RK, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell B, Badcock K, Badcock K, Benes V, Botstein D, Bowman S, Bruckner M, Carpenter J, Cherry JM, et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 387 (Suppl.): 103-105. PMID:9169875
Dietrich FS, Mulligan J, Hennessy K, Yelton MA, Allen E, Araujo R, Aviles E, Berno A, Brennan T, Carpenter J, Chen E, Cherry JM, et al. (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome V. Nature 387 (Suppl.): 78-81. PMID:9169868 PMCID:PMC3057095
Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D (1997) Genetic and Physical Maps of Saccharomyces cerevisiae. Nature 387 (Suppl.): 67-73. PMID:9169866PMCID:PMC3057085
Somerville C, Flanders D, Cherry JM (1997) Plant Biology in the Post-Gutenberg Era. Plant Physiology 113:1015-1022. PMID:9112765; PMCID: PMC158224
Cherry JM (1995) Genetic nomenclature guide. Saccharomyces cerevisiae. in Trends Genetics Nomenclature Guide, Trends Genetics, pages 11-12. PMID:7660459
Cherry JM (1994) The Internet and Electronic Arabidopsis Information Resources, in Arabidopsis, edited by E. M. Meyerowitz and C. R. Somerville. Cold Spring Harbor Laboratory Press, pages 1149-1159.
Cherry JM, Cartinhour SW (1994) ACEDB, A tool for biological information., in Automated DNA Sequencing and Analysis, edited by M. Adams, C. Fields, and C. Venter. Academic Press, pages 347-356. full text
Hauge BM, Hanley SM, Cartinhour S, Cherry JM, Goodman HM, Koornneef M, Stam P, Chang C, Kempin S, Medrano L, Meyerowitz EM (1993) An integrated genetic/RFLP map of the Arabidopsis thaliana genome. Plant Journal 3:745-754 doi:10.1111/j.1365-313X.1993.00745.x. full text
Cherry JM, Cartinhour SW, Goodman HM (1992) AAtDB, An Arabidopsis thaliana Database. Plant Molecular Biology Reporter 10: 308-309,409-410. abstract
Rong BL, Pavan-Langston D, Weng QP, Martinez R, Cherry JM, Dunkel EC (1991) Detection of herpes simplex virus thymidine kinase and latency-associated transcript gene sequences in human herpetic corneas by polymerase chain reaction amplification. Invest. Ophthalmol. Vis. Sci. 32:1808-1815. PMID: 1851732 abstract
Cherry JM (1991) Codon Usage Table for Xenopus laevis. Methods in Cell Biology 36:675-677. PMID:1811159; doi: 10.1016/s0091-679x(08)60304-0
Couture S, Ellington AD, Gerber AS, Cherry JM, Doudna JA, Green R, Hanna M, Pace U, Rajagopal J, Szostak JW (1990) Mutational Analysis of Conserved Nucleotides in a Self-splicing Group I Intron., J. Mol. Biol. 215:345-358. PMID:1700131; doi: 10.1016/s0022-2836(05)80356-0
Schultes NP, Ellington AD, Cherry JM, Szostak JW (1990) Saccharomyces cerevisiae homoserine kinase is homologous to prokaryotic homoserine kinases., Gene 96:177-180. PMID:2176637; doi: 10.1016/0378-1119(90)90250-u
Doudna JA, Gerber AS, Cherry JM, Szostak JW (1987) Genetic Dissection of an RNA Enzyme., Cold Spring Harb. Symp. Quant. Biol. 52:173-180. PMID:2456876; doi: 10.1101/sqb.1987.052.01.022
Cherry JM, Blackburn EH (1985) The Internally Located Telomeric Sequences in the Germ-Line Chromosomes of Tetrahymena are at the Ends of Transposon-like Elements., Cell 43:747-758. PMID: 3000613 PMID:3000613; doi: 10.1016/0092-8674(85)90248-x
Blackburn EH, Budarf ML, Challoner PB, Cherry JM, Howard EA, Katzen AL, Pan WC, Ryan T (1983) DNA Termini in Ciliate Macronuclei., Cold Spring Harb. Symp. Quant. Biol. 47:1195-1207. PMID: 6407801 PMID:6407801; doi: 10.1101/sqb.1983.047.01.135
Cherry JM, Mackellar W, Moore DJ, Crane FL, Joacobsen LB, Schirrmacher V (1981) Evidence for a Plasma Membrane Redox System on Intact Ascites Tumor Cells with Different Metastatic Capacity., Biochim. Biophys. Acta 634:11-18. PMID:7470494; PDF; doi: 10.1016/0005-2728(81)90123-7
Cherry JM, Buckhout TJ, and Moore DJ (1978) The Absence of Gangliosides in a Higher Plant., Experientia 34:1433-1434. PDF