Differences

This shows you the differences between two versions of the page.

--- aboutus [2009/12/23 12:33]
biogridadmin
+++ aboutus [2023/10/16 15:39] (current)
biogridadmin [BioGRID Team]
@@ Line 1: / Line 1: @@
 ====== About the BioGRID ======
-The Biological General Repository for Interaction Datasets (BioGRID) database ([[http://www.thebiogrid.org]]) was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 250,000 interactions from major model organism species, as derived from both high-throughput studies and conventional focused studies. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations. The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database, Flybase and Entrez Gene. Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction.
+The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (**[[https://thebiogrid.org|thebiogrid.org]]**). BioGRID currently holds over **[[statistics|1,740,000 interactions]]** curated from both high-throughput datasets and individual focused studies, as derived from over 70,000+ publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.5 web interface contains new search and display features that enable rapid queries across multiple data types and sources. BioGRID provides interaction data to several model organism databases, resources such as **[[http://www.ncbi.nlm.nih.gov/gene|Entrez-Gene]]**, **[[http://www.yeastgenome.org/|SGD]]**, **[[http://www.arabidopsis.org/|TAIR]]**, **[[http://flybase.org/|FlyBase]]** and other **[[https://wiki.thebiogrid.org/doku.php/partners|interaction meta-databases]]**. The entire BioGRID 3.2 data collection may be **[[http://thebiogrid.org/download.php|downloaded in multiple file formats]]**, including **[[http://www.imexconsortium.org|IMEx]]** compatible PSI MI XML. For developers, BioGRID interactions are also available via a **[[biogridrest|REST based Web Service]]** and **[[biogridplugin2|Cytoscape plugin]]**. All BioGRID documentation is available online in the **[[https://wiki.thebiogrid.org|BioGRID Wiki]]**.
 ** Contact Information **
-  * **EMAIL**: [[biogridadmin@gmail.com]]
+  * **EMAIL**: **[[support@thebiogrid.org]]**
-  * **FAX**: Attention BIOGRID Administrator C/O Mike Tyers @ 416-586-8869
+  * **TWITTER**: **[[http://twitter.com/#!/biogrid|@biogrid]]**
+  * **YOUTUBE**: **[[https://www.youtube.com/channel/UCIdwfNwL9gi4oLBUqDB189g|BioGRID]]**
+  * **GITHUB**: **[[https://github.com/BioGRID|BioGRID]]**
 ===== BioGRID Team =====
-  * **Andrew Chatr-Aryamontri**, [curator, Edinburgh]{{ globe2.png}}
+  * **Lorrie Boucher** [curator, Toronto]
-  * **Andrew Winter**, [curator, Edinburgh]
+  * **Bobby-Joe Breitkreutz** [software engineer, Toronto]
-  * **Bobby-Joe Breitkretuz**, [software engineer, Toronto]
+  * **Christie Chang** [curator, Princeton]
-  * **Chris Stark**, [software engineer, Toronto]
+  * **Andrew Chatr-Aryamontri** [curator, Montreal]
-  * **Jennifer Rust**, [curator, Princeton]
+  * **Kara Dolinski** [co-principal investigator, Princeton]
-  * **Julie Nixon**, [curator, Edinburgh]
+  * **Sonam Dolma** [curator, Toronto]
-  * **Kara Dolinski**, [co-principal investigator, Princeton]
+  * **Nadine Kolas** [curator, Toronto]
-  * **Lorrie Boucher**, [curator, Toronto]
+  * **Genie Leung** [curator, Toronto]
-  * **Michael Livstone**, [curator, Princeton]
+  * **Lara O’Donnell** [curator, Toronto]
-  * **Mike Tyers**, [principal investigator, Edinburgh]
+  * **Rose Oughtred** [curator, Princeton]
-  * **Rose Oughtred**, [curator, Princeton]
+  * **Jennifer Rust** [curator, Princeton]
-  * **Teresa Reguly**, [curator, Toronto]
+  * **Chris Stark** [software engineer, Toronto]
+  * **Mike Tyers** [principal investigator, Montreal]
+  * **Andrew Willems** [curator, Toronto]
+  * **Frederick Zhang** [curator, Toronto]
+==== Alumni ====
+  * **Ashton Breitkreutz** [curator, Toronto]
+  * **Daici Chen** [curator, Montreal]
+  * **Sven Heinicke** [software engineer, Princeton]
+  * **Jodi Hirschman** [curator, Princeton]
+  * **Michael Livstone** [curator, Princeton]
+  * **Rochelle McAdam** [curator, Toronto]
+  * **Julie Nixon** [curator, Edinburgh]
+  * **Sara Oster** [curator, Toronto]
+  * **Lindsay Ramage** [curator, Edinburgh]
+  * **Teresa Reguly** [curator, Toronto]
+  * **Adnane Sellam** [curator, Montreal]
+  * **Jean Tang** [curator, Toronto]
+  * **Chandra Theesfeld** [curator, Princeton]
+  * **Andrew Winter** [curator, Edinburgh]
 ===== BioGRID Funding =====
-{{:nih.png|}}{{ :cihr_logo_big_e.png?315|}}{{ :new_bbsrc_colour.gif?315|}}
+[[https://orip.nih.gov/|{{:nih_orip.png|}}]][[http://www.cihr-irsc.gc.ca/|{{:cihr_logo_big_e.png:?225|}}]]
+NIH - **#R01 RR024031**
+===== BioGRID Publications =====
+{{ :newspaper.png}}
+  * Oughtred R, Rust J, Chang C, Breitkreutz BJ, Stark C, Willems A, Boucher L, Leung G, Kolas N, Zhang F, Dolma S, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M. **The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions**.  Protein Sci. 2020 Oct 18. [ [[https://pubmed.ncbi.nlm.nih.gov/33070389/|Pubmed]], [[https://doi.org/10.1002/pro.3978|Protein Science]] ]
+  * Oughtred R, Stark C, Breitkreutz BJ, Rust J, Boucher L, Chang C, Kolas N, O'Donnell L, Leung G, McAdam R, Zhang F, Dolma S, Willems A, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M. **The BioGRID interaction database: 2019 update**. Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541 [ [[https://www.ncbi.nlm.nih.gov/pubmed/30476227|Pubmed]], [[https://academic.oup.com/nar/article/47/D1/D529/5204333|NAR]] ]
+  * Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O'Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M. **The BioGRID interaction database: 2017 update**. Nucleic Acids Res. 2016 Dec 14;2017(1) [ [[https://www.ncbi.nlm.nih.gov/pubmed/27980099|Pubmed]], [[http://nar.oxfordjournals.org/content/45/D1/D369|NAR]] ]
+  * Oughtred R, Chatr-Aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M. **Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions**. Cold Spring Harb Protoc. 2016 Jan 4;2016(1):pdb.prot088880 [ [[http://www.ncbi.nlm.nih.gov/pubmed/26729909|Pubmed]] ]
+  * Oughtred R, Chatr-Aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M. **BioGRID: A Resource for Studying Biological Interactions in Yeast**. Cold Spring Harb Protoc. 2016 Jan 4;2016(1):pdb.top080754 [ [[http://www.ncbi.nlm.nih.gov/pubmed/26729913|Pubmed]] ]
+  * Wildenhain J, Spitzer M, Dolma S, Jarvik N, White R, Roy M, Griffiths E, Bellows DS, Wright GD, Tyers M. **Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning.** Cell Systems. Dec. 23, 2015, 1(6):383-95. [ [[http://www.ncbi.nlm.nih.gov/pubmed/27136353|Pubmed]] ]
+  * Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M. **The BioGRID interaction database: 2015 update.** Nucleic Acids Research. Nov. 2014, [ [[http://www.ncbi.nlm.nih.gov/pubmed/25428363|Pubmed]] ]
+  * Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Tyers M. **The PhosphoGRID Saccharomyces cerevisiae Protein Phosphorylation Site Database: Version 2.0 Update.** Database (Oxford) May 2013; [ [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653121/|Pubmed]] ]
+  * Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, Reguly T, Breitkreutz A, Sellam A, Chen D, Chang C, Rust JM, Livstone MS, Oughtred R, Dolinski K, Tyers M. **The BioGRID Interaction Database: 2013 update.** Nucleic Acids Res. 2012 Nov 30. [ [[http://www.ncbi.nlm.nih.gov/pubmed/23203989|Pubmed]] ]
+  * Winter AG, Wildenhain J, Tyers M. **BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID.** Bioinformatics, 2011 Apr 1. [ [[http://www.ncbi.nlm.nih.gov/pubmed/21300700|Pubmed]] ]
+  * Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. **The BioGRID Interaction Database: 2011 update.** Nucleic Acids Res. 2010 Nov 11. [ [[http://www.ncbi.nlm.nih.gov/pubmed/21071413|Pubmed]] ]
+  * Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M.  **A global protein kinase and phosphatase interaction network in yeast.** Science. 2010 May 21;328(5981):1043-6. [ [[http://www.ncbi.nlm.nih.gov/pubmed/20489023|Pubmed]] ]
+  * Stark C, Ting-Cheng Su, Breitkreutz A, Lourenco P, Dahabieh M, Breitkreutz BJ, Tyers M, Sadowski I. **PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.** Database. 2010 Jan; Vol. 2010 [ [[http://www.ncbi.nlm.nih.gov/pubmed/20428315|Pubmed]] ]
+  * Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H. **Recurated protein interaction datasets.** Nat Methods. 2009 Jan;6(1):39-46. [ [[http://www.ncbi.nlm.nih.gov/pubmed/19935838|Pubmed]] ]
+  * Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M. **The BioGRID Interaction Database: 2008 update.** Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40. Epub 2007 Nov 13. [ [[http://www.ncbi.nlm.nih.gov/pubmed/18000002|Pubmed]] ]
+  * Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. **Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.** J Biol. 2006;5(4):11. Epub 2006 Jun 8. [ [[http://www.ncbi.nlm.nih.gov/pubmed/16762047|Pubmed]] ]
+  * Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. **BioGRID: a general repository for interaction datasets.** Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9. [ [[http://www.ncbi.nlm.nih.gov/pubmed/16381927|Pubmed]] ]
+  * Breitkreutz BJ, Stark C, Tyers M. **The GRID: the General Repository for Interaction Datasets.** Genome Biol. 2003;4(3):R23. Epub 2003 Feb 27. [ [[http://www.ncbi.nlm.nih.gov/pubmed/12620108|Pubmed]] ]
+  * Breitkreutz BJ, Stark C, Tyers M. **Osprey: a network visualization system.** Genome Biol. 2003;4(3):R23. Epub 2003 Feb 27. [ [[http://www.ncbi.nlm.nih.gov/pubmed/12620107|Pubmed]] ]
+===== BioGRID Affiliations =====
+{{ globe2.png}}
+| [[https://www.systemsbiology.org/people/faculty/aitchison-lab/|John Aitchison Lab]]    | [[http://sites.utoronto.ca/andrewslab/people.shtml|Brenda Andrews Lab]]     | [[http://baderlab.org/Home|Gary Bader Lab]]        | [[http://www.bahlerlab.info/|Jürg Bähler Lab]]    |
+| [[https://www.jax.org/research-and-faculty/research-labs/the-blake-lab|Judy Blake Lab]]    | [[http://www.bs.jhmi.edu/MBG/boekelab/|Jef Boeke Lab]]     | [[http://sites.utoronto.ca/boonelab/|Charlie Boone Lab]]        | [[http://www.princeton.edu/genomics/botstein/|David Botstein Lab]]    |
+| [[http://mint.bio.uniroma2.it/mint/Welcome.do|Gianni Cesarini Lab]]    | [[https://cherrylab.stanford.edu/|Mike Cherry Lab]]     | [[http://proteome.wayne.edu/index.html|Russ Finley Lab]]      | [[http://www.embl.de/research/units/scb/gavin/members/?s_personId=4074|Anne-Claude Gavin Lab]]    |
+| [[http://virus.chem.ucla.edu/|Bill Gelbart Lab]]    | [[http://gingraslab.lunenfeld.ca|Anne-Claude Gingras Lab]]     | [[http://www.ebi.ac.uk/~hhe/|Henning Hermjakob Lab]]      | [[http://www.arabidopsis.org/about/staff.jsp|Eva Huala Lab]]    |
+| [[http://chianti.ucsd.edu/idekerlab/|Trey Ideker Lab]]    | [[https://harper.hms.harvard.edu/|Wade Harper Lab]]    | [[http://www.morrislab.ca/|Quaid Morris Lab]]      | [[http://pawsonlab.mshri.on.ca/|Tony Pawson Lab]]    |
+| [[http://www.bc.biol.ethz.ch/research/peter/people/matthias-peter.html|Matthias Peter Lab]]    | [[https://labs.oicr.on.ca/francis-lab|Francis Ouellette Lab]]     | [[https://dpb.carnegiescience.edu/labs/rhee-lab|Sue Rhee Lab]]      | [[http://biochem.ubc.ca/person/ivan-sadowski/|Ivan Sadowski Lab]]    |
+| [[http://www.sanderlab.org/#/|Chris Sander Lab]]    | [[http://fafner.stanford.edu/~sherlock/|Gavin Sherlock Lab]]     | [[http://snyderlab.stanford.edu/|Mike Snyder Lab]]      | [[https://labs.oicr.on.ca/stein-lab|Lincoln Stein Lab]]    |
+| [[http://wormlab.caltech.edu/|Paul Sternberg Lab]]    | [[http://www.cnio.es/ing/grupos/plantillas/curriculum.asp?pag=1002|Alfonso Valencia Lab]]     | [[http://ion.uoregon.edu/content/westerfield-laboratory|Monte Westerfield Lab]]      | [[http://wodaklab.org/ws/|Shoshana Wodak Lab]]    |
+| [[http://research.lunenfeld.ca/woodgett/|Jim Woodgett Lab]]    |[[http://yaffelab.mit.edu/|Mike Yaffe Lab]]  | [[http://function.princeton.edu/|Olga Troyanskaya Lab]]    |     |