The BioPAX data exchange format is the joint work of the BioPAX workgroup: Mirit Aladjem, (2008)
Gary D. Bader, Eric Brauner, Michael P. Cary, Kam Dahlquist, Emek Demir, Ken Fukuda, ...
At present, there are over 215 Internet-accessible databases that store biological pathway data. Biologists often need to use information from many of these to support their research, but since each...
344 Review TRENDS in Cell Biology Vol.13 No.7 July 2003 (2008)
Gary D. Bader, Adrian Heilbut, Brenda Andrews, Mike Tyers, Timothy Hughes, Charles Boone
Functional genomics and proteomics: charting a multidimensional map of the yeast cell q
A Specificity Map for the PDZ Domain Family (2008)
Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, ...
PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides,...
BMC Biology BioMed Central (2008)
Samuel Kerrien, Ra Orchard, Luisa Montecchi-palazzi, Bruno Ar, Antony F Quinn, Nisha Vinod, ...
Software Broadening the horizon – level 2.5 of the HUPO-PSI format for
808 RESEARCH ARTICLE Global Mapping of the Yeast Genetic Interaction Network (2008)
Amy Hin, Yan Tong, Guillaume Lesage, Gary D. Bader, Huiming Ding, Hong Xu, ...
A genetic interaction network containing �1000 genes and �4000 interactions was mapped by crossing mutations in 132 different query genes into a set of �4700 viable gene yeast deletion mutants...
Cytoscape ESP: simple search of complex biological networks (2008)
Ashkenazi, Maital, Bader, Gary D., Kuchinsky, Allan, Moshelion, Menachem, States, David J.
Summary: Cytoscape enhanced search plugin (ESP) enables searching complex biological networks on multiple attribute fields using logical operators and wildcards. Queries use an intuitive syntax and...
Article type Methodology article (2007)
Bmc Bioinformatics, Gary D Bader, Michel Dumontier, Hao C Lieu, Ruth Isserlin, Christopher Wv Hogue, ...
This 'Manuscript PDF ' corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below....
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions (2007)
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats,...
Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, ...
cPath: open source software for collecting, storing, and querying biological pathways (2006)
Cerami, Ethan G, Bader, Gary D, Gross, Benjamin E, Sander, Chris
Abstract Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220...
Pathguide: a Pathway Resource List (2006)
Gary D. Bader, Michael P. Cary, Chris S
Pathguide: the Pathway Resource List
Pathguide: a Pathway Resource List (2006)
Bader, Gary D., Cary, Michael P., Sander, Chris
Pathguide: the Pathway Resource List (http://pathguide.org) is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include...
Donaldson, Ian, Martin, Joel, De Bruijn, Berry, Wolting, Cheryl, Lay, Vicki, Tuekam, Brigitte, ...
Abstract Background The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are...
An automated method for finding molecular complexes in large protein interaction networks (2003)
Bader, Gary D, Hogue, Christopher WV
Abstract Background Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks....
BMC Bioinformatics Methodology article (2003)
Gary D Bader, Christopher Wv Hogue
Background: Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial...
BIND: the Biomolecular Interaction Network Database (2003)
Bader, Gary D., Betel, Doron, Hogue, Christopher W. V.
The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit...
Michalickova, Katerina, Bader, Gary D, Dumontier, Michel, Lieu, Hao, Betel, Doron, Isserlin, Ruth, ...
Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for...
BIND--The Biomolecular Interaction Network Database (2001)
Bader, Gary D., Donaldson, Ian, Wolting, Cheryl, Ouellette, B. F. Francis, Pawson, Tony, Hogue, Christopher W. V.
The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the...
Bader, Gary D., Hogue, Christopher W. V.
* To whom correspondence should be addressed. Motivation: Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins, protein domains and protein...
BIND—The Biomolecular Interaction Network Database
Bader, Gary D., Donaldson, Ian, Wolting, Cheryl, Ouellette, B. F. Francis, Pawson, Tony, Hogue, Christopher W. V.
The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND...
SeqHound: biological sequence and structure database as a platform for bioinformatics research
Michalickova, Katerina, Bader, Gary D, Dumontier, Michel, Lieu, Hao, Betel, Doron, Isserlin, Ruth, ...
BIND: the Biomolecular Interaction Network Database
Bader, Gary D., Betel, Doron, Hogue, Christopher W. V.
The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit...
Pathguide: a Pathway Resource List
Bader, Gary D., Cary, Michael P., Sander, Chris
Pathguide: the Pathway Resource List () is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic...
cPath: open source software for collecting, storing, and querying biological pathways
Cerami, Ethan G, Bader, Gary D, Gross, Benjamin E, Sander, Chris
BIND—The Biomolecular Interaction Network Database
Bader, Gary D., Donaldson, Ian, Wolting, Cheryl, Ouellette, B. F. Francis, Pawson, Tony, Hogue, Christopher W. V.
The Biomolecular Interaction Network Database (BIND; http://binddb.org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND...
SeqHound: biological sequence and structure database as a platform for bioinformatics research
Michalickova, Katerina, Bader, Gary D, Dumontier, Michel, Lieu, Hao, Betel, Doron, Isserlin, Ruth, ...
BIND: the Biomolecular Interaction Network Database
Bader, Gary D., Betel, Doron, Hogue, Christopher W. V.
The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit...
Pathguide: a Pathway Resource List
Bader, Gary D., Cary, Michael P., Sander, Chris
Pathguide: the Pathway Resource List () is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic...
cPath: open source software for collecting, storing, and querying biological pathways
Cerami, Ethan G, Bader, Gary D, Gross, Benjamin E, Sander, Chris
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
Mathew, Jomol P, Taylor, Barry S, Bader, Gary D, Pyarajan, Saiju, Antoniotti, Marco, Chinnaiyan, Arul M, ...
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Cytoscape ESP: simple search of complex biological networks
Ashkenazi, Maital, Bader, Gary D., Kuchinsky, Allan, Moshelion, Menachem, States, David J.
Summary: Cytoscape enhanced search plugin (ESP) enables searching complex biological networks on multiple attribute fields using logical operators and wildcards. Queries use an intuitive syntax and...
A Specificity Map for the PDZ Domain Family
Tonikian, Raffi, Zhang, Yingnan, Sazinsky, Stephen L, Currell, Bridget, Yeh, Jung-Hua, Reva, Boris, ...
PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides,...
Tonikian, Raffi, Xin, Xiaofeng, Toret, Christopher P., Gfeller, David, Landgraf, Christiane, Panni, Simona, ...
A genome-scale specificity and interaction map for yeast SH3 domain-containing proteins reveal how family members show selective binding to target proteins and predicts the dynamic localization of...