Peer-reviewed Journals

2009

Positive Selection of Tyrosine Loss in Metazoan Evolution.
Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R
Science. 2009 Jul 9. [Epub ahead of print]
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION

2008

A Specificity Map for the PDZ Domain Family.
Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A. Held, Brent A. Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C. Chan, Somasekar Seshagiri, Laurence A. Lasky, Chris Sander, Charles Boone, Gary D. Bader, Sachdev S. Sidhu
PLoS Biology Vol. 6, No. 9, e239
PubMed Abstract - PDF
PROTEIN-PROTEIN INTERACTION ANALYSIS
Cytoscape ESP: simple search of complex biological networks.
Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ
Bioinformatics 2008 Jun 15;24(12):1465-6
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Computational prediction of protein-protein interactions.
Skrabanek L, Saini HK, Bader GD, Enright AJ
Molecular Biotechnology 2008 Jan;38(1):1-17
PubMed Abstract - PDF
REVIEW

2007

Integration of biological networks and gene expression data using Cytoscape
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
Nature Protocols 2007;2(10):2366-82
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H
BMC Biology 2007 Oct 9;5(1):44
PubMed Abstract - PDF
DATA STANDARD
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas Jde L, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H
Nat Biotechnol. 2007 Aug;25(8):894-8
PubMed Abstract - PDF
DATA STANDARD
Germ-line DNA copy number variation frequencies in a large North American population
Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S
Hum Genet. 2007 Jul 19
PubMed Abstract - PDF
GENOMICS
From bytes to bedside: data integration and computational biology for translational cancer research
Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B
PLoS Comput Biol. 2007 Feb 23;3(2):e12
PubMed Abstract - PDF
CANCER REVIEW
NetMatch: a Cytoscape Plugin for Searching Biological Networks
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D
Bioinformatics 2007 Apr 1;23(7):910-2
PubMed Abstract - PDF
Download software
NETWORK ANALYSIS SOFTWARE
Computational prediction of cancer-gene function
Hu P, Bader G, Wigle DA, Emili A
Nature Reviews Cancer 2007 Jan;7(1):23-34. Epub 2006 Dec 14
PubMed Abstract - PDF
CANCER REVIEW

2006

cPath: open source software for collecting, storing, and querying biological pathways
Cerami EG, Bader GD, Gross BE, Sander C
BMC Bioinformatics 2006, 7:497
PubMed Abstract - PDF
PATHWAY SOFTWARE
Pathguide: a Pathway Resource List
Bader GD, Cary MP, Sander C
Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6
PubMed Abstract - PDF
PATHWAY WEBSITE

2005

Pathway information for systems biology
Cary MP, Bader GD, Sander C
FEBS Lett. 2005 Mar 21;579(8):1815-20
PubMed Abstract - PDF
PATHWAY REVIEW

2004

Global Mapping of the Yeast Genetic Interaction Network
Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C
Science 2004 Feb 6;303(5659):808-813
PubMed Abstract - PDF
Science Perspective PDF
GENETIC INTERACTION NETWORK ANALYSIS
The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R
Nature Biotechnology 2004 Feb;22(2):177-83
PubMed Abstract - PDF
DATA STANDARD

2003

Playing tag with the yeast proteome
Andrews BJ, Bader GD, Boone C
Nature Biotechnology Nov;21(11):1297-1299
PubMed Abstract - PDF
REVIEW
Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell
Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C
Trends in Cell Biology Jul, 2003 13(7):344-56
PubMed Abstract - PDF
REVIEW
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine
Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW
BMC Bioinformatics Mar 27, 2003 4(1):11
PubMed Abstract - PDF
TEXT MINING SOFTWARE
Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
Sidhu SS, Bader GD, Boone C
Current Opinion in Chemical Biology 2003 Feb;7(1):97-102
PubMed Abstract - PDF
REVIEW
An automated method for finding molecular complexes in large protein interaction networks
Bader GD, Hogue CWV
BMC Bioinformatics 2003 Jan 13;4(1):2
PubMed Abstract - PDF
ALGORITHM
BIND-The Biomolecular Interaction Network Database
Bader GD, Betel D, Hogue CWV
Nucleic Acids Research Jan 1, 2003 31(1):248-250
PubMed Abstract - PDF
INTERACTION DATABASE

2002

SeqHound: biological sequence and structure database as a platform for bioinformatics research
Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW
BMC Bioinformatics 2002, 3:32 (25 October 2002)
PubMed Abstract - PDF
PROTEIN DATABASE
Analyzing yeast protein–protein interaction data obtained from different sources
Bader GD, Hogue CW
Nature Biotechnology 2002 Oct;20(10):991-997
PubMed Abstract - PDF
META-ANALYSIS
A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules
Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G
Science 2002 Jan 11;295(5553):321-324
PubMed Abstract - PDF
Science Perspective PDF
PROTEIN INTERACTION PREDICTION
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M
Nature 2002 Jan 10;415(6868): 180-183
PubMed Abstract - PDF
Nature News and Views PDF
PROTEIN INTERACTION NETWORK ANALYSIS

2001

Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C
Science 2001 Dec 14;294(5550):2364-8
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
BIND - The Biomolecular Interaction Network Database
Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW
Nucleic Acids Research Jan 1, 2001 29(1):242-245
PubMed Abstract - PDF
INTERACTION DATABASE

2000

BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways
Bader GD, Hogue CW
Bioinformatics. 2000 May;16(5):465-77
PubMed Abstract - PDF
INTERACTION DATABASE

Textbook Chapters

2008

Exploring Biological Networks with Cytoscape Software
Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and Gary D. Bader
Current Protocols in Bioinformatics - PubMed Abstract - PDF
John Wiley & Sons, Inc.
NETWORK ANALYSIS SOFTWARE

2006

BioPAX - Biological Pathway Data Exchange Format
Gary D. Bader, Michael Cary, Chris Sander
Encyclopedia of Genomics, Proteomics and Bioinformatics
Humana Press, New Jersey
DATA STANDARD

2005

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Rowan Christmas, Iliana Avila-Campillo, Hamid Bolouri, Benno Schwikowski, Mark Anderson, Ryan Kelley, Nerius Landys, Chris Workman, Trey Ideker, Ethan Cerami, Rob Sheridan, Gary D. Bader, and Chris Sander
Am Assoc Cancer Res Educ Book 2005: 12-16
NETWORK ANALYSIS SOFTWARE
Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes
Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone
in Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.
Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA
GENETIC INTERACTION NETWORK ANALYSIS

2004

Interaction Databases, in Genomics and Bioinformatics, 2nd Edition
Gary D. Bader, Christopher W.V. Hogue
in Volume 5B of the Series: Biotechnology, 2nd Edition.
Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany
INTERACTION DATABASE
Intermolecular Interactions and Biological Pathways
Gary D. Bader, Anton J. Enright
in Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey
INTERACTION DATABASE
Computational Prediction of Protein-Protein Interactions
Anton J. Enright, Lucy Skrabanek, Gary D. Bader
in The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)
PROTEIN INTERACTION PREDICTION

2003

Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions
Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone
in Handbook of Cell Signaling
Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)
PROTEIN INTERACTION PREDICTION

2002

Interaction Databases
Gary D. Bader, Christopher W.V. Hogue
Chapter 18, in Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)
Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.
Wiley-VCH, Germany
INTERACTION DATABASE