Databases > biodbcore-000100

ready Saccharomyces Genome Database

Abbreviation:SGD


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Conditions of Use

Applies to: Data use

Data Versioning

Data Release

Data Curation

Data Access




Connectivity
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No guidelines defined

Models and Formats




Credit

Record Maintainer

  • This record is maintained by stacia

Funds

Maintains

Grant Number(s)

  • 2U41HG002273-13 (National Human Genome Research Institute)

  • 5U41HG001315-18 (National Human Genome Research Institute)


Publications

From one to many: expanding the Saccharomyces cerevisiae reference genome panel.

Engel SR., Weng S., Binkley G., Paskov K., Song G., Cherry JM.
Database (Oxford). 2016

View Paper (PubMed)

The Saccharomyces Genome Database Variant Viewer.

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.
Nucleic Acids Res. 2016

View Paper (PubMed)

The Saccharomyces Genome Database: A Tool for Discovery.

Cherry JM.
Cold Spring Harb Protoc. 2015

View Paper (PubMed)

The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.

Cherry JM.
Cold Spring Harb Protoc. 2015

View Paper (PubMed)

The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.

Cherry JM.
Cold Spring Harb Protoc. 2015

View Paper (PubMed)

The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

Cherry JM.
Cold Spring Harb Protoc. 2015

View Paper (PubMed)

The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes.

Cherry JM.
Cold Spring Harb Protoc. 2015

View Paper (PubMed)

Biocuration at the Saccharomyces Genome Database.

Skrzypek MS., Nash RS.
Genesis. 2015

View Paper (PubMed)

AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae.

Song G., Dickins BJ., Demeter J., Engel S., Dunn B., Cherry JM.
PLoS One. 2015

View Paper (PubMed)

The complex portal - an encyclopaedia of macromolecular complexes.

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.
Nucleic Acids Res. 2014

View Paper (PubMed)

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Chibucos MC., Mungall CJ., Balakrishnan R., Christie KR., Huntley RP., White O., Blake JA., Lewis SE., Giglio M.
Database (Oxford). 2014

View Paper (PubMed)

Saccharomyces Genome Database provides new regulation data.

Costanzo MC., Engel SR., Wong ED., Lloyd P., Karra K., Chan ET., Weng S., Paskov KM., Roe GR., Binkley G., Hitz BC., Cherry JM.
Nucleic Acids Res. 2014

View Paper (PubMed)

The reference genome sequence of Saccharomyces cerevisiae: then and now.

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.
G3 (Bethesda). 2014

View Paper (PubMed)

A guide to best practices for Gene Ontology (GO) manual annotation.

Balakrishnan R., Harris MA., Huntley R., Van Auken K., Cherry JM.
Database (Oxford). 2013

View Paper (PubMed)

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database.

Engel SR., Cherry JM.
Database (Oxford). 2013

View Paper (PubMed)

The YeastGenome app: the Saccharomyces Genome Database at your fingertips.

Wong ED., Karra K., Hitz BC., Hong EL., Cherry JM.
Database (Oxford). 2013

View Paper (PubMed)

YeastMine - An integrated data warehouse for S. cerevisiae data as a multi-purpose tool-kit.

Balakrishnan R., Park J., Karra K., Hitz BC., Binkley G., Hong EL., Sullivan J., Micklem G., Cherry JM.
Database (Oxford). 2012

View Paper (PubMed)

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report.

Chan ET., Cherry JM.
Database (Oxford). 2012

View Paper (PubMed)

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.

Park J., Costanzo MC., Balakrishnan R., Cherry JM., Hong EL.
Database (Oxford). 2012

View Paper (PubMed)

Saccharomyces Genome Database: the genomics resource of budding yeast.

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.
Nucleic Acids Res. 2012

View Paper (PubMed)

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.

Costanzo MC., Park J., Balakrishnan R., Cherry JM., Hong EL.
Database (Oxford). 2011

View Paper (PubMed)

Saccharomyces Genome Database provides mutant phenotype data.

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.
Nucleic Acids Res. 2010

View Paper (PubMed)

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.

Christie KR., Hong EL., Cherry JM.
Trends Microbiol. 2009

View Paper (PubMed)

Using Model Organism Databases (MODs).

Engel SR.
Current Protocols Essential Laboratory Techniques 2009

View Paper (DOI)

New mutant phenotype data curation system in the Saccharomyces Genome Database.

Costanzo MC., Skrzypek MS., Nash R., Wong E., Binkley G, Engel SR., Hitz B., Hong EL., Cherry JM., and the Saccharomyces Genome Database Project.
Database (Oxford). 2009

View Paper (PubMed)

Gene Ontology annotations at SGD: new data sources and annotation methods.

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.
Nucleic Acids Res. 2008

View Paper (PubMed)

Expanded protein information at SGD: new pages and proteome browser.

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.
Nucleic Acids Res. 2007

View Paper (PubMed)

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.

Fisk DG., Ball CA., Dolinski K., Engel SR., Hong EL., Issel-Tarver L., Schwartz K., Sethuraman A., Botstein D., Cherry JM.
Yeast. 2006

View Paper (PubMed)

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

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.
Nucleic Acids Res. 2006

View Paper (PubMed)

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).

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.
Nucleic Acids Res. 2005

View Paper (PubMed)

Saccharomyces genome database: underlying principles and organisation.

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.
Brief Bioinform. 2004

View Paper (PubMed)

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

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.
Nucleic Acids Res. 2004

View Paper (PubMed)

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.

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.
Nucleic Acids Res. 2003

View Paper (PubMed)

Saccharomyces Genome Database

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.
Methods Enzymol. 2002

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Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

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.
Nucleic Acids Res. 2002

View Paper (PubMed)

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data.

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.
Nucleic Acids Res. 2001

View Paper (PubMed)

Integrating functional genomic information into the Saccharomyces genome database.

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

View Paper (PubMed)

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.

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

View Paper (PubMed)

Comparison of the complete protein sets of worm and yeast: orthology and divergence.

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

View Paper (PubMed)

Expanding yeast knowledge online.

Dolinski K., Ball CA., Chervitz SA., Dwight SS., Harris MA., Roberts S., Roe T., Cherry JM., Botstein D.
Yeast. 1998

View Paper (PubMed)

SGD: Saccharomyces Genome Database.

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

View Paper (PubMed)

Yeast as a model organism.

Botstein D., Chervitz SA., Cherry JM.
Science. 1997

View Paper (PubMed)

Molecular linguistics: extracting information from gene and protein sequences.

Botstein D., Cherry JM.
Proc Natl Acad Sci U S A. 1997

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Genetic and physical maps of Saccharomyces cerevisiae.

Cherry JM., Ball C., Weng S., Juvik G., Schmidt R., Adler C., Dunn B., Dwight S., Riles L., Mortimer RK., Botstein D.
Nature. 1997

View Paper (PubMed)

Genetic nomenclature guide. Saccharomyces cerevisiae.

Cherry JM.
Trends Genet. 1995

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