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Gary Bader

Research Profile

Occupations

Activities & Behaviors

Procedures

Protein Interaction Mapping

Chemicals & Drugs

Concepts & Ideas

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Publications

TOP 3
J Montojo; K Zuberi; H Rodriguez; F Kazi; G Wright; S L Donaldson; Quaid Morris; Gary Bader
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
Natalie Yeung; Melissa S Cline; Allan Kuchinsky; Michael E Smoot; Gary Bader
Exploring biological networks with Cytoscape software.
Maital Ashkenazi; Gary Bader; Allan Kuchinsky; Menachem Moshelion; David J States
Cytoscape ESP: simple search of complex biological networks.

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All Publications

2010: J Montojo; K Zuberi; H Rodriguez; F Kazi; G Wright; S L Donaldson; Quaid Morris; Gary Bader
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
Bioinformatics (Oxford, England) 2010;26(22):2927-8.
2008: Natalie Yeung; Melissa S Cline; Allan Kuchinsky; Michael E Smoot; Gary Bader
Exploring biological networks with Cytoscape software.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2008;Chapter 8():Unit 8.13.
2008: Maital Ashkenazi; Gary Bader; Allan Kuchinsky; Menachem Moshelion; David J States
Cytoscape ESP: simple search of complex biological networks.
Bioinformatics (Oxford, England) 2008;24(12):1465-6.
2008: Lucy Skrabanek; Harpreet K Saini; Gary Bader; Anton J Enright
Computational prediction of protein-protein interactions.
Molecular biotechnology 2008;38(1):1-17.
2007: George Zogopoulos; Kevin C H Ha; Faisal Naqib; Sara Moore; Hyeja Kim; Alexandre Montpetit; Frederick Robidoux; Philippe Laflamme; Michelle Cotterchio; Celia Greenwood; Stephen W Scherer; Brent Zanke; Thomas J Hudson; Gary Bader; Steven Gallinger
Germ-line DNA copy number variation frequencies in a large North American population.
Human genetics 2007;122(3-4):345-53.
2007: Sandra Orchard; Lukasz Salwinski; Samuel Kerrien; Luisa Montecchi-Palazzi; Matthias Oesterheld; Volker Stümpflen; Arnaud CEOL; Andrew Chatr-aryamontri; John Armstrong; Peter Woollard; John J Salama; Susan Moore; Jérôme Wojcik; Gary Bader; Marc Vidal; Michael E Cusick; Mark Gerstein; Anne-Claude Gavin; Giulio Superti-Furga; Jack Greenblatt; Joel Bader; Peter Uetz; Mike Tyers; Pierre Legrain; Stan Fields; Nicola Mulder; Michael K Gilson; Michael Niepmann; Lyle Burgoon; Javier De Las Rivas; Carlos Prieto; Victoria M Perreau; Chris Hogue; Hans-Werner Mewes; Rolf Apweiler; Ioannis Xenarios; David Eisenberg; Gianni Cesareni; Henning Hermjakob
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Nature biotechnology 2007;25(8):894-8.
2007: Alfredo Ferro; Rosalba Giugno; Giuseppe Pigola; Alfredo Pulvirenti; D Skripin; Gary Bader; Dennis Shasha
NetMatch: a Cytoscape plugin for searching biological networks.
Bioinformatics (Oxford, England) 2007;23(7):910-2.
2007: Jomol P Mathew; Barry S Taylor; Gary Bader; Saiju Pyarajan; Marco Antoniotti; Arul M Chinnaiyan; Chris Sander; Steven J Burakoff; Bud Mishra
From bytes to bedside: data integration and computational biology for translational cancer research.
PLoS computational biology 2007;3(2):e12.
2007: Melissa S Cline; Michael Smoot; Ethan Cerami; Kuchinsky Allan; 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 Bader
Integration of biological networks and gene expression data using Cytoscape.
Nature protocols 2007;2(10):2366-82.
2007: Samuel Kerrien; Sandra Orchard; Luisa Montecchi-Palazzi; Bruno Aranda; Antony F Quinn; Nisha Vinod; Gary 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 K Gilson; John Armstrong; Peter Woollard; Christopher Hogue; David Eisenberg; Gianni Cesareni; Rolf Apweiler; Henning Hermjakob
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
BMC biology 2007;5():44.
2007: Pingzhao Hu; Gary Bader; Dennis Wigle; Andrew Emili
Computational prediction of cancer-gene function.
Nature reviews. Cancer 2007;7(1):23-34.
2006: Ethan G Cerami; Gary Bader; Benjamin E Gross; Chris Sander
cPath: open source software for collecting, storing, and querying biological pathways.
BMC bioinformatics 2006;7():497.
2006: Gary Bader; Michael P Cary; Chris Sander
Pathguide: a pathway resource list.
Nucleic acids research 2006;34(Database issue):D504-6.
2005: Michael P Cary; Gary Bader; Chris Sander
Pathway information for systems biology.
FEBS letters 2005;579(8):1815-20.
2004: Amy Hin Yan Tong; Guillaume Lesage; Gary Bader; Huiming Ding; Hong Xu; Xiaofeng Xin; James Young; Gabriel F Berriz; Renee L Brost; Michael Chang; YiQun Chen; Xin Cheng; Gordon Chua; Helena Friesen; Debra S Goldberg; Jennifer Haynes; Christine Humphries; Grace He; Shamiza Hussein; Lizhu Ke; Nevan Krogan; Zhijian Li; Joshua N Levinson; Hong Lu; Patrice Ménard; Christella Munyana; Ainslie B Parsons; Owen Ryan; Raffi Tonikian; Tania Roberts; Anne-Marie Sdicu; Jesse Shapiro; Bilal Sheikh; Bernhard Suter; Sharyl L Wong; Lan V Zhang; Hongwei Zhu; Christopher G Burd; Sean Munro; Chris Sander; Jasper Rine; Jack Greenblatt; Matthias Peter; Anthony Bretscher; Graham Bell; Frederick P Roth; Grant W Brown; Brenda Andrews; Howard Bussey; Charles Boone
Global mapping of the yeast genetic interaction network.
Science (New York, N.Y.) 2004;303(5659):808-13.
2004: Henning Hermjakob; Luisa Montecchi-Palazzi; Gary Bader; Jérôme Wojcik; Lukasz Salwinski; Arnaud CEOL; Susan Moore; Sandra Orchard; Ugis Sarkans; Christian von Mering; Bernd Roechert; Sylvain Poux; Eva Jung; Henning Mersch; Paul Kersey; Michael Lappe; Yixue Li; Rong Zeng; Debashis Rana; Macha Nikolski; Holger Husi; Christine Brun; K Shanker; Seth G N Grant; Chris Sander; Peer Bork; Weimin Zhu; Akhilesh Pandey; Alvis Brazma; Bernard Jacq; Marc Vidal; David Sherman; Pierre Legrain; Gianni Cesareni; Ioannis Xenarios; David Eisenberg; Boris Steipe; Chris Hogue; Rolf Apweiler
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Nature biotechnology 2004;22(2):177-83.
2003: Brenda J Andrews; Gary Bader; Charles Boone
Playing tag with the yeast proteome.
Nature biotechnology 2003;21(11):1297-9.
2003: Gary Bader; Adrian Heilbut; Brenda Andrews; Mike Tyers; Timothy Hughes; Charles Boone
Functional genomics and proteomics: charting a multidimensional map of the yeast cell.
Trends in cell biology 2003;13(7):344-56.
2003: Ian Donaldson; Joel Martin; Berry de Bruijn; Cheryl Wolting; Vicki Lay; Brigitte Tuekam; Shudong Zhang; Berivan Baskin; Gary Bader; Katerina Michalickova; Tony Pawson; Christopher W V Hogue
PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine.
BMC bioinformatics 2003;4():11.
2003: Gary Bader; Christopher W V Hogue
An automated method for finding molecular complexes in large protein interaction networks.
BMC bioinformatics 2003;4():2.
2003: Gary Bader; Doron Betel; Christopher W V Hogue
BIND: the Biomolecular Interaction Network Database.
Nucleic acids research 2003;31(1):248-50.
2002: Katerina Michalickova; Gary Bader; Michel Dumontier; Hao Lieu; Doron Betel; Ruth Isserlin; Christopher W V Hogue
SeqHound: biological sequence and structure database as a platform for bioinformatics research.
BMC bioinformatics 2002;3():32.
2002: Amy Hin Yan Tong; Becky Drees; Giuliano Nardelli; Gary Bader; Barbara Brannetti; Luisa Castagnoli; Marie Evangelista; Silvia Ferracuti; Bryce Nelson; Serena Paoluzi; Michele Quondam; Adriana Zucconi; Christopher W V Hogue; Stanley Fields; Charles Boone; Gianni Cesareni
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.
Science (New York, N.Y.) 2002;295(5553):321-4.
2002: Yuen Ho; Albrecht Gruhler; Adrian Heilbut; Gary Bader; Lynda Moore; Sally-Lin Adams; Anna Millar; Paul Taylor; Keiryn Bennett; Kelly Boutilier; Lingyun Yang; Cheryl Wolting; Ian Donaldson; Søren Schandorff; Juanita Shewnarane; Mai Vo; Joanne Taggart; Marilyn Goudreault; Brenda Muskat; Cris Alfarano; Danielle Dewar; Zhen Lin; Katerina Michalickova; Andrew R Willems; Holly Sassi; Peter A Nielsen; Karina J Rasmussen; Jens R Andersen; Lene E Johansen; Lykke H Hansen; Hans Jespersen; Alexandre Podtelejnikov; Eva Nielsen; Janne Crawford; Vibeke Poulsen; Birgitte D Sørensen; Jesper Matthiesen; Ronald Hendrickson; Frank Gleeson; Tony Pawson; Michael F Moran; Daniel Durocher; Matthias Mann; Christopher W V Hogue; Daniel Figeys; Mike Tyers
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
Nature 2002;415(6868):180-3.
2001: Amy Hin Yan Tong; Marie Evangelista; Ainslie B Parsons; H Xu; Gary Bader; Nicolas Pagé; M Robinson; S Raghibizadeh; Christopher W V Hogue; Howard Bussey; Brenda Andrews; Mike Tyers; Charles Boone
Systematic genetic analysis with ordered arrays of yeast deletion mutants.
Science (New York, N.Y.) 2001;294(5550):2364-8.
2001: Gary Bader; I Donaldson; Cheryl Wolting; B F Ouellette; Tony Pawson; Christopher W V Hogue
BIND--The Biomolecular Interaction Network Database.
Nucleic acids research 2001;29(1):242-5.
2000: Gary Bader; Christopher W V Hogue
BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.
Bioinformatics (Oxford, England) 2000;16(5):465-77.