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Peer-reviewed Articles

2014

  1. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.
    Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A.
    Mol Biosyst. 2014 Oct
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  2. Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K.
    Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-Awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E.
    EMBO Mol Med. 2014 Oct 20. pii: e201404402. doi: 10.15252/emmm.201404402
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  3. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
    James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack F. Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary Bader, Mohan Babu
    Bioinformatics (2014) doi: 10.1093/bioinformatics/btu671
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  4. GeneMANIA: Fast gene network construction and function prediction for Cytoscape
    Jason Montojo,Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
    F1000Res. 2014 Jul 1;3:153
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  5. Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.
    Isserlin R, Merico D, Voisin V, Bader GD
    F1000Res. 2014 Jul 1;3:141
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  6. Intercellular network structure and regulatory motifs in the human hematopoietic system
    Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW
    Mol Syst Biol. 2014 Jul 15;10(7):741
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  7. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
    Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM
    Nature. 2014 Jul 24;511(7510):428-34
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  8. Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma
    Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB
    Cancer Cell. 2014 Jun 17. pii: S1535-6108(14)00220-7
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  9. Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction
    Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q
    Front Genet. 2014 May 16;5:123
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  10. A draft map of the human proteome
    Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A
    Nature. 2014 May 29;509(7502):575-81
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  11. Mapping the cellular response to small molecules using chemogenomic fitness signatures
    Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G
    Science 2014 Apr 11;344(6180):208-11
    PubMed Abstract - PDF
    CHEMICAL GENOMICS

  12. Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs
    Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD
    PLoS One. 2014 Apr 10;9(4):e94507
    PubMed Abstract - PDF
    FUNCTIONAL MUTATION ANALYSIS

  13. HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
    Leung A, Bader GD, Reimand J
    Bioinformatics. 2014 Apr 8
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  14. Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition
    Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project
    Cancer Cell. 2014 Mar 17;25(3):393-405
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  15. Highlights of B/D-HPP and HPP Resource Pillar Workshops at Yokohama 12th Annual HUPO World Congress of Proteomics
    Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS
    Proteomics. 2014 May;14(9):975-88
    PubMed Abstract - PDF
    PROTEOMICS

  16. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
    Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD
    Nature. 2014 Feb 27;506(7489):445-50
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

2013

  1. TCGA pan-cancer project, thread 2: Network models
    Reimand J, Bader GD, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton
    Nature Genetics (2013) doi:10.1038/ng.2787
    CANCER MUTATIONS, NETWORKS

  2. Coordinate microRNA-mediated regulation of protein complexes in prostate cancer
    Alshalalfa M, Bader GD, Bismar TA, Alhajj R
    PLoS One. 2013 Dec 31;8(12):e84261
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  3. Comprehensive identification of mutational cancer driver genes across 12 tumor types
    Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N
    Sci Rep. 2013 Oct 2;3:2650
    PubMed Abstract - PDF
    CANCER MUTATIONS

  4. The mutational landscape of phosphorylation signaling in cancer
    Reimand J, Wagih O, Bader GD
    Sci Rep. 2013 Oct 2;3:2651
    PubMed Abstract - PDF
    CANCER MUTATIONS, NETWORKS

  5. Using biological pathway data with paxtools
    Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.
    PLoS Comput Biol. 2013;9(9):e1003194
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  6. The BioPAX Validator
    Rodchenkov I, Demir E, Sander C, Bader GD
    Bioinformatics. 2013 Oct 15;29(20):2659-60
    PubMed Abstract - PDF
    DATA STANDARD

  7. Computational approaches to identify functional genetic variants in cancer genomes
    Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group
    Nature Methods (2013) doi:10.1038/nmeth.2562
    PubMed Abstract - PDF
    CANCER MUTATIONS

  8. GeneMANIA prediction server 2013 update
    Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q
    Nucleic Acids Res. 2013 Jul;41(Web Server issue):W115-22
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  9. Cytoscape App Store
    Lotia S, Montojo J, Dong Y, Bader GD, Pico AR
    Bioinformatics. 2013 May 15;29(10):1350-1
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  10. SH3 interactome conserves general function over specific form
    Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD
    Mol Syst Biol. 2013 Apr 2;9:652
    Pubmed Abstract - PDF
    Interactions in Intact Database
    PROTEIN INTERACTION PREDICTION

  11. Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells
    Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD.
    PLoS One. 2013;8(3):e58367
    Pubmed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  12. Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
    Reimand J, Bader GD
    Mol Syst Biol. 2013;9:637
    PubMed Abstract - PDF
    Research Highlight in Genome Medicine (2013)
    CANCER MUTATIONS, SIGNALING NETWORKS

  13. Predicting PDZ domain mediated protein interactions from structure
    Hui S, Xing X, Bader GD
    BMC Bioinformatics. 2013 Jan 21;14:27
    PubMed Abstract - PDF
    PROTEIN INTERACTION PREDICTION

  14. Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation
    Karagiannis GS, Weile J, Bader GD, Minta J.
    BMC Cardiovasc Disord. 2013 Jan 16;13:4
    PubMed Abstract - PDF
    PATHWAY AND NETWORK ANALYSIS

  15. 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 Feb 15;29(4):513-4
    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
    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;1:e00078
    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
    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
    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
    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 Sep 3;1:e26
    PubMed Abstract - 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 - PDF
    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
    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 Nov 15;26(22):2927-8
    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 GD, 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 Jul 15;466(7304):368-72
    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
    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
    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 Nov;122(3-4):345-53
    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
    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

2014

  1. Biological network exploration with Cytoscape 3
    Su G, Morris JH, Demchak B, Bader GD
    Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-8.13.24 - PubMed Abstract - PDF
    NETWORK ANALYSIS SOFTWARE

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. 2013 Omar Wagih - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - PDF, University of Toronto, Department of Computer Science

  2. 2013 Shirley Hui - Computational Prediction of PDZ Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Molecular Genetics

  3. 2013 Ron Ammar - Understanding Genome Structure and Response to Perturbation - PDF, University of Toronto, Department of Molecular Genetics

  4. 2013 Anastasia Baryshnikova - Mapping Genetic Interaction Networks in Yeast - PDF, University of Toronto, Department of Molecular Genetics

  5. 2012 Chris Tan - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - PDF, University of Toronto, Department of Molecular Genetics

  6. 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

Publications (last edited 2014-11-03 14:00:05 by RuthIsserlin)

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