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
Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases.
Chris Soon Heng Tan, Bernd Bodenmiller, Adrian Pasculescu, Marko Jovanovic, Michael O. Hengartner, Claus Jørgensen, Gary D. Bader, Ruedi Aebersold, Tony Pawson, and Rune Linding
Science Signaling 2(81):r39 (2009)
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

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+== 2009 ==
 1. '''Positive Selection of Tyrosine Loss in Metazoan Evolution.'''<<BR>>'''Tan CS''', Pasculescu A, Lim WA, Pawson T, '''Bader GD''', Linding R<<BR>>[[http://www.sciencemag.org/cgi/content/abstract/1174301v2|Science. 2009 Jul 9. [Epub ahead of print]]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19589966|PubMed Abstract]] - [[attachment:2009_Tan_TyrosineLoss_Science.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK EVOLUTION'''

 1. '''Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases.'''<<BR>>'''Chris Soon Heng Tan''', Bernd Bodenmiller, Adrian Pasculescu, Marko Jovanovic, Michael O. Hengartner, Claus Jørgensen, '''Gary D. Bader''', Ruedi Aebersold, Tony Pawson, and Rune Linding<<BR>>[[http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2/81/ra39|Science Signaling 2(81):r39 (2009)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19638616|PubMed Abstract]] - [[attachment:2009_Tan_ComparativePhosphoProteomics_ScienceSignaling_Jul.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK EVOLUTION'''
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-. '''Cytoscape ESP: simple search of complex biological networks.'''[[BR]]Ashkenazi M, '''Bader GD''', Kuchinsky A, Moshelion M, States DJ[[BR]][http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn208v1 Bioinformatics. 2008 Apr 28][[BR]][http://www.ncbi.nlm.nih.gov/pubmed/18445605 PubMed Abstract] - [attachment:2008_Ashkenazi_CytoscapeESP_Bioinformatics.pdf PDF][[BR]]'''NETWORK ANALYSIS SOFTWARE'''
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-. '''Computational prediction of protein-protein interactions.'''[[BR]]Skrabanek L, Saini HK, '''Bader GD''', Enright AJ[[BR]][http://humanapress.com/index.php?option=com_journalshome&task=articledetails&category=journals&article_code=MB:38:1:1 Mol Biotechnol. 2008 Jan;38(1):1-17][[BR]][http://www.ncbi.nlm.nih.gov/pubmed/18095187 PubMed Abstract] - [attachment:2008_Skrabanek_MolBiotech_PPI.pdf PDF][[BR]]'''REVIEW'''
+. '''A Specificity Map for the PDZ Domain Family.'''<<BR>>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<<BR>>[[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060239|PLoS Biology Vol. 6, No. 9, e239]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18828675|PubMed Abstract]] - [[attachment:2008_Tonikian_PDZSpecificityMap_PlosBiology.pdf|PDF]]<<BR>>'''PROTEIN-PROTEIN INTERACTION ANALYSIS'''

 1. '''Cytoscape ESP: simple search of complex biological networks.'''<<BR>>Ashkenazi M, '''Bader GD''', Kuchinsky A, Moshelion M, States DJ<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn208v1|Bioinformatics 2008 Jun 15;24(12):1465-6]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18445605|PubMed Abstract]] - [[attachment:2008_Ashkenazi_CytoscapeESP_Bioinformatics.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Computational prediction of protein-protein interactions.'''<<BR>>Skrabanek L, Saini HK, '''Bader GD''', Enright AJ<<BR>>[[http://humanapress.com/index.php?option=com_journalshome&task=articledetails&category=journals&article_code=MB:38:1:1|Molecular Biotechnology 2008 Jan;38(1):1-17]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18095187|PubMed Abstract]] - [[attachment:2008_Skrabanek_MolBiotech_PPI.pdf|PDF]]<<BR>>'''REVIEW'''
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-. '''Integration of biological networks and gene expression data using Cytoscape'''[[BR]]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'''[[BR]][http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html Nat Protoc. 2007;2(10):2366-82][[BR]][http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17947979 PubMed Abstract] - [attachment:2007_Cytoscape_Cline_NatureProtocols_Oct.pdf PDF][[BR]]'''NETWORK ANALYSIS SOFTWARE'''
+. '''Integration of biological networks and gene expression data using Cytoscape'''<<BR>>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'''<<BR>>[[http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html|Nature Protocols 2007;2(10):2366-82]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17947979|PubMed Abstract]] - [[attachment:2007_Cytoscape_Cline_NatureProtocols_Oct.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''
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-. '''Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions'''[[BR]]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[[BR]][http://www.biomedcentral.com/1741-7007/5/44/abstract BMC Biology 2007 Oct 9;5(1):44][[BR]][http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17925023 PubMed Abstract] - [attachment:2007_Kerrien_PSIMI_BMCBiology.pdf PDF][[BR]]'''DATA STANDARD'''
+. '''Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions'''<<BR>>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<<BR>>[[http://www.biomedcentral.com/1741-7007/5/44/abstract|BMC Biology 2007 Oct 9;5(1):44]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17925023|PubMed Abstract]] - [[attachment:2007_Kerrien_PSIMI_BMCBiology.pdf|PDF]]<<BR>>'''DATA STANDARD'''
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-. '''The minimum information required for reporting a molecular interaction experiment (MIMIx)'''[[BR]]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[[BR]][http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html Nat Biotechnol. 2007 Aug;25(8):894-8][[BR]][http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17687370 PubMed Abstract] - [attachment:2007_MIMIx_OrchardEtAl_NatBiotech_August.pdf PDF][[BR]]'''DATA STANDARD'''
+. '''The minimum information required for reporting a molecular interaction experiment (MIMIx)'''<<BR>>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<<BR>>[[http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html|Nat Biotechnol. 2007 Aug;25(8):894-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17687370|PubMed Abstract]] - [[attachment:2007_MIMIx_OrchardEtAl_NatBiotech_August.pdf|PDF]]<<BR>>'''DATA STANDARD'''
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-. '''Germ-line DNA copy number variation frequencies in a large North American population'''[[BR]]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[[BR]][http://www.springerlink.com/content/f57t61764r0t21mv/ Hum Genet. 2007 Jul 19][[BR]][http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17638019 PubMed Abstract] - [attachment:2007_Germ-lineDNACopyNumberVariationFrequenciesInALargeNorthAmericanPopulation_Zogopoulos_Bader_Gallinder_HumanGenetics.pdf PDF][[BR]]'''GENOMICS'''
+. '''Germ-line DNA copy number variation frequencies in a large North American population'''<<BR>>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<<BR>>[[http://www.springerlink.com/content/f57t61764r0t21mv/|Hum Genet. 2007 Jul 19]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17638019|PubMed Abstract]] - [[attachment:2007_Germ-lineDNACopyNumberVariationFrequenciesInALargeNorthAmericanPopulation_Zogopoulos_Bader_Gallinder_HumanGenetics.pdf|PDF]]<<BR>>'''GENOMICS'''
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-. '''From bytes to bedside: data integration and computational biology for translational cancer research'''[[BR]]Mathew JP, Taylor BS, '''Bader GD''', Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B[[BR]][http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030012 PLoS Comput Biol. 2007 Feb 23;3(2):e12][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17319736 PubMed Abstract] - [attachment:2007_MatthewTaylorBader_TranslationalReview_PLoSCompBio_Feb.pdf PDF][[BR]]'''CANCER REVIEW'''
+. '''From bytes to bedside: data integration and computational biology for translational cancer research'''<<BR>>Mathew JP, Taylor BS, '''Bader GD''', Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B<<BR>>[[http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030012|PLoS Comput Biol. 2007 Feb 23;3(2):e12]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17319736|PubMed Abstract]] - [[attachment:2007_MatthewTaylorBader_TranslationalReview_PLoSCompBio_Feb.pdf|PDF]]<<BR>>'''CANCER REVIEW'''
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-. '''!NetMatch: a Cytoscape Plugin for Searching Biological Networks'''[[BR]]Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, '''Bader GD''', Shasha D[[BR]][http://bioinformatics.oxfordjournals.org/cgi/reprint/btm032v1 Bioinformatics. 2007 Feb 3;][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17277332 PubMed Abstract] - [attachment:2007_NetMatch-ACytoscapePluginForSearchingBiologicalNetworks_Ferro_Guigno_Bader_Shasha_Apr.pdf PDF][[BR]][:Software/NetMatch:Download software][[BR]]'''NETWORK ANALYSIS SOFTWARE'''
+. '''!NetMatch: a Cytoscape Plugin for Searching Biological Networks'''<<BR>>Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, '''Bader GD''', Shasha D<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/reprint/btm032v1|Bioinformatics 2007 Apr 1;23(7):910-2]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17277332|PubMed Abstract]] - [[attachment:2007_NetMatch-ACytoscapePluginForSearchingBiologicalNetworks_Ferro_Guigno_Bader_Shasha_Apr.pdf|PDF]]<<BR>>[[Software/NetMatch|Download software]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''
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-. '''Computational prediction of cancer-gene function'''[[BR]]Hu P, '''Bader G''', Wigle DA, Emili A[[BR]][http://www.nature.com/nrc/journal/v7/n1/abs/nrc2036.html Nature Reviews Cancer 2007 Jan;7(1):23-34. Epub 2006 Dec 14][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17167517 PubMed Abstract] - [attachment:2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf PDF][[BR]]'''CANCER REVIEW'''
+. '''Computational prediction of cancer-gene function'''<<BR>>Hu P, '''Bader G''', Wigle DA, Emili A<<BR>>[[http://www.nature.com/nrc/journal/v7/n1/abs/nrc2036.html|Nature Reviews Cancer 2007 Jan;7(1):23-34. Epub 2006 Dec 14]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17167517|PubMed Abstract]] - [[attachment:2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf|PDF]]<<BR>>'''CANCER REVIEW'''
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-. '''cPath: open source software for collecting, storing, and querying biological pathways'''[[BR]]Cerami EG, '''Bader GD''', Gross BE, Sander C[[BR]][http://www.biomedcentral.com/1471-2105/7/497/abstract BMC Bioinformatics 2006, 7:497][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17101041 PubMed Abstract] - [attachment:2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf PDF][[BR]]'''PATHWAY SOFTWARE'''
+. '''cPath: open source software for collecting, storing, and querying biological pathways'''<<BR>>Cerami EG, '''Bader GD''', Gross BE, Sander C<<BR>>[[http://www.biomedcentral.com/1471-2105/7/497/abstract|BMC Bioinformatics 2006, 7:497]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17101041|PubMed Abstract]] - [[attachment:2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf|PDF]]<<BR>>'''PATHWAY SOFTWARE'''
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-. '''Pathguide: a Pathway Resource List'''[[BR]]'''Bader GD''', Cary MP, Sander C[[BR]][http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D504 Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16381921&query_hl=14&itool=pubmed_docsum PubMed Abstract] - [attachment:2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf PDF][[BR]]'''PATHWAY WEBSITE'''
+. '''Pathguide: a Pathway Resource List'''<<BR>>'''Bader GD''', Cary MP, Sander C<<BR>>[[http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D504|Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16381921&query_hl=14&itool=pubmed_docsum|PubMed Abstract]] - [[attachment:2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf|PDF]]<<BR>>'''PATHWAY WEBSITE'''
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-. '''Pathway information for systems biology'''[[BR]]Cary MP, '''Bader GD''', Sander C[[BR]][http://www.febsletters.org/retrieve/pii/S0014579305001705 FEBS Lett. 2005 Mar 21;579(8):1815-20][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15763557&query_hl=14&itool=pubmed_docsum PubMed Abstract] - [attachment:2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf PDF][[BR]]'''PATHWAY REVIEW'''
+. '''Pathway information for systems biology'''<<BR>>Cary MP, '''Bader GD''', Sander C<<BR>>[[http://www.febsletters.org/retrieve/pii/S0014579305001705|FEBS Lett. 2005 Mar 21;579(8):1815-20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15763557&query_hl=14&itool=pubmed_docsum|PubMed Abstract]] - [[attachment:2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf|PDF]]<<BR>>'''PATHWAY REVIEW'''
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-. '''Global Mapping of the Yeast Genetic Interaction Network'''[[BR]]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[[BR]][http://www.sciencemag.org/cgi/content/full/303/5659/808 Science 2004 Feb 6;303(5659):808-813][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870 PubMed Abstract] - [attachment:2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf PDF][[BR]][attachment:2004_SGA_Hartwell_comment.pdf Science Perspective PDF][[BR]]'''GENETIC INTERACTION NETWORK ANALYSIS'''
+. '''Global Mapping of the Yeast Genetic Interaction Network'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/full/303/5659/808|Science 2004 Feb 6;303(5659):808-813]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870|PubMed Abstract]] - [[attachment:2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf|PDF]]<<BR>>[[attachment:2004_SGA_Hartwell_comment.pdf|Science Perspective PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''
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-. '''The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data'''[[BR]]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[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 Nature Biotechnology 2004 Feb;22(2):177-83][[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 PubMed Abstract] - [attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf PDF][[BR]]'''DATA STANDARD'''
+. '''The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data'''<<BR>>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<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147|Nature Biotechnology 2004 Feb;22(2):177-83]]<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147|PubMed Abstract]] - [[attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf|PDF]]<<BR>>'''DATA STANDARD'''
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-. '''Playing tag with the yeast proteome'''[[BR]]Andrews BJ, '''Bader GD''', Boone C[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v21/n11/full/nbt1103-1297.html Nature Biotechnology Nov;21(11):1297-1299][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14595360 PubMed Abstract] - [attachment:2003_OsheaWeissmanReview_NatureBiotech.pdf PDF][[BR]]'''REVIEW'''
+. '''Playing tag with the yeast proteome'''<<BR>>Andrews BJ, '''Bader GD''', Boone C<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v21/n11/full/nbt1103-1297.html|Nature Biotechnology Nov;21(11):1297-1299]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14595360|PubMed Abstract]] - [[attachment:2003_OsheaWeissmanReview_NatureBiotech.pdf|PDF]]<<BR>>'''REVIEW'''
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-. '''Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell'''[[BR]]'''Bader GD''', Heilbut A, Andrews B, Tyers M, Hughes T, Boone C[[BR]][http://linkinghub.elsevier.com/retrieve/pii/S0962892403001272 Trends in Cell Biology Jul, 2003 13(7):344-56][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12837605&dopt=Abstract PubMed Abstract] - [attachment:2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf PDF][[BR]]'''REVIEW'''
+. '''Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell'''<<BR>>'''Bader GD''', Heilbut A, Andrews B, Tyers M, Hughes T, Boone C<<BR>>[[http://linkinghub.elsevier.com/retrieve/pii/S0962892403001272|Trends in Cell Biology Jul, 2003 13(7):344-56]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12837605&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf|PDF]]<<BR>>'''REVIEW'''
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-. '''PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine'''[[BR]]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[[BR]][http://www.biomedcentral.com/1471-2105/4/11 BMC Bioinformatics Mar 27, 2003 4(1):11][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12689350&dopt=Abstract PubMed Abstract] - [attachment:PreBIND_BMC2003.pdf PDF][[BR]]'''TEXT MINING SOFTWARE'''
+. '''PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine'''<<BR>>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<<BR>>[[http://www.biomedcentral.com/1471-2105/4/11|BMC Bioinformatics Mar 27, 2003 4(1):11]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12689350&dopt=Abstract|PubMed Abstract]] - [[attachment:PreBIND_BMC2003.pdf|PDF]]<<BR>>'''TEXT MINING SOFTWARE'''
-Line 49:
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-. '''Functional genomics of intracellular peptide recognition domains with combinatorial biology methods'''[[BR]]Sidhu SS, '''Bader GD''', Boone C[[BR]][http://linkinghub.elsevier.com/retrieve/pii/S136759310200011X Current Opinion in Chemical Biology 2003 Feb;7(1):97-102][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12547433&dopt=Abstract PubMed Abstract] - [attachment:2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf PDF][[BR]]'''REVIEW'''
+. '''Functional genomics of intracellular peptide recognition domains with combinatorial biology methods'''<<BR>>Sidhu SS, '''Bader GD''', Boone C<<BR>>[[http://linkinghub.elsevier.com/retrieve/pii/S136759310200011X|Current Opinion in Chemical Biology 2003 Feb;7(1):97-102]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12547433&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf|PDF]]<<BR>>'''REVIEW'''
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-. '''An automated method for finding molecular complexes in large protein interaction networks'''[[BR]]'''Bader GD''', Hogue CWV[[BR]][http://www.biomedcentral.com/1471-2105/4/2 BMC Bioinformatics 2003 Jan 13;4(1):2][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract PubMed Abstract] - [attachment:2003_BaderHogue_MCODE.pdf PDF][[BR]]'''ALGORITHM'''
+. '''An automated method for finding molecular complexes in large protein interaction networks'''<<BR>>'''Bader GD''', Hogue CWV<<BR>>[[http://www.biomedcentral.com/1471-2105/4/2|BMC Bioinformatics 2003 Jan 13;4(1):2]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_BaderHogue_MCODE.pdf|PDF]]<<BR>>'''ALGORITHM'''
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-. '''BIND-The Biomolecular Interaction Network Database'''[[BR]]'''Bader GD''', Betel D, Hogue CWV[[BR]][http://nar.oupjournals.org/cgi/content/abstract/31/1/248 Nucleic Acids Research Jan 1, 2003 31(1):248-250][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519993&dopt=Abstract PubMed Abstract] - [attachment:2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf PDF][[BR]]'''INTERACTION DATABASE'''
+. '''BIND-The Biomolecular Interaction Network Database'''<<BR>>'''Bader GD''', Betel D, Hogue CWV<<BR>>[[http://nar.oupjournals.org/cgi/content/abstract/31/1/248|Nucleic Acids Research Jan 1, 2003 31(1):248-250]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519993&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf|PDF]]<<BR>>'''INTERACTION DATABASE'''
-Line 57:
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-. '''!SeqHound: biological sequence and structure database as a platform for bioinformatics research'''[[BR]]Michalickova K, '''Bader GD''', Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW[[BR]][http://www.biomedcentral.com/1471-2105/3/32 BMC Bioinformatics 2002, 3:32 (25 October 2002)][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract PubMed Abstract] - [attachment:2002_SeqHound_BMCBioinfo.pdf PDF][[BR]]'''PROTEIN DATABASE'''
+. '''!SeqHound: biological sequence and structure database as a platform for bioinformatics research'''<<BR>>Michalickova K, '''Bader GD''', Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW<<BR>>[[http://www.biomedcentral.com/1471-2105/3/32|BMC Bioinformatics 2002, 3:32 (25 October 2002)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract|PubMed Abstract]] - [[attachment:2002_SeqHound_BMCBioinfo.pdf|PDF]]<<BR>>'''PROTEIN DATABASE'''
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-. '''Analyzing yeast protein–protein interaction data obtained from different sources'''[[BR]]'''Bader GD''', Hogue CW[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v20/n10/abs/nbt1002-991.html&dynoptions=doi1040752166 Nature Biotechnology 2002 Oct;20(10):991-997][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12355115&dopt=Abstract PubMed Abstract] - [attachment:BaderHogueNBT2002.pdf PDF][[BR]]'''META-ANALYSIS'''
+. '''Analyzing yeast protein–protein interaction data obtained from different sources'''<<BR>>'''Bader GD''', Hogue CW<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v20/n10/abs/nbt1002-991.html&dynoptions=doi1040752166|Nature Biotechnology 2002 Oct;20(10):991-997]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12355115&dopt=Abstract|PubMed Abstract]] - [[attachment:BaderHogueNBT2002.pdf|PDF]]<<BR>>'''META-ANALYSIS'''
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-. '''A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules'''[[BR]]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[[BR]][http://www.sciencemag.org/cgi/content/abstract/295/5553/321 Science 2002 Jan 11;295(5553):321-324][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743162&dopt=Abstract PubMed Abstract] - [attachment:SH3ScienceJan11_2002.pdf PDF][[BR]][attachment:Perspective_ScienceJan11_2002.pdf Science Perspective PDF][[BR]]'''PROTEIN INTERACTION PREDICTION'''
+. '''A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/abstract/295/5553/321|Science 2002 Jan 11;295(5553):321-324]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743162&dopt=Abstract|PubMed Abstract]] - [[attachment:SH3ScienceJan11_2002.pdf|PDF]]<<BR>>[[attachment:Perspective_ScienceJan11_2002.pdf|Science Perspective PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''
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-. '''Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry'''[[BR]]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[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v415/n6868/abs/415180a_fs.html Nature 2002 Jan 10;415(6868): 180-183][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11805837&dopt=Abstract PubMed Abstract] - [attachment:HMS-PCI-Nature-Jan10_2002.pdf PDF][[BR]][attachment:HMS-PCINewsAndViews-NatureJan10_2002.pdf Nature News and Views PDF][[BR]]'''PROTEIN INTERACTION NETWORK ANALYSIS'''
+. '''Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry'''<<BR>>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<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v415/n6868/abs/415180a_fs.html|Nature 2002 Jan 10;415(6868): 180-183]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11805837&dopt=Abstract|PubMed Abstract]] - [[attachment:HMS-PCI-Nature-Jan10_2002.pdf|PDF]]<<BR>>[[attachment:HMS-PCINewsAndViews-NatureJan10_2002.pdf|Nature News and Views PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK ANALYSIS'''
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-. '''Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants'''[[BR]]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[[BR]][http://www.sciencemag.org/cgi/content/abstract/294/5550/2364 Science 2001 Dec 14;294(5550):2364-8][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743205&dopt=Abstract PubMed Abstract] - [attachment:SGA_ScienceVol294-2001.pdf PDF][[BR]]'''GENETIC INTERACTION NETWORK ANALYSIS'''
+. '''Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/abstract/294/5550/2364|Science 2001 Dec 14;294(5550):2364-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743205&dopt=Abstract|PubMed Abstract]] - [[attachment:SGA_ScienceVol294-2001.pdf|PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''
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-. '''BIND - The Biomolecular Interaction Network Database'''[[BR]]'''Bader GD''', Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW[[BR]][http://nar.oupjournals.org/cgi/content/abstract/29/1/242 Nucleic Acids Research Jan 1, 2001 29(1):242-245][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11125103&dopt=Abstract PubMed Abstract] - [attachment:BIND_NAR_2001.pdf PDF][[BR]]'''INTERACTION DATABASE'''
+. '''BIND - The Biomolecular Interaction Network Database'''<<BR>>'''Bader GD''', Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW<<BR>>[[http://nar.oupjournals.org/cgi/content/abstract/29/1/242|Nucleic Acids Research Jan 1, 2001 29(1):242-245]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11125103&dopt=Abstract|PubMed Abstract]] - [[attachment:BIND_NAR_2001.pdf|PDF]]<<BR>>'''INTERACTION DATABASE'''
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-. '''BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways'''[[BR]]'''Bader GD''', Hogue CW[[BR]][http://bioinformatics.oupjournals.org/cgi/content/abstract/16/5/465 Bioinformatics. 2000 May;16(5):465-77][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10871269&dopt=Abstract PubMed Abstract] - [attachment:BIND_Spec_2000.pdf PDF][[BR]]'''INTERACTION DATABASE'''
+. '''BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways'''<<BR>>'''Bader GD''', Hogue CW<<BR>>[[http://bioinformatics.oupjournals.org/cgi/content/abstract/16/5/465|Bioinformatics. 2000 May;16(5):465-77]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10871269&dopt=Abstract|PubMed Abstract]] - [[attachment:BIND_Spec_2000.pdf|PDF]]<<BR>>'''INTERACTION DATABASE'''
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+== 2008 ==

 1. '''Exploring Biological Networks with Cytoscape Software'''<<BR>>'''Natalie Yeung''', Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and '''Gary D. Bader'''<<BR>>[[http://mrw.interscience.wiley.com/emrw/9780471250951/cp/cpbi/article/bi0813/current/abstract|Current Protocols in Bioinformatics]] - [[http://www.ncbi.nlm.nih.gov/pubmed/18819078|PubMed Abstract]] - [[attachment:CytoscapeCurrProtocolsProof-YeungBader_Sep2008.pdf|PDF]]<<BR>>John Wiley & Sons, Inc.<<BR>>'''NETWORK ANALYSIS SOFTWARE'''
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-. '''BioPAX - Biological Pathway Data Exchange Format'''[[BR]]'''Gary D. Bader''', Michael Cary, Chris Sander[[BR]][http://www.mrw.interscience.wiley.com/ggpb/articles/g408117/frame.html Encyclopedia of Genomics, Proteomics and Bioinformatics][[BR]]Humana Press, New Jersey[[BR]]'''DATA STANDARD'''
+. '''BioPAX - Biological Pathway Data Exchange Format'''<<BR>>'''Gary D. Bader''', Michael Cary, Chris Sander<<BR>>[[http://www.mrw.interscience.wiley.com/ggpb/articles/g408117/frame.html|Encyclopedia of Genomics, Proteomics and Bioinformatics]]<<BR>>Humana Press, New Jersey<<BR>>'''DATA STANDARD'''
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-. '''Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks'''[[BR]]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[[BR]][http://educationbook.aacrjournals.org/cgi/content/full/2005/1/12 Am Assoc Cancer Res Educ Book 2005: 12-16][[BR]]'''NETWORK ANALYSIS SOFTWARE'''
+. '''Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks'''<<BR>>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<<BR>>[[http://educationbook.aacrjournals.org/cgi/content/full/2005/1/12|Am Assoc Cancer Res Educ Book 2005: 12-16]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''
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-. '''Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes'''[[BR]]'''Gary D. Bader''', Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone[[BR]]in [http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155 Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.][[BR]]Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA[[BR]]'''GENETIC INTERACTION NETWORK ANALYSIS'''
+. '''Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes'''<<BR>>'''Gary D. Bader''', Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone<<BR>>in [[http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155|Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.]]<<BR>>Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''
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-. '''Interaction Databases, in Genomics and Bioinformatics, 2nd Edition'''[[BR]]'''Gary D. Bader''', Christopher W.V. Hogue[[BR]]in [http://www.wiley-vch.de/books/biotech/con_v05b.html Volume 5B of the Series: Biotechnology, 2nd Edition.][[BR]]Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany[[BR]]'''INTERACTION DATABASE'''
+. '''Interaction Databases, in Genomics and Bioinformatics, 2nd Edition'''<<BR>>'''Gary D. Bader''', Christopher W.V. Hogue<<BR>>in [[http://www.wiley-vch.de/books/biotech/con_v05b.html|Volume 5B of the Series: Biotechnology, 2nd Edition.]]<<BR>>Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany<<BR>>'''INTERACTION DATABASE'''
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-. '''Intermolecular Interactions and Biological Pathways'''[[BR]]'''Gary D. Bader''', Anton J. Enright[[BR]]in [http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey][[BR]]'''INTERACTION DATABASE'''
+. '''Intermolecular Interactions and Biological Pathways'''<<BR>>'''Gary D. Bader''', Anton J. Enright<<BR>>in [[http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html|Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey]]<<BR>>'''INTERACTION DATABASE'''
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+Line 109:
-. '''Computational Prediction of Protein-Protein Interactions'''[[BR]]Anton J. Enright, Lucy Skrabanek, '''Gary D. Bader'''[[BR]]in [http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1 The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)][[BR]]'''PROTEIN INTERACTION PREDICTION'''
+. '''Computational Prediction of Protein-Protein Interactions'''<<BR>>Anton J. Enright, Lucy Skrabanek, '''Gary D. Bader'''<<BR>>in [[http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1|The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''
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-. '''Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions'''[[BR]]'''Gary D. Bader''', Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone[[BR]]in [http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462 Handbook of Cell Signaling][[BR]]Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)[[BR]]'''PROTEIN INTERACTION PREDICTION'''
+. '''Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions'''<<BR>>'''Gary D. Bader''', Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone<<BR>>in [[http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462|Handbook of Cell Signaling]]<<BR>>Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)<<BR>>'''PROTEIN INTERACTION PREDICTION'''
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-. '''Interaction Databases'''[[BR]]'''Gary D. Bader''', Christopher W.V. Hogue[[BR]]Chapter 18, in [http://www.wiley-vch.de/books/biotech/vol_05b.html Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)][[BR]]Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.[[BR]]Wiley-VCH, Germany[[BR]]'''INTERACTION DATABASE'''
+. '''Interaction Databases'''<<BR>>'''Gary D. Bader''', Christopher W.V. Hogue<<BR>>Chapter 18, in [[http://www.wiley-vch.de/books/biotech/vol_05b.html|Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)]]<<BR>>Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.<<BR>>Wiley-VCH, Germany<<BR>>'''INTERACTION DATABASE'''