Peer-reviewed Journals

2008

1. Cytoscape ESP: simple search of complex biological networks.BRAshkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJBR[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]BRNETWORK ANALYSIS SOFTWARE

2. Computational prediction of protein-protein interactions.BRSkrabanek L, Saini HK, Bader GD, Enright AJBR[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]BRREVIEW

2007

1. Integration of biological networks and gene expression data using CytoscapeBRCline 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 GDBR[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]BRNETWORK ANALYSIS SOFTWARE

2. Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular InteractionsBRKerrien 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 HBR[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]BRDATA STANDARD

3. The minimum information required for reporting a molecular interaction experiment (MIMIx)BROrchard 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 HBR[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]BRDATA STANDARD

4. Germ-line DNA copy number variation frequencies in a large North American populationBRZogopoulos 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 SBR[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]BRGENOMICS

5. From bytes to bedside: data integration and computational biology for translational cancer researchBRMathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra BBR[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]BRCANCER REVIEW

6. NetMatch: a Cytoscape Plugin for Searching Biological NetworksBRFerro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha DBR[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]BRNETWORK ANALYSIS SOFTWARE

7. Computational prediction of cancer-gene functionBRHu P, Bader G, Wigle DA, Emili ABR[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]BRCANCER REVIEW

2006

1. cPath: open source software for collecting, storing, and querying biological pathwaysBRCerami EG, Bader GD, Gross BE, Sander CBR[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]BRPATHWAY SOFTWARE

2. Pathguide: a Pathway Resource ListBRBader GD, Cary MP, Sander CBR[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]BRPATHWAY WEBSITE

2005

1. Pathway information for systems biologyBRCary MP, Bader GD, Sander CBR[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]BRPATHWAY REVIEW

2004

1. Global Mapping of the Yeast Genetic Interaction NetworkBRTong 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 CBR[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]BRGENETIC INTERACTION NETWORK ANALYSIS

2. The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction dataBRHermjakob 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 RBR[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]BRDATA STANDARD

2003

1. Playing tag with the yeast proteomeBRAndrews BJ, Bader GD, Boone CBR[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]BRREVIEW

2. Functional Genomics and Proteomics: Charting a Multidimensional Map of the CellBRBader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone CBR[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]BRREVIEW

3. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machineBRDonaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CWBR[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]BRTEXT MINING SOFTWARE

4. Functional genomics of intracellular peptide recognition domains with combinatorial biology methodsBRSidhu SS, Bader GD, Boone CBR[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]BRREVIEW

5. An automated method for finding molecular complexes in large protein interaction networksBRBader GD, Hogue CWVBR[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]BRALGORITHM

6. BIND-The Biomolecular Interaction Network DatabaseBRBader GD, Betel D, Hogue CWVBR[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]BRINTERACTION DATABASE

2002

1. SeqHound: biological sequence and structure database as a platform for bioinformatics researchBRMichalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CWBR[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]BRPROTEIN DATABASE

2. Analyzing yeast protein–protein interaction data obtained from different sourcesBRBader GD, Hogue CWBR[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]BRMETA-ANALYSIS

3. A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition ModulesBRTong 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 GBR[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]BRPROTEIN INTERACTION PREDICTION

4. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometryBRHo 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 MBR[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]BRPROTEIN INTERACTION NETWORK ANALYSIS

2001

1. Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion MutantsBRTong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone CBR[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]BRGENETIC INTERACTION NETWORK ANALYSIS

2. BIND - The Biomolecular Interaction Network DatabaseBRBader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CWBR[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]BRINTERACTION DATABASE

2000

1. BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathwaysBRBader GD, Hogue CWBR[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]BRINTERACTION DATABASE

Textbook Chapters

2006

1. BioPAX - Biological Pathway Data Exchange FormatBRGary D. Bader, Michael Cary, Chris SanderBR[http://www.mrw.interscience.wiley.com/ggpb/articles/g408117/frame.html Encyclopedia of Genomics, Proteomics and Bioinformatics]BRHumana Press, New JerseyBRDATA STANDARD

2005

1. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksBRRowan 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 SanderBR[http://educationbook.aacrjournals.org/cgi/content/full/2005/1/12 Am Assoc Cancer Res Educ Book 2005: 12-16]BRNETWORK ANALYSIS SOFTWARE

2. Exploiting Synthetic Genetic Interactions to Predict Pathways and ComplexesBRGary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles BooneBRin [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.]BREd. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USABRGENETIC INTERACTION NETWORK ANALYSIS

2004

1. Interaction Databases, in Genomics and Bioinformatics, 2nd EditionBRGary D. Bader, Christopher W.V. HogueBRin [http://www.wiley-vch.de/books/biotech/con_v05b.html Volume 5B of the Series: Biotechnology, 2nd Edition.]BREds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, GermanyBRINTERACTION DATABASE

2. Intermolecular Interactions and Biological PathwaysBRGary D. Bader, Anton J. EnrightBRin [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]BRINTERACTION DATABASE

3. Computational Prediction of Protein-Protein InteractionsBRAnton J. Enright, Lucy Skrabanek, Gary D. BaderBRin [http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1 The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)]BRPROTEIN INTERACTION PREDICTION

2003

1. Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein InteractionsBRGary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles BooneBRin [http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462 Handbook of Cell Signaling]BREds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)BRPROTEIN INTERACTION PREDICTION

2002

1. Interaction DatabasesBRGary D. Bader, Christopher W.V. HogueBRChapter 18, in [http://www.wiley-vch.de/books/biotech/vol_05b.html Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)]BREds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.BRWiley-VCH, GermanyBRINTERACTION DATABASE