Peer-reviewed Journals

2010

1. The Genetic Landscape of a Cell
   Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C
   Science. 2010 Jan 22;327(5964):425-31
   PubMed Abstract - PDF
   GENETIC INTERACTION NETWORK ANALYSIS

2. NetPath: a public resource of curated signal transduction pathways
   Kandasamy K, Mohan S, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro DJ, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman A, Keshava Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu S, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A
   Genome Biology 2010 Jan 12;11(1):R3
   PubMed Abstract - PDF
   PATHWAY DATABASE

3. DRYGIN: a database of quantitative genetic interaction networks in yeast
   Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C
   Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. Epub 2009 Oct 30
   PubMed Abstract - PDF
   GENETIC INTERACTION NETWORK DATABASE

2009

1. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins
   Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C
   PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218
   PubMed Abstract - PDF
   PROTEIN-PROTEIN INTERACTION ANALYSIS

2. How to visually interpret biological data using networks
   Merico D, Gfeller D, Bader GD
   Nature Biotechnology 2009 Oct 27, 921-924
   PubMed Abstract - PDF
   Data: http://www.baderlab.org/NetworkPrimerNBT
   NETWORK PRIMER

3. Rapid evolution of functional complexity in a domain family
   Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS
   Science Signaling 2009 Sep 8;2(87):ra50
   PubMed Abstract - PDF
   PROTEIN INTERACTION NETWORK EVOLUTION

4. Positive Selection of Tyrosine Loss in Metazoan Evolution
   Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R
   Science. Sep 25;325(5948):1686-8. Epub 2009 Jul 9
   PubMed Abstract - PDF
   PROTEIN INTERACTION NETWORK EVOLUTION

5. Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases
   Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R
   Science Signaling 2(81):r39 (2009)
   PubMed Abstract - PDF
   PROTEIN INTERACTION NETWORK EVOLUTION

2008

1. A Specificity Map for the PDZ Domain Family
   Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS.
   PLoS Biology Vol. 6, No. 9, e239
   PubMed Abstract - PDF
   PROTEIN-PROTEIN INTERACTION ANALYSIS

2. 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

3. 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

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

1. 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

2. 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

1. 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

1. 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

2. 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

1. Playing tag with the yeast proteome
   Andrews BJ, Bader GD, Boone C
   Nature Biotechnology Nov;21(11):1297-1299
   PubMed Abstract - PDF
   REVIEW

2. 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

3. 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

4. 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

5. 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

6. 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

1. 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

2. 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

3. 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

4. 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

1. 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

2. 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

1. 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

1. 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

1. 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

1. 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

2. 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

1. 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

2. 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

3. 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

1. 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

1. 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