Peer-reviewed Journals

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions,
Aranda B, Blankenburg H, Kerrien S, Brinkman FSL, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock REW, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M & Hermjakob H;
Nature Methods 8, 528–529 (2011)
Pubmed Abstract
PROTEIN INTERACTION
Response to Comment on Positive Selection of Tyrosine Loss in Metazoan Evolution,
Tan CS, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD and Linding R;
Science 332(6032):917, 20 May 2011
The multiple-specificity landscape of modular peptide recognition domains,
Gfeller D., Butty F., Wierzbicka M., Verschueren E., Vanhee P., Huang H., Ernst A., Dar N., Stagljar I., Serrano L., Sidhu S.S., Bader G.D., Kim P.M.;
Molecular Systems Biology 7:484, 26 April 2011
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks,
Oesper L., Merico D., Isserlin R., Bader G.D.;
Source Code for Biology and Medicine 2011, 6:7, 7 April 2011
NETWORK ANALYSIS SOFTWARE
Protein Complexes are Central in the Yeast Genetic Landscape,
Michaut M., Baryshnikova A., Costanzo M., Myers C.L., Andrews B.J., Boone C., Bader G.D.;
PLoS Computational Biology 7(2): e1001092 Feb 24 2011
February 2011 Issue Cover
GENETIC INTERACTION NETWORK ANALYSIS
Bringing order to protein disorder through comparative genomics and genetic interactions
Bellay J*, Han S*, Michaut M*, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM
Genome Biology 12(2):R14 Feb 15 2011
PubMed Abstract
PROTEIN DISORDER AND COMPARATIVE GENOMICS
Too Many Roads Not Taken
Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH
Nature (470) 163-165 Feb 9 2011
PubMed Abstract - PDF
Full Paper on arxiv.org
BIBLIOMETRIC ANALYSIS
The Biomolecular Interaction Network Database in PSI-MI 2.5
Isserlin R, El-Badrawi RA, Bader GD
Database 2011; doi: 10.1093/database/baq037
PubMed Abstract - PDF
PROTEIN INTERACTION DATABASE

2010

A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence
Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD
Bioinformatics 2010 Dec 2
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Merico D, Isserlin R, Stueker O, Emili A, Bader GD
PLoS One. 2010 Nov 15;5(11):e13984
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology
Jain S, Bader GD
BMC Bioinformatics. 2010 Nov 15;11(1):562
PubMed Abstract -PDF
PROTEIN INTERACTION PREDICTION
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL
Nat Methods. 2010 Nov 14
PubMed Abstract -PDF
GENETIC INTERACTION NETWORK ANALYSIS
Pathway Commons, a web resource for biological pathway data
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C
Nucleic Acids Res. 2010 Nov 10
PubMed Abstract -PDF
PATHWAY DATABASE
Proteome scanning to predict PDZ domain interactions using support vector machines
Hui S, Bader GD
BMC Bioinformatics. 2010 Oct 12;11(1):50
PubMed Abstract -PDF
PROTEIN INTERACTION PREDICTION
GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD
Bioinformatics. 2010 Oct 5
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Dynamic interaction networks in a hierarchically organized tissue
Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW
Mol Syst Biol. 2010 Oct 5;6:417
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling
Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, Gfeller D, Bader G, Sidhu S, Vandekerckhove J, Gettemans J, Sudol M
Biochem J. 2010 Sep 24
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
The BioPAX community standard for pathway data sharing
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Novère NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD
Nat Biotechnol. 2010 Sep;28(9):935-42
PubMed Abstract - PDF
DATA STANDARD
Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS.
Mol. BioSyst., 2010, Advance Article
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Cytoscape Web: an interactive web-based network browser
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD
Bioinformatics. 2010 Jul 23
PubMed Abstract - PDF
NETWORK VISUALIZATION
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W214-20
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Functional impact of global rare copy number variation in autism spectrum disorders.
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C
Nature. 2010 Jun 9 (Epub ahead of print)
PubMed Abstract - PDF
Nature Blogs - In the news (The Globe and Mail)
PATHWAY AND NETWORK ANALYSIS
A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans.
Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ
Nat Chem Biol. 2010 May 30
PubMed Abstract - PDF
NCB_News&Views.pdf
CHEMICAL GENOMICS
International network of cancer genome projects
International Cancer Genome Consortium
Nature. 2010 Apr 15;464(7291):993-8
PubMed Abstract - PDF
CANCER GENOMICS
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A.
Proteomics 2010, March 10(6):1316-27
Pubmed Abstract - PDF
PATHWAY ANALYSIS
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
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
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

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
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
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
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
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

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
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

Theses

2011 Xiaojian Shao - Prediction of Protein-Nucleic Acids and Protein-Protein Interactions Using Kernel Methods - PDF (in Mandarin), China Agricultural University and the University of Toronto

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+== 2011 ==
 1. '''PSICQUIC and PSISCORE: accessing and scoring molecular interactions''', <<BR>> Aranda B, Blankenburg H, Kerrien S,  Brinkman FSL,	Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock REW, '''Isserlin R''', Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, '''Michaut M''', O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M,	 Velankar S, Winter A, Wu G, '''Bader GD''', Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M & Hermjakob H; <<BR>> [[http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1637.html|Nature Methods 8, 528–529 (2011)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21716279|Pubmed Abstract]]<<BR>> '''PROTEIN INTERACTION''' 

 1. '''Response to Comment on ''Positive Selection of Tyrosine Loss in Metazoan Evolution''''', <<BR>>  '''Tan CS''', Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, '''Bader GD''' and Linding R; <<BR>>[[http://www.sciencemag.org/content/332/6032/917.2.full|Science 332(6032):917, 20 May 2011]] <<BR>>

 1. '''The multiple-specificity landscape of modular peptide recognition domains''', <<BR>>'''Gfeller D.''', Butty F., Wierzbicka M., Verschueren E., Vanhee P., Huang H., Ernst A., Dar N., Stagljar I., Serrano L., Sidhu S.S., '''Bader G.D.''', Kim P.M.; <<BR>>[[http://www.nature.com/msb/journal/v7/n1/full/msb201118.html|Molecular Systems Biology 7:484, 26 April 2011]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/21525870|PubMed Abstract]] - [[attachment:2011_Gfeller.pdf|PDF]]<<BR>> '''PROTEIN INTERACTION PREDICTION'''

 1. '''!WordCloud: a Cytoscape plugin to create a visual semantic summary of networks''', <<BR>>Oesper L., '''Merico D.''', '''Isserlin R.''', '''Bader G.D.'''; <<BR>>[[http://www.scfbm.org/content/6/1/7/abstract|Source Code for Biology and Medicine 2011, 6:7, 7 April 2011]] <<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Protein Complexes are Central in the Yeast Genetic Landscape''', <<BR>>'''Michaut M.''', Baryshnikova A., Costanzo M., Myers C.L., Andrews B.J., Boone C., '''Bader G.D.'''; <<BR>>[[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001092|PLoS Computational Biology 7(2): e1001092 Feb 24 2011]] <<BR>> [[http://www.ploscompbiol.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcbi.v07.i02|February 2011 Issue Cover]] <<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''Bringing order to protein disorder through comparative genomics and genetic interactions'''<<BR>>Bellay J*, Han S*, '''Michaut M*''', Kim T, Costanzo M, Andrews BJ, Boone C, '''Bader GD''', Myers CL, Kim PM<<BR>>[[http://genomebiology.com/2011/12/2/R14/abstract|Genome Biology 12(2):R14 Feb 15 2011]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21324131|PubMed Abstract]]<<BR>>'''PROTEIN DISORDER AND COMPARATIVE GENOMICS'''

 1. '''Too Many Roads Not Taken'''<<BR>>Edwards AM, '''Isserlin R''', '''Bader GD''', Frye SV, Willson TM, Yu FH <<BR>>[[http://www.nature.com/nature/journal/v470/n7333/full/470163a.html|Nature (470) 163-165 Feb 9 2011]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21307913|PubMed Abstract]] - [[attachment:nature_comment_Feb2011.pdf|PDF]]<<BR>>[[http://arxiv.org/abs/1102.0448|Full Paper on arxiv.org]]<<BR>> '''BIBLIOMETRIC ANALYSIS'''

 1. '''The Biomolecular Interaction Network Database in PSI-MI 2.5'''<<BR>>'''Isserlin R''', '''El-Badrawi RA''', '''Bader GD'''<<BR>>[[http://database.oxfordjournals.org/cgi/content/abstract/baq037?ijkey=5ex1hxBFa242Q8L&keytype=ref|Database 2011; doi: 10.1093/database/baq037]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21233089|PubMed Abstract]] - [[http://database.oxfordjournals.org/content/2011/baq037.full.pdf?keytype=ref&ijkey=5ex1hxBFa242Q8L|PDF]]<<BR>>'''PROTEIN INTERACTION DATABASE'''
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+. '''A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence'''<<BR>>'''Shao X''', '''Tan CS''', Voss C, Li SS, Deng N, '''Bader GD'''<<BR>>[[http://bioinformatics.oxfordjournals.org/content/early/2010/12/02/bioinformatics.btq657.abstract|Bioinformatics 2010 Dec 2]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21127034|PubMed Abstract]] - [[attachment:2010_ShaoTanBader-PDZAffinity_Bioinformatics.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''
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-. '''The Genetic Landscape of a Cell'''<<BR>>Michael Costanzo,1,2,* Anastasia Baryshnikova,1,2,* Jeremy Bellay,3 Yungil Kim,3 Eric D. Spear,4 Carolyn S. Sevier,4 Huiming Ding,1,2 Judice L.Y. Koh,1,2 Kiana Toufighi,1,2 Sara Mostafavi,1,5 Jeany Prinz,1,2 Robert P. St. Onge,6 Benjamin VanderSluis,3 Taras Makhnevych,7 Franco J. Vizeacoumar,1,2 Solmaz Alizadeh,1,2 Sondra Bahr,1,2 Renee L. Brost,1,2 Yiqun Chen,1,2 Murat Cokol,8 Raamesh Deshpande,3 Zhijian Li,1,2 Zhen-Yuan Lin,9 Wendy Liang,1,2 Michaela Marback,1,2 Jadine Paw,1,2 Bryan-Joseph San Luis,1,2 Ermira Shuteriqi,1,2 Amy Hin Yan Tong,1,2 Nydia van Dyk,1,2 Iain M. Wallace,1,2,10 Joseph A. Whitney,1,5 Matthew T. Weirauch,11 Guoqing Zhong,1,2 Hongwei Zhu,1,2 Walid A. Houry,7 Michael Brudno,1,5 Sasan Ragibizadeh,12 Balázs Papp,13 Csaba Pál,13 Frederick P. Roth,8 Guri Giaever,2,10 Corey Nislow,1,2 Olga G. Troyanskaya,14 Howard Bussey,15 Gary D. Bader,1,2 Anne-Claude Gingras,9 Quaid D. Morris,1,2,5 Philip M. Kim,1,2 Chris A. Kaiser,4 Chad L. Myers,3, Brenda J. Andrews,1,2 Charles Boone<<BR>>[[http://www.sciencemag.org/cgi/content/short/327/5964/425|Vol. 327. no. 5964, pp. 425 - 431, Science 22 January 2010]]<<BR>>[[PubMed Abstract]] - [[attachment:2010_CostanzoBaryshnikova_GeneticLandscapeOfTheCell_Science_Jan.pdf|PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''
+. '''Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation'''<<BR>>'''Merico D''', '''Isserlin R''', '''Stueker O''', Emili A, '''Bader GD'''<<BR>>[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013984|PLoS One. 2010 Nov 15;5(11):e13984]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21085593|PubMed Abstract]] -[[attachment:2010_MericoIsserlinStuekerBader-EnrichmentMap_PLoSOne.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''
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-. '''NetPath: a public resource of curated signal transduction pathways'''<<BR>>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<<BR>>[[http://genomebiology.com/2010/11/1/R3|Genome Biology 2010 Jan 12;11(1):R3]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20067622|PubMed Abstract]] - [[attachment:2010_Kandasamy_NetPath_GenomeBiol_Jan.pdf|PDF]]<<BR>>'''PATHWAY DATABASE'''
+. '''An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology'''<<BR>>'''Jain S, Bader GD'''<<BR>>[[http://www.biomedcentral.com/1471-2105/11/562|BMC Bioinformatics. 2010 Nov 15;11(1):562]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21078182|PubMed Abstract]] -[[attachment:2010_JainBader-SemanticSimilarityGO_BMCBioinformatics.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''

 1. '''Quantitative analysis of fitness and genetic interactions in yeast on a genome scale'''<<BR>>'''Baryshnikova A''', Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, '''Bader GD''', Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL<<BR>>[[http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1534.html|Nat Methods. 2010 Nov 14]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21076421|PubMed Abstract]] -[[attachment:2010_BaryshnikovaMyers-SGAScore_NatMethods.pdf|PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''Pathway Commons, a web resource for biological pathway data'''<<BR>>Cerami EG, Gross BE, Demir E, '''Rodchenkov I''', Babur O, Anwar N, Schultz N, '''Bader GD''', Sander C<<BR>>[[http://nar.oxfordjournals.org/content/early/2010/11/10/nar.gkq1039.long|Nucleic Acids Res. 2010 Nov 10]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21071392|PubMed Abstract]] -[[attachment:2010_CeramiBaderSander-PathwayCommons_NAR.pdf|PDF]]<<BR>>'''PATHWAY DATABASE'''

 1. '''Proteome scanning to predict PDZ domain interactions using support vector machines'''<<BR>>'''Hui S''', '''Bader GD'''<<BR>>[[http://www.biomedcentral.com/1471-2105/11/507|BMC Bioinformatics. 2010 Oct 12;11(1):50]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20939902|PubMed Abstract]] -[[attachment:2010_HuiBader-ProteomeScanningPDZ_BMCBioinformatics.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''

 1. '''GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop'''<<BR>>'''Montojo J''', '''Zuberi K''', '''Rodriguez H''', '''Kazi F''', '''Wright G''', '''Donaldson SL''', Morris Q, '''Bader GD'''<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/reprint/btq562|Bioinformatics. 2010 Oct 5]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20926419|PubMed Abstract]] -[[attachment:2010_GeneMANIA_Cytoscape_Plugin_Montojo_Bioinformatics_Oct.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Dynamic interaction networks in a hierarchically organized tissue'''<<BR>>Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, '''Bader GD''', Zandstra PW<<BR>>[[http://www.nature.com/msb/journal/v6/n1/full/msb201071.html|Mol Syst Biol. 2010 Oct 5;6:417]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20924352|PubMed Abstract]] - [[attachment:2010_KirouacZandstra_DynamicCellCellInteractionNetworks_MSB_Oct.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling'''<<BR>>Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, '''Gfeller D''', '''Bader G''', Sidhu S, Vandekerckhove J, Gettemans J, Sudol M<<BR>>[[http://www.biochemj.org/bj/imps/abs/BJ20100870.htm|Biochem J. 2010 Sep 24]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20868367|PubMed Abstract]] - [[attachment:2010_OkaSudol_YAP2_ZO2_BJ_Oct.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''

 1. '''The BioPAX community standard for pathway data sharing'''<<BR>>Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, '''Rodchenkov I''', Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, '''Donaldson S''', Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, !McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Novère NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, '''Bader GD'''<<BR>>[[http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html|Nat Biotechnol. 2010 Sep;28(9):935-42]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20829833|PubMed Abstract]] - [[attachment:2010_Demir_BioPAX_NatBiotech_Sep.pdf|PDF]]<<BR>>'''DATA STANDARD'''

 1. '''Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing'''<<BR>>Ernst A, '''Gfeller D''', Kan Z, Seshagiri S, Kim PM, '''Bader GD''', Sidhu SS.<<BR>>[[http://pubs.rsc.org/en/Content/ArticleLanding/2010/MB/C0MB00061B|Mol. BioSyst., 2010, Advance Article]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20714644|PubMed Abstract]] - [[attachment:2010_ErnstSidhu_PDZSpecificityEvolution_MBS_Aug.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK EVOLUTION'''

 1. '''Cytoscape Web: an interactive web-based network browser'''<<BR>>'''Lopes CT''', '''Franz M''', '''Kazi F''', '''Donaldson SL''', Morris Q, '''Bader GD'''<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/reprint/btq430v1|Bioinformatics. 2010 Jul 23]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20656902|PubMed Abstract]] - [[attachment:2010_CytoscapeWeb_Lopes_Bioinformatics_Jul.pdf|PDF]]<<BR>>'''NETWORK VISUALIZATION'''

 1. '''The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function'''<<BR>>Warde-Farley D, '''Donaldson SL''', '''Comes O''', '''Zuberi K''', '''Badrawi R''', '''Chao P''', '''Franz M''', Grouios C, '''Kazi F''', '''Lopes CT''', '''Maitland A''', Mostafavi S, '''Montojo J''', '''Shao Q''', '''Wright G''', '''Bader GD''', Morris Q<<BR>>[[http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_2/W214|Nucleic Acids Res. 2010 Jul 1;38 Suppl:W214-20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20576703|PubMed Abstract]] - [[attachment:2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Functional impact of global rare copy number variation in autism spectrum disorders.'''<<BR>>Pinto D, Pagnamenta AT, Klei L, Anney R, '''Merico D''', Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, '''Bader GD''', Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09146.html|Nature. 2010 Jun 9 (Epub ahead of print)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20531469|PubMed Abstract]] - [[attachment:2010_AutismNature.pdf|PDF]]<<BR>>[[http://blogs.nature.com/news/thegreatbeyond/2010/06/rare_genetic_variants_linked_t.html|Nature Blogs]] - [[http://www.theglobeandmail.com/news/national/autism-caused-by-wide-array-of-rare-gene-changes-study/article1597861/|In the news (The Globe and Mail)]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans.'''<<BR>>Burns AR, '''Wallace IM''', Wildenhain J, Tyers M, Giaever G, '''Bader GD''', Nislow C, Cutler SR, Roy PJ<<BR>>[[http://www.nature.com/nchembio/journal/vaop/ncurrent/abs/nchembio.380.html|Nat Chem Biol. 2010 May 30]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20512140|PubMed Abstract]] - [[attachment:2010_BurnsWallace_bioaccumulationWorms_May.pdf|PDF]]<<BR>>[[attachment:NCB_News&Views.pdf]]<<BR>>'''CHEMICAL GENOMICS'''

 1. '''International network of cancer genome projects'''<<BR>>International Cancer Genome Consortium<<BR>>[[http://www.nature.com/nature/journal/v464/n7291/full/nature08987.html|Nature. 2010 Apr 15;464(7291):993-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20393554|PubMed Abstract]] - [[attachment:2010_ICGC.pdf|PDF]]<<BR>>'''CANCER GENOMICS'''

 1. '''Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps'''<<BR>>'''Isserlin R''', '''Merico D''', Alikhani-Koupaei R, Gramolini A, '''Bader GD''', Emili A.<<BR>>[[http://www3.interscience.wiley.com/journal/123269335/abstract|Proteomics 2010, March 10(6):1316-27]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20127684|Pubmed Abstract]] - [[attachment:2010_EM_proteomics.pdf|PDF]]<<BR>>'''PATHWAY ANALYSIS'''

 1. '''The Genetic Landscape of a Cell'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/short/327/5964/425|Science. 2010 Jan 22;327(5964):425-31]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20093466|PubMed Abstract]] - [[attachment:2010_CostanzoBaryshnikova_GeneticLandscapeOfTheCell_Science_Jan.pdf|PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''!NetPath: a public resource of curated signal transduction pathways'''<<BR>>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<<BR>>[[http://genomebiology.com/2010/11/1/R3|Genome Biology 2010 Jan 12;11(1):R3]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/20067622|PubMed Abstract]] - [[attachment:2010_Kandasamy_NetPath_GenomeBiol_Jan.pdf|PDF]]<<BR>>'''PATHWAY DATABASE'''
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+. '''Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins'''<<BR>>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<<BR>>[[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000218|PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19841731|PubMed Abstract]] - [[attachment:2009_Tonikian_YeastSH3_PLoSBiology_Oct.pdf|PDF]]<<BR>>'''PROTEIN-PROTEIN INTERACTION ANALYSIS'''
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-. '''Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins'''<<BR>>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<<BR>>[[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000218|PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19841731|PubMed Abstract]] - [[attachment:2009_Tonikian_YeastSH3_PLoSBiology_Oct.pdf|PDF]]<<BR>>'''PROTEIN-PROTEIN INTERACTION ANALYSIS'''

 1. '''How to visually interpret biological data using networks'''<<BR>> '''Merico D''', '''Gfeller D''', '''Bader GD'''<<BR>>[[http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1567.html|Nature Biotechnology 2009 Oct 27, 921-924]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19816451|PubMed Abstract]] - [[attachment:2009_Merico_Primer_NatBiotech_Oct.pdf|PDF]]<<BR>> Data: [[http://www.baderlab.org/NetworkPrimerNBT|http://www.baderlab.org/NetworkPrimerNBT]]<<BR>>'''NETWORK PRIMER'''
+. '''How to visually interpret biological data using networks'''<<BR>> '''Merico D''', '''Gfeller D''', '''Bader GD'''<<BR>>[[http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1567.html|Nature Biotechnology 2009 Oct 27, 921-924]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19816451|PubMed Abstract]] - [[attachment:2009_Merico_Primer_NatBiotech_Oct.pdf|PDF]]<<BR>> Data: http://www.baderlab.org/NetworkPrimerNBT <<BR>> '''NETWORK PRIMER'''
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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'''
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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'''
+= Theses =
 1. 2011 '''Xiaojian Shao''' - Prediction of Protein-Nucleic Acids and Protein-Protein Interactions Using Kernel Methods - [[attachment:PhDThesis(XiaojianShao).pdf|PDF]] (in Mandarin), China Agricultural University and the University of Toronto