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Peer-reviewed Articles

2013

1. GESTODIFFERENT: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process
   Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi and Giancarlo Mauri
   Bioinformatics (2013) doi: 10.1093/bioinformatics/bts726
   PubMed Abstract PDF
   NETWORK SIMULATION

2012

1. The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community
   Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS
   J Proteome Res. 2013 Jan 4;12(1):23-7. doi: 10.1021/pr301151m. Epub 2012 Dec 21
   PubMed Abstract PDF
   PROTEOMICS

2. Chromatin is an ancient innovation conserved between Archaea and Eukarya
   Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C
   eLife. 2012 Dec 13. DOI: http://dx.doi.org/10.7554/eLife.00078
   PubMed Abstract PDF
   ANALYSIS OF ARCHAEAL CHROMATIN

3. Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion
   Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L
   Cell Stem Cell. 2012 Nov 7. doi:pii: S1934-5909(12)00537-1. 10.1016/j.stem.2012.09.001
   PubMed Abstract PDF
   PATHWAY AND NETWORK ANALYSIS

4. A travel guide to Cytoscape plugins
   Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T
   Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6
   PubMed Abstract PDF
   PATHWAY AND NETWORK ANALYSIS

5. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
   Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R
   BMC Syst Biol. 2012 Aug 28;6:112. doi: 10.1186/1752-0509-6-112
   PubMed Abstract PDF
   PATHWAY AND NETWORK ANALYSIS

6. Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice
   Xiong X, Chorzalska A, Dubielecka PM, White JR, Vedvyas Y, Hedvat CV, Haimovitz-Friedman A, Koutcher JA, Reimand J, Bader GD, Sawicki JA, Kotula L
   Oncogenesis (2012) 1, e26; doi:10.1038/oncsis.2012.28
   PDF
   CANCER GENOMICS

7. Subgroup-specific structural variation across 1,000 medulloblastoma genomes
   Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD
   Nature. 2012 Aug 2;488(7409):49-56
   PubMed Abstract
   PATHWAY AND NETWORK ANALYSIS

8. A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals
   Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ
   Stem Cells. 2012 Jun 13 doi: 10.1002/stem.1144
   PubMed Abstract PDF
   PATHWAY AND NETWORK ANALYSIS

9. Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction
   Michaut M, Bader GD
   PLoS Comput Biol 8(6): e1002559
   PubMed Abstract PDF
   GENETIC INTERACTIONS

10. Domain-mediated protein interaction prediction: From genome to network
    Reimand J, Hui S, Jain S, Law B, Bader GD
    FEBS Lett. 2012 May 3
    PubMed Abstract PDF
    PROTEIN INTERACTIONS

11. Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer
    Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E
    Proc Natl Acad Sci U S A. 2012 Mar 28
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS

12. Phosphorylation sites of higher stoichiometry are more conserved
    Tan CS, Bader GD
    Nat Methods. 2012 Mar 27;9(4):317
    PubMed Abstract -PDF
    PHOSPHOPROTEOMICS

13. Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry
    Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE
    PLoS Genet. 2012 Mar;8(3):e1002562
    PubMed Abstract -PDF
    PATHWAY AND NETWORK ANALYSIS

2011

1. MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
   Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM
   Nucleic Acids Res. 2011 Dec 30
   PubMed Abstract -PDF
   DOMAIN SPECIFICITY SOFTWARE

2. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
   Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A
   Stand Genomic Sci. 2011 Nov 30;5(2):230-42
   PubMed Abstract -PDF
   DATA STANDARD

3. clusterMaker: a multi-algorithm clustering plugin for Cytoscape
   Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE
   BMC Bioinformatics. 2011 Nov 9;12(1):436
   PubMed Abstract -PDF
   NETWORK ANALYSIS SOFTWARE

4. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms
   Iain M. Wallace, Malene L. Urbanus, Genna M. Luciani,Andrew R. Burns,Mitchell K.L. Han, Hao Wang, Kriti Arora, Lawrence E. Heisler, Michael Proctor, Robert P. St. Onge, Terry Roemer, Peter J. Roy,Carolyn L. Cummins, Gary D. Bader, Corey Nislow, Guri Giaever
   Cell Chemistry & Biology 2011 18, 1273–1283
   PubMed Abstract - PDF
   Chemistry & Biology 2011 18:10, 1204-1205 Commentary on paper
   CHEMICAL GENOMICS

5. NetSlim: high-confidence curated signaling maps
   Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Sameer Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A
   Database (Oxford). 2011 Sep 29;2011(0):bar032
   PubMed Abstract - PDF
   PATHWAY DATABASE

6. Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
   Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM
   Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011
   PubMed Abstract - PDF
   PATHWAY ANALYSIS

7. A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway
   Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, Pandey A
   Database (Oxford). 2011 Jul 8;2011
   PubMed Abstract -PDF
   PATHWAY DATABASE

8. PSICQUIC and PSISCORE: accessing and scoring molecular interactions
   Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, 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 2011 Jun 29;8(7):528-9
   Pubmed Abstract PDF
   PROTEIN INTERACTIONS

9. 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
   PDF
   NETWORK EVOLUTION

10. 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 SS, Bader GD, Kim PM
    Molecular Systems Biology 7:484, 26 April 2011
    PubMed Abstract - PDF
    PROTEIN INTERACTION PREDICTION

11. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks
    Oesper L, Merico D, Isserlin R, Bader GD
    Source Code for Biology and Medicine 2011, 6:7, 7 April 2011
    PubMed Abstract -PDF
    NETWORK ANALYSIS SOFTWARE

12. Protein Complexes are Central in the Yeast Genetic Landscape
    Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD
    PLoS Computational Biology 7(2): e1001092 Feb 24 2011
    February 2011 Issue Cover
    PubMed Abstract - PDF
    GENETIC INTERACTION NETWORK ANALYSIS

13. 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 - PDF
    PROTEIN DISORDER AND COMPARATIVE GENOMICS

14. 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

15. 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

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. International network of cancer genome projects
    International Cancer Genome Consortium
    Nature. 2010 Apr 15;464(7291):993-8
    PubMed Abstract - PDF
    CANCER GENOMICS

17. 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

18. 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

19. 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

20. 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

2011

1. Displaying chemical information on a biological network using cytoscape
   Wallace IM, Bader GD, Giaever G, Nislow C
   Methods Mol Biol. 2011;781:363-76 - PubMed Abstract - PDF Supplemental Website
   NETWORK ANALYSIS SOFTWARE

2. Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
   Merico D, Isserlin R, Bader GD
   Methods Mol Biol. 2011;781:257-77 - PubMed Abstract - PDF
   NETWORK ANALYSIS SOFTWARE

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)
   PDF
   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

Theses

1. 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