Literature DB >> 26729913

BioGRID: A Resource for Studying Biological Interactions in Yeast.

Rose Oughtred1, Andrew Chatr-aryamontri2, Bobby-Joe Breitkreutz3, Christie S Chang1, Jennifer M Rust1, Chandra L Theesfeld1, Sven Heinicke1, Ashton Breitkreutz3, Daici Chen2, Jodi Hirschman1, Nadine Kolas3, Michael S Livstone1, Julie Nixon4, Lara O'Donnell3, Lindsay Ramage4, Andrew Winter4, Teresa Reguly3, Adnane Sellam2, Chris Stark3, Lorrie Boucher3, Kara Dolinski1, Mike Tyers5.   

Abstract

The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental evidence codes, an intuitive search interface, and visualization tools enable the discovery of individual gene, protein, or biological network function. BioGRID houses interaction data for the major model organism species--including yeast, nematode, fly, zebrafish, mouse, and human--with particular emphasis on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as pioneer eukaryotic models for network biology. BioGRID has achieved comprehensive curation coverage of the entire literature for these two major yeast models, which is actively maintained through monthly curation updates. As of September 2015, BioGRID houses approximately 335,400 biological interactions for budding yeast and approximately 67,800 interactions for fission yeast. BioGRID also supports an integrated posttranslational modification (PTM) viewer that incorporates more than 20,100 yeast phosphorylation sites curated through its sister database, the PhosphoGRID.
© 2016 Cold Spring Harbor Laboratory Press.

Entities:  

Mesh:

Substances:

Year:  2016        PMID: 26729913      PMCID: PMC5975956          DOI: 10.1101/pdb.top080754

Source DB:  PubMed          Journal:  Cold Spring Harb Protoc        ISSN: 1559-6095


  27 in total

1.  GenBank: update.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

3.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

4.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.

Authors:  Philippe Lamesch; Tanya Z Berardini; Donghui Li; David Swarbreck; Christopher Wilks; Rajkumar Sasidharan; Robert Muller; Kate Dreher; Debbie L Alexander; Margarita Garcia-Hernandez; Athikkattuvalasu S Karthikeyan; Cynthia H Lee; William D Nelson; Larry Ploetz; Shanker Singh; April Wensel; Eva Huala
Journal:  Nucleic Acids Res       Date:  2011-12-02       Impact factor: 16.971

5.  Saccharomyces Genome Database: the genomics resource of budding yeast.

Authors:  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; Rob S Nash; Julie Park; Marek S Skrzypek; Matt Simison; Shuai Weng; Edith D Wong
Journal:  Nucleic Acids Res       Date:  2011-11-21       Impact factor: 16.971

6.  BioGRID: a general repository for interaction datasets.

Authors:  Chris Stark; Bobby-Joe Breitkreutz; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

7.  Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

Authors:  Teresa Reguly; Ashton Breitkreutz; Lorrie Boucher; Bobby-Joe Breitkreutz; Nizar N Batada; Gary C Hon; Chad L Myers; Ainslie Parsons; Helena Friesen; Rose Oughtred; Amy Tong; Chris Stark; Yuen Ho; David Botstein; Brenda Andrews; Charles Boone; Olga G Troyanskya; Trey Ideker; Kara Dolinski; Mike Tyers
Journal:  J Biol       Date:  2006-06-08

8.  Reactome knowledgebase of human biological pathways and processes.

Authors:  Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft; Bernard de Bono; Phani Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alex Kanapin; Suzanna Lewis; Shahana Mahajan; Bruce May; Esther Schmidt; Imre Vastrik; Guanming Wu; Ewan Birney; Lincoln Stein; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2008-11-03       Impact factor: 16.971

9.  The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.

Authors:  Ivan Sadowski; Bobby-Joe Breitkreutz; Chris Stark; Ting-Cheng Su; Matthew Dahabieh; Sheetal Raithatha; Wendy Bernhard; Rose Oughtred; Kara Dolinski; Kris Barreto; Mike Tyers
Journal:  Database (Oxford)       Date:  2013-05-13       Impact factor: 3.451

10.  Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Authors:  Samuel Kerrien; Sandra Orchard; Luisa Montecchi-Palazzi; Bruno Aranda; Antony F Quinn; Nisha Vinod; Gary D Bader; Ioannis Xenarios; Jérôme Wojcik; David Sherman; Mike Tyers; John J Salama; Susan Moore; Arnaud Ceol; Andrew Chatr-Aryamontri; Matthias Oesterheld; Volker Stümpflen; Lukasz Salwinski; Jason Nerothin; Ethan Cerami; Michael E Cusick; Marc Vidal; Michael Gilson; John Armstrong; Peter Woollard; Christopher Hogue; David Eisenberg; Gianni Cesareni; Rolf Apweiler; Henning Hermjakob
Journal:  BMC Biol       Date:  2007-10-09       Impact factor: 7.431

View more
  23 in total

1.  Mal-Light: Enhancing Lysine Malonylation Sites Prediction Problem Using Evolutionary-based Features.

Authors:  Wakil Ahmad; Easin Arafat; Ghazaleh Taherzadeh; Alok Sharma; Shubhashis Roy Dipta; Abdollah Dehzangi; Swakkhar Shatabda
Journal:  IEEE Access       Date:  2020-04-22       Impact factor: 3.367

2.  Investigating genetic-and-epigenetic networks, and the cellular mechanisms occurring in Epstein-Barr virus-infected human B lymphocytes via big data mining and genome-wide two-sided NGS data identification.

Authors:  Cheng-Wei Li; Bo-Ren Jheng; Bor-Sen Chen
Journal:  PLoS One       Date:  2018-08-22       Impact factor: 3.240

3.  dbSAP: single amino-acid polymorphism database for protein variation detection.

Authors:  Ruifang Cao; Yan Shi; Shuangguan Chen; Yimin Ma; Jiajun Chen; Juan Yang; Geng Chen; Tieliu Shi
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

4.  Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid.

Authors:  Victor E Balderas-Hernández; Kevin Correia; Radhakrishnan Mahadevan
Journal:  J Ind Microbiol Biotechnol       Date:  2018-06-06       Impact factor: 3.346

Review 5.  Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae.

Authors:  Christopher D Putnam; Richard D Kolodner
Journal:  Genetics       Date:  2017-07       Impact factor: 4.562

6.  Cellular responses to proteostasis perturbations reveal non-optimal feedback in chaperone networks.

Authors:  Asmita Ghosh; Abhilash Gangadharan; Monika Verma; Sarada Das; Latika Matai; Devi Prasanna Dash; Debasis Dash; Koyeli Mapa; Kausik Chakraborty
Journal:  Cell Mol Life Sci       Date:  2019-01-25       Impact factor: 9.261

7.  Overview of the interactive task in BioCreative V.

Authors:  Qinghua Wang; Shabbir S Abdul; Lara Almeida; Sophia Ananiadou; Yalbi I Balderas-Martínez; Riza Batista-Navarro; David Campos; Lucy Chilton; Hui-Jou Chou; Gabriela Contreras; Laurel Cooper; Hong-Jie Dai; Barbra Ferrell; Juliane Fluck; Socorro Gama-Castro; Nancy George; Georgios Gkoutos; Afroza K Irin; Lars J Jensen; Silvia Jimenez; Toni R Jue; Ingrid Keseler; Sumit Madan; Sérgio Matos; Peter McQuilton; Marija Milacic; Matthew Mort; Jeyakumar Natarajan; Evangelos Pafilis; Emiliano Pereira; Shruti Rao; Fabio Rinaldi; Karen Rothfels; David Salgado; Raquel M Silva; Onkar Singh; Raymund Stefancsik; Chu-Hsien Su; Suresh Subramani; Hamsa D Tadepally; Loukia Tsaprouni; Nicole Vasilevsky; Xiaodong Wang; Andrew Chatr-Aryamontri; Stanley J F Laulederkind; Sherri Matis-Mitchell; Johanna McEntyre; Sandra Orchard; Sangya Pundir; Raul Rodriguez-Esteban; Kimberly Van Auken; Zhiyong Lu; Mary Schaeffer; Cathy H Wu; Lynette Hirschman; Cecilia N Arighi
Journal:  Database (Oxford)       Date:  2016-09-01       Impact factor: 3.451

8.  Multiple-Molecule Drug Design Based on Systems Biology Approaches and Deep Neural Network to Mitigate Human Skin Aging.

Authors:  Shan-Ju Yeh; Jin-Fu Lin; Bor-Sen Chen
Journal:  Molecules       Date:  2021-05-26       Impact factor: 4.411

9.  The Unicellular Ancestry of Groucho-Mediated Repression and the Origins of Metazoan Transcription Factors.

Authors:  Richard R Copley
Journal:  Genome Biol Evol       Date:  2016-06-27       Impact factor: 3.416

10.  Modelling the Structure and Dynamics of Biological Pathways.

Authors:  Laura O'Hara; Alessandra Livigni; Thanos Theo; Benjamin Boyer; Tim Angus; Derek Wright; Sz-Hau Chen; Sobia Raza; Mark W Barnett; Paul Digard; Lee B Smith; Tom C Freeman
Journal:  PLoS Biol       Date:  2016-08-10       Impact factor: 8.029

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.