Computational Biology Center Publications

Gary Bader

Computational Prediction of Protein-Protein Interactions (2005)

Enright AJ, Skrabanek L, Bader GD

In: The Proteomics Protocols Handbook

Humana Press Inc

ISBN: 1-58829-343-2

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The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data (2004)

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

Nat Biotechnol. 2004 Feb;22(2):177-83.

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Global Mapping of the Yeast Genetic Interaction Network (2004)

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):808-13.

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Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions (2003)

Bader GD, Tong AHY, Cesareni G, Hogue CWV, Fields S, Boone C

In: Handbook of Cell Signalling

Bradshaw R, Dennis E (eds)

Academic/Elsevier Press

ISBN: 0-12-124546-2

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BIND-The Biomolecular Interaction Network Database (2003)

Bader GD, Betel D, Hogue CWV

[PubMed Abstract] [Full Text] [PDF]

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An automated method for finding molecular complexes in large protein interaction networks (2003)

Bader GD, Hogue CWV

[PubMed Abstract] [Full Text] [PDF]

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Functional genomics of intracellular peptide recognition domains with combinatorial biology method (2003)

Sidhu SS, Bader GD, Boone C

[PubMed Abstract] [Full Text] [PDF]

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PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine (2003)

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

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Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell (2003)

Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C

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Playing tag with the yeast proteome (2003)

Andrews BJ, Bader GD, Boone C

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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry (2002)

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

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A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules (2002)

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] [Full Text] [PDF]

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Analyzing yeast protein protein interaction data obtained from different sources (2002)

Bader GD, Hogue CW

Nature Biotechnology 2002 Oct;20(10): 991-997

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SeqHound: biological sequence and structure database as a platform for bioinformatics research (2002)

Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW

BMC Bioinformatics 2002, 3:32 (25 October 2002)

[PubMed Abstract] [Full Text] [PDF]