Integration of new alternative reference strain genome sequences into the Saccharomyces genome database.

Maria C. Costanzo

Giltae Song Rama Balakrishnan Gail Binkley Maria C. Costanzo Kyla S. Dalusag Janos Demeter Stacia R. Engel Sage T. Hellerstedt Kalpana Karra Benjamin C. Hitz Robert S. Nash Kelley M. Paskov Travis K. Sheppard Marek S. Skrzypek Shuai Weng Edith D. Wong J. Michael Cherry Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. 2016 2016 Database J. Biol. Databases Curation https://doi.org/10.1093/database/baw074 https://www.wikidata.org/entity/Q36955745 db/journals/biodb/biodb2016.html#SongBBCDDEHKHNP16

Travis K. Sheppard Benjamin C. Hitz Stacia R. Engel Giltae Song Rama Balakrishnan Gail Binkley Maria C. Costanzo Kyla S. Dalusag Janos Demeter Sage T. Hellerstedt Kalpana Karra Robert S. Nash Kelley M. Paskov Marek S. Skrzypek Shuai Weng Edith D. Wong J. Michael Cherry The Saccharomyces Genome Database Variant Viewer. 698-702 2016 44 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkv1250 https://www.wikidata.org/entity/Q36434900 db/journals/nar/nar44.html#SheppardHESBBCD16

Birgit H. M. Meldal Oscar Forner-Martinez Maria C. Costanzo Jose M. Dana Janos Demeter Marine Dumousseau Selina S. Dwight Anna Gaulton Luana Licata Anna N. Melidoni Sylvie Ricard-Blum Bernd Roechert Marek S. Skrzypek Manu Tiwari Sameer Velankar Edith D. Wong Henning Hermjakob Sandra E. Orchard The complex portal - an encyclopaedia of macromolecular complexes. 479-484 2015 43 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gku975 https://www.wikidata.org/entity/Q35254891 db/journals/nar/nar43.html#MeldalFCDDDDGLMRRSTVWHO15

Maria C. Costanzo Stacia R. Engel Edith D. Wong Paul Lloyd Kalpana Karra Esther T. Chan Shuai Weng Kelley M. Paskov Greg R. Roe Gail Binkley Benjamin C. Hitz J. Michael Cherry Saccharomyces genome database provides new regulation data. 717-725 2014 42 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkt1158 https://www.wikidata.org/entity/Q30699640 db/journals/nar/nar42.html#CostanzoEWLKCWPRBHC14

Julie Park Maria C. Costanzo Rama Balakrishnan J. Michael Cherry Eurie L. Hong CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. 2012 2012 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bas001 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308158/ https://www.wikidata.org/entity/Q35840949 db/journals/biodb/biodb2012.html#ParkCBCH12

J. Michael Cherry Eurie L. Hong Craig Amundsen Rama Balakrishnan Gail Binkley Esther T. Chan Karen R. Christie Maria C. Costanzo Selina S. Dwight Stacia R. Engel Dianna G. Fisk Jodi E. Hirschman Benjamin C. Hitz Kalpana Karra Cynthia J. Krieger Stuart R. Miyasato Robert S. Nash Julie Park Marek S. Skrzypek Matt Simison Shuai Weng Edith D. Wong Saccharomyces Genome Database: the genomics resource of budding yeast. 700-705 2012 40 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkr1029 https://www.wikidata.org/entity/Q29616757 db/journals/nar/nar40.html#CherryHABBCCCDEFHHKKMNPSSWW12

Maria C. Costanzo Julie Park Rama Balakrishnan J. Michael Cherry Eurie L. Hong Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. 2011 2011 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bar004 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067894/ https://www.wikidata.org/entity/Q34742703 db/journals/biodb/biodb2011.html#CostanzoPBCH11

Martha B. Arnaud Marcus C. Chibucos Maria C. Costanzo Jonathan Crabtree Diane O. Inglis Adil Lotia Joshua Orvis Prachi Shah Marek S. Skrzypek Gail Binkley Stuart R. Miyasato Jennifer R. Wortman Gavin Sherlock The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. 420-427 2010 38 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkp751 https://www.wikidata.org/entity/Q33601074 db/journals/nar/nar38.html#ArnaudCCCILOSSBMWS10

Marek S. Skrzypek Martha B. Arnaud Maria C. Costanzo Diane O. Inglis Prachi Shah Gail Binkley Stuart R. Miyasato Gavin Sherlock New tools at the Candida Genome Database: biochemical pathways and full-text literature search. 428-432 2010 38 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkp836 https://www.wikidata.org/entity/Q33600871 db/journals/nar/nar38.html#SkrzypekACISBMS10

Stacia R. Engel Rama Balakrishnan Gail Binkley Karen R. Christie Maria C. Costanzo Selina S. Dwight Dianna G. Fisk Jodi E. Hirschman Benjamin C. Hitz Eurie L. Hong Cynthia J. Krieger Michael S. Livstone Stuart R. Miyasato Robert S. Nash Rose Oughtred Julie Park Marek S. Skrzypek Shuai Weng Edith D. Wong Kara Dolinski David Botstein J. Michael Cherry Saccharomyces Genome Database provides mutant phenotype data. 433-436 2010 38 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkp917 https://www.wikidata.org/entity/Q33515788 db/journals/nar/nar38.html#EngelBBCCDFHHHKLMNOPSWWDBC10

Maria C. Costanzo Marek S. Skrzypek Robert S. Nash Edith D. Wong Gail Binkley Stacia R. Engel Benjamin C. Hitz Eurie L. Hong J. Michael Cherry New mutant phenotype data curation system in the Saccharomyces Genome Database. 2009 2009 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bap001 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790299/ https://www.wikidata.org/entity/Q56890161 db/journals/biodb/biodb2009.html#CostanzoSNWBEHHC09

Eurie L. Hong Rama Balakrishnan Qing Dong Karen R. Christie Julie Park Gail Binkley Maria C. Costanzo Selina S. Dwight Stacia R. Engel Dianna G. Fisk Jodi E. Hirschman Benjamin C. Hitz Cynthia J. Krieger Michael S. Livstone Stuart R. Miyasato Robert S. Nash Rose Oughtred Marek S. Skrzypek Shuai Weng Edith D. Wong Kathy K. Zhu Kara Dolinski David Botstein J. Michael Cherry Gene Ontology annotations at SGD: new data sources and annotation methods. 577-581 2008 36 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkm909 https://www.wikidata.org/entity/Q24650193 db/journals/nar/nar36.html#HongBDCPBCDEFHHKLMNOSWWZDBC08

Martha B. Arnaud Maria C. Costanzo Marek S. Skrzypek Prachi Shah Gail Binkley Christopher Lane Stuart R. Miyasato Gavin Sherlock Sequence resources at the Candida Genome Database. 452-456 2007 35 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkl899 https://www.wikidata.org/entity/Q35179231 db/journals/nar/nar35.html#ArnaudCSSBLMS07

Robert S. Nash Shuai Weng Benjamin C. Hitz Rama Balakrishnan Karen R. Christie Maria C. Costanzo Selina S. Dwight Stacia R. Engel Dianna G. Fisk Jodi E. Hirschman Eurie L. Hong Michael S. Livstone Rose Oughtred Julie Park Marek S. Skrzypek Chandra L. Theesfeld Gail Binkley Qing Dong Christopher Lane Stuart R. Miyasato Anand Sethuraman Mark Schroeder Kara Dolinski David Botstein J. Michael Cherry Expanded protein information at SGD: new pages and proteome browser. 468-471 2007 35 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkl931 https://www.wikidata.org/entity/Q35179250 db/journals/nar/nar35.html#NashWHBCCDEFHHLOPSTBDLMSSDBC07

Jodi E. Hirschman Rama Balakrishnan Karen R. Christie Maria C. Costanzo Selina S. Dwight Stacia R. Engel Dianna G. Fisk Eurie L. Hong Michael S. Livstone Robert S. Nash Julie Park Rose Oughtred Marek S. Skrzypek Barry Starr Chandra L. Theesfeld Jennifer M. Williams Rey Andrada Gail Binkley Qing Dong Christopher Lane Stuart R. Miyasato Anand Sethuraman Mark Schroeder Mayank K. Thanawala Shuai Weng Kara Dolinski David Botstein J. Michael Cherry Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. 442-445 2006 34 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkj117 https://www.wikidata.org/entity/Q25256245 db/journals/nar/nar34.html#HirschmanBCCDEFHLNPOSSTWABDLMSSTWDBC06

Martha B. Arnaud Maria C. Costanzo Marek S. Skrzypek Gail Binkley Christopher Lane Stuart R. Miyasato Gavin Sherlock The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. 358-363 2005 33 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gki003 https://www.wikidata.org/entity/Q24792812 db/journals/nar/nar33.html#ArnaudCSBLMS05

Rama Balakrishnan Karen R. Christie Maria C. Costanzo Kara Dolinski Selina S. Dwight Stacia R. Engel Dianna G. Fisk Jodi E. Hirschman Eurie L. Hong Robert S. Nash Rose Oughtred Marek S. Skrzypek Chandra L. Theesfeld Gail Binkley Qing Dong Christopher Lane Anand Sethuraman Shuai Weng David Botstein J. Michael Cherry Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). 374-377 2005 33 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gki023 https://www.wikidata.org/entity/Q24793481 db/journals/nar/nar33.html#BalakrishnanCCDDEFHHNOSTBDLSWBC05

Selina S. Dwight Rama Balakrishnan Karen R. Christie Maria C. Costanzo Kara Dolinski Stacia R. Engel Becket Feierbach Dianna G. Fisk Jodi E. Hirschman Eurie L. Hong Laurie Issel-Tarver Robert S. Nash Anand Sethuraman Barry Starr Chandra L. Theesfeld Rey Andrada Gail Binkley Qing Dong Christopher Lane Mark Schroeder Shuai Weng David Botstein J. Michael Cherry Saccharomyces genome database: Underlying principles and organisation. 9-22 2004 5 Briefings Bioinform. 1 db/journals/bib/bib5.html#DwightBCCDEFFHHINSSTABDLSWBC04 https://doi.org/10.1093/bib/5.1.9 https://www.wikidata.org/entity/Q34569310

Karen R. Christie Shuai Weng Rama Balakrishnan Maria C. Costanzo Kara Dolinski Selina S. Dwight Stacia R. Engel Becket Feierbach Dianna G. Fisk Jodi E. Hirschman Eurie L. Hong Laurie Issel-Tarver Robert S. Nash Anand Sethuraman Barry Starr Chandra L. Theesfeld Rey Andrada Gail Binkley Qing Dong Christopher Lane Mark Schroeder David Botstein J. Michael Cherry Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. 311-314 2004 32 Nucleic Acids Res. Database-Issue db/journals/nar/nar32.html#ChristieWBCDDEFFHHINSSTABDLSBC04 https://doi.org/10.1093/nar/gkh033 https://www.wikidata.org/entity/Q29619138

Shuai Weng Qing Dong Rama Balakrishnan Karen R. Christie Maria C. Costanzo Kara Dolinski Selina S. Dwight Stacia R. Engel Dianna G. Fisk Eurie L. Hong Laurie Issel-Tarver Anand Sethuraman Chandra L. Theesfeld Rey Andrada Gail Binkley Christopher Lane Mark Schroeder David Botstein J. Michael Cherry Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. 216-218 2003 31 Nucleic Acids Res. 1 db/journals/nar/nar31.html#WengDBCCDDEFHISTABLSBC03 https://doi.org/10.1093/nar/gkg054 https://www.wikidata.org/entity/Q39790370

Qing Dong Rama Balakrishnan Gail Binkley Karen R. Christie Maria C. Costanzo Kara Dolinski Selina S. Dwight Stacia R. Engel Dianna G. Fisk Jodi E. Hirschman Eurie L. Hong Robert S. Nash Laurie Issel-Tarver Anand Sethuraman Chandra L. Theesfeld Shuai Weng David Botstein J. Michael Cherry Gene Function, Metabolic Pathways and Comparative Genomics in Yeast. 437-438 2003 conf/csb/2003 CSB https://doi.org/10.1109/CSB.2003.1227362 https://doi.ieeecomputersociety.org/10.1109/CSB.2003.1227362 db/conf/csb/csb2003.html#DongBBCCDDEFHHNISTWBC03

Maria C. Costanzo Matthew E. Crawford Jodi E. Hirschman Janice E. Kranz Philip Olsen Laura S. Robertson Marek S. Skrzypek Burkhard R. Braun Kelley Lennon-Hopkins Pinar Kondu Carey Lengieza Jodi E. Lew-Smith Michael Tillberg James I. Garrels YPDTM, PombePDTM and WormPDTM: model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information. 75-79 2001 29 Nucleic Acids Res. 1 db/journals/nar/nar29.html#CostanzoCHKORSBHKLLTG01 https://doi.org/10.1093/nar/29.1.75 https://www.wikidata.org/entity/Q24606435

Maria C. Costanzo Jennifer D. Hogan Michael E. Cusick Brian P. Davis Ann M. Fancher Peter E. Hodges Pinar Kondu Carey Lengieza Jodi E. Lew-Smith Carol Lingner Kevin Roberg-Perez Michael Tillberg Joan E. Brooks James I. Garrels The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. 73-76 2000 28 Nucleic Acids Res. 1 db/journals/nar/nar28.html#CostanzoHCDFHKLLLRTBG00 https://doi.org/10.1093/nar/28.1.73 https://www.wikidata.org/entity/Q33610188

Craig Amundsen Rey Andrada Martha B. Arnaud Rama Balakrishnan Gail Binkley David Botstein Burkhard R. Braun Joan E. Brooks Esther T. Chan J. Michael Cherry Marcus C. Chibucos Karen R. Christie Jonathan Crabtree Matthew E. Crawford Michael E. Cusick Kyla S. Dalusag Jose M. Dana Brian P. Davis Janos Demeter Kara Dolinski Qing Dong Selina S. Dwight Stacia R. Engel Ann M. Fancher Becket Feierbach Dianna G. Fisk Oscar Forner-Martinez James I. Garrels Anna Gaulton Sage T. Hellerstedt Henning Hermjakob Jodi E. Hirschman Benjamin C. Hitz Peter E. Hodges Jennifer D. Hogan Eurie L. Hong Diane O. Inglis Laurie Issel-Tarver Kalpana Karra Pinar Kondu Janice E. Kranz Cynthia J. Krieger Christopher Lane Carey Lengieza Kelley Lennon-Hopkins Jodi E. Lew-Smith Luana Licata Carol Lingner Michael S. Livstone Paul Lloyd Adil Lotia Birgit MeldalBirgit H. M. Meldal Anna N. Melidoni Stuart R. Miyasato Robert S. Nash Philip Olsen Sandra E. Orchard Joshua Orvis Rose Oughtred Julie Park Kelley M. Paskov Sylvie Ricard-Blum Kevin Roberg-Perez Laura S. Robertson Greg RoeGreg R. Roe Bernd Roechert Mark Schroeder Anand Sethuraman Prachi Shah Travis K. Sheppard Gavin Sherlock Matt Simison Marine SivadeMarine Dumousseau Marek S. Skrzypek Giltae Song Barry Starr Mayank K. Thanawala Chandra L. Theesfeld Michael Tillberg Manu Tiwari Sameer Velankar Shuai Weng Jennifer M. Williams Edith D. Wong Jennifer R. Wortman Kathy K. Zhu