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Contents

Peer-reviewed Articles
Textbook Chapters
Theses

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Peer-reviewed Articles

2014

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. doi: 10.3389/fgene.2014.00123. eCollection 2014.
PubMed PDF
PATHWAY AND NETWORK ANALYSIS
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. doi: 10.1038/nature13302
Pubmed PDF
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. doi: 10.1126/science.1250217.
Pubmed PDF
CHEMICAL GENOMICS
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. doi: 10.1371/journal.pone.0094507. eCollection 2014.
Pubmed PDF
PROTEIN INTERACTION PREDICTION
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 Mar 4. doi: 10.1002/pmic.201400041.
Pubmed PDF

2013

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
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
Nature Scientific Reports (2013) doi:10.1038/srep02650
PubMed Abstract PDF
CANCER MUTATIONS
The mutational landscape of phosphorylation signaling in cancer
Reimand J, Wagih O, Bader GD
Nature Scientific Reports (2013) doi:10.1038/srep02650
PubMed Abstract PDF
CANCER MUTATIONS, NETWORKS
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. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19.
Pubmed PDF
PATHWAY AND NETWORK ANALYSIS
The BioPAX Validator.
Rodchenkov I, Demir E, Sander C, Bader GD.
Bioinformatics. 2013 Oct 15;29(20):2659-60. doi: 10.1093/bioinformatics/btt452. Epub 2013 Aug 5.
Pubmed PDF
DATA STANDARD
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
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. doi: 10.1093/nar/gkt533.
Pubmed PDF
PATHWAY AND NETWORK ANALYSIS
Cytoscape App Store.
Lotia S, Montojo J, Dong Y, Bader GD, Pico AR.
Pubmed Abstract
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. doi: 10.1038/msb.2013.9.
Pubmed abstract Xin_SH3inter_MSB.pdf
Interactions in Intact Database
PROTEIN INTERACTION PREDICTION
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. doi: 10.1371/journal.pone.0058367. Epub 2013 Mar 8.
Pubmed abstract PDF
PATHWAY AND NETWORK ANALYSIS
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
Reimand J, Bader GD
Molecular Systems Biology (2013) doi:10.1038/msb.2012.68
PubMed Abstract PDF
Research Highlight in Genome Medicine (2013)
CANCER MUTATIONS, SIGNALING NETWORKS
Predicting PDZ domain mediated protein interactions from structure
Hui S, Xing X, Bader GD
BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-27
PubMed Abstract PDF
PROTEIN INTERACTION PREDICTION
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. doi: 10.1186/1471-2261-13-4
PubMed Abstract PDF
PATHWAY AND NETWORK ANALYSIS
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

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

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
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
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
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
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
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
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
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
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
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
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
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
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
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

2011

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
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

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)
PDF
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

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

-  ⇤ ← Revision 17 as of 2007-02-18 02:58:10 → 
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+   ← Revision 192 as of 2014-06-10 15:22:15 → ⇥
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+Additions are marked like this.
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-= Peer-reviewed Journals =
+#acl All:read
<<TableOfContents(1)>>

See who's cited our work at [[http://scholar.google.com/citations?hl=en&user=22M9eisAAAAJ&view_op=list_works&pagesize=100|Google Scholar]]

= Peer-reviewed Articles =

== 2014 ==
 1. '''Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction.'''<<BR>> '''Montojo J''', '''Zuberi K''', Shao Q, '''Bader GD''', Morris Q.<<BR>>[[http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00123/abstract|Front Genet. 2014 May 16;5:123. doi: 10.3389/fgene.2014.00123. eCollection 2014.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24904632|PubMed]][[attachment:montojoFrontgenet_2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>>
 1. '''A draft map of the human proteome.<<BR>>'''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.<<BR>>[[http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html|Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24870542|Pubmed]][[attachment:pandeymay2014.pdf|PDF]]<<BR>>
 1. '''Mapping the cellular response to small molecules using chemogenomic fitness signatures.'''<<BR>>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.<<BR>>[[http://www.sciencemag.org/content/344/6180/208.long|Science. 2014 Apr 11;344(6180):208-11. doi: 10.1126/science.1250217.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24723613|Pubmed]][[attachment:Lee_Science.pdf|PDF]]<<BR>>'''CHEMICAL GENOMICS'''<<BR>>

 1. '''Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs.'''<<BR>> Gfeller D, Ernst A, Jarvik N, Sidhu SS, '''Bader GD'''. <<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0094507|PLoS One. 2014 Apr 10;9(4):e94507. doi: 10.1371/journal.pone.0094507. eCollection 2014.]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24722214|Pubmed]][[attachment:gfeller_plosone2014.pdf|PDF]] <<BR>> '''PROTEIN INTERACTION PREDICTION'''<<BR>>

 1. '''Highlights of B/D-HPP and HPP Resource Pillar Workshops at Yokohama 12th Annual HUPO World Congress of Proteomics.'''<<BR>>Aebersold R, '''Bader GD''', Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS.<<BR>>[[http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400041/abstract;jsessionid=43053F08858E874C4B022564ED7ABAA4.f04t02?systemMessage=Wiley+Online+Library+will+be+disrupted+Saturday%2C+15+March+from+10%3A00-12%3A00+GMT+%2806%3A00-08%3A00+EDT%29+for+essential+maintenance|Proteomics. 2014 Mar 4. doi: 10.1002/pmic.201400041.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24596128|Pubmed]][[attachment:abersold_prot.pdf|PDF]]<<BR>>

== 2013 ==
 1. '''TCGA pan-cancer project, thread 2: Network models.'''<<BR>>'''Reimand J, Bader GD,''' Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton<<BR>>[[http://www.nature.com/ng/2013/131017/full/ng.2787.html|Nature Genetics (2013) doi:10.1038/ng.2787]] <<BR>> '''CANCER MUTATIONS, NETWORKS''' <<BR>>
 
 1. '''Comprehensive identification of mutational cancer driver genes across 12 tumor types'''<<BR>>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<<BR>>[[http://www.nature.com/srep/2013/131002/srep02650/full/srep02650.html|Nature Scientific Reports (2013)  doi:10.1038/srep02650]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24084849|PubMed Abstract]] [[attachment:Tamborero_SciRep_TCGA-pancancer.pdf|PDF]]<<BR>> '''CANCER MUTATIONS''' <<BR>>
 
 1. '''The mutational landscape of phosphorylation signaling in cancer'''<<BR>>'''Reimand J, Wagih O, Bader GD'''<<BR>>[[http://www.nature.com/srep/2013/131002/srep02651/full/srep02651.html|Nature Scientific Reports (2013)  doi:10.1038/srep02650]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24089029|PubMed Abstract]] [[attachment:Reimand_SciRep_TCGA-pancancer.pdf|PDF]]<<BR>> '''CANCER MUTATIONS, NETWORKS''' <<BR>>

 1. '''Using biological pathway data with paxtools.'''<<BR>>Demir E, Babur O, '''Rodchenkov I''', Aksoy BA, Fukuda KI, Gross B, Sümer OS, '''Bader GD''', Sander C.<<BR>>[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003194|PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24068901|Pubmed]][[attachment:Demir_paxtools_ploone.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>>

 1. '''The BioPAX Validator.'''<<BR>> '''Rodchenkov I''', Demir E, Sander C, '''Bader GD.'''<<BR>>[[http://bioinformatics.oxfordjournals.org/content/29/20/2659.long|Bioinformatics. 2013 Oct 15;29(20):2659-60. doi: 10.1093/bioinformatics/btt452. Epub 2013 Aug 5.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23918249|Pubmed]][[attachment:Rodchenkov_valid_bioinfo.pdf|PDF]]<<BR>>'''DATA STANDARD'''<<BR>>

 1. '''Computational approaches to identify functional genetic variants in cancer genomes'''<<BR>>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 <<BR>>[[http://www.nature.com/nmeth/journal/v10/n8/full/nmeth.2562.html|Nature Methods (2013) doi:10.1038/nmeth.2562]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/23900255|PubMed Abstract]] [[attachment:GonzalezPerez_cancer_mutations_NatMeth.pdf|PDF]]<<BR>> '''CANCER MUTATIONS''' <<BR>>

 1. '''GeneMANIA prediction server 2013 update.'''<<BR>> '''Zuberi K''', '''Franz M''', '''Rodriguez H''', '''Montojo J''', '''Lopes CT''', '''Bader GD''', Morris Q. <<BR>> [[http://nar.oxfordjournals.org/content/41/W1/W115.long|Nucleic Acids Res. 2013 Jul;41(Web Server issue):W115-22. doi: 10.1093/nar/gkt533.]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/23794635|Pubmed]][[attachment:Zuberi_genemanis_NAR.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>>

 1. '''Cytoscape App Store.'''<<BR>> Lotia S, '''Montojo J''', '''Dong Y''', '''Bader GD''', Pico AR.<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23595664|Pubmed Abstract]]<<BR>>

 1. '''SH3 interactome conserves general function over specific form.'''<<BR>>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'''<<BR>>[[http://www.nature.com/msb/journal/v9/n1/full/msb20139.html|Mol Syst Biol. 2013 Apr 2;9:652. doi: 10.1038/msb.2013.9.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23549480|Pubmed abstract]][[attachment:Xin_SH3inter_MSB.pdf]]<<BR>>[[http://www.ebi.ac.uk/intact/search/do/search?searchString=pubid:23549480| Interactions in Intact Database]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''

 1. '''Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells.'''<<BR>>Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, '''Voisin V''', Jitkova Y, Gronda M, Hurren R, Laister RC, '''Bader GD''', Minden MD, Schimmer AD.<<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058367|PLoS One. 2013;8(3):e58367. doi: 10.1371/journal.pone.0058367. Epub 2013 Mar 8.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23520503|Pubmed abstract]][[attachment:Jhas_leuk_plosone.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers'''<<BR>>'''Reimand J, Bader GD'''<<BR>>[[http://www.nature.com/msb/journal/v9/n1/full/msb201268.html|Molecular Systems Biology (2013)  doi:10.1038/msb.2012.68]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23340843|PubMed Abstract]] [[attachment:Reimand_MSB_phosphomutations.pdf|PDF]]<<BR>> [[http://genomemedicine.com/content/5/2/19/abstract|Research Highlight in Genome Medicine (2013)]]  <<BR>>
 '''CANCER MUTATIONS, SIGNALING NETWORKS''' <<BR>>

 1. '''Predicting PDZ domain mediated protein interactions from structure'''<<BR>>'''Hui S, Xing X, Bader GD'''<<BR>> [[http://www.biomedcentral.com/1471-2105/14/27/abstract|BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-27]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23336252|PubMed Abstract]] [[attachment:pdz-struct-2013.pdf|PDF]] <<BR>>'''PROTEIN INTERACTION PREDICTION'''

 1. '''Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation.'''<<BR>>Karagiannis GS, Weile J, '''Bader GD''', Minta J.<<BR>>[[http://www.biomedcentral.com/1471-2261/13/4|BMC Cardiovasc Disord. 2013 Jan 16;13:4. doi: 10.1186/1471-2261-13-4]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23324130|PubMed Abstract]][[attachment:WeileBMC.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''


 1. '''GESTODIFFERENT: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process'''<<BR>>Marco Antoniotti, '''Gary D. Bader''', Giulio Caravagna, Silvia Crippa, Alex Graudenzi and Giancarlo Mauri<<BR>> [[http://bioinformatics.oxfordjournals.org/content/early/2013/01/03/bioinformatics.bts726.abstract|Bioinformatics (2013) doi: 10.1093/bioinformatics/bts726]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23292740|PubMed Abstract]] [[attachment:GESTODIFFERENT.pdf|PDF]] <<BR>>'''NETWORK SIMULATION'''

== 2012 ==

 1. '''The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community'''<<BR>>Aebersold R, '''Bader GD''', Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS<<BR>> [[http://pubs.acs.org/doi/abs/10.1021/pr301151m|J Proteome Res. 2013 Jan 4;12(1):23-7. doi: 10.1021/pr301151m. Epub 2012 Dec 21]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23259511|PubMed Abstract]] [[attachment:hupo-bdhpp.pdf|PDF]] <<BR>>'''PROTEOMICS'''

 1. '''Chromatin is an ancient innovation conserved between Archaea and Eukarya'''<<BR>>'''Ammar R''', Torti D, Tsui K, Gebbia M, Durbic T, '''Bader GD''', Giaever G, Nislow C<<BR>> [[http://elife.elifesciences.org/content/1/e00078|eLife. 2012 Dec 13. DOI: http://dx.doi.org/10.7554/eLife.00078]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23240084|PubMed Abstract]] [[attachment:e00078.full (1).pdf|PDF]] <<BR>>'''ANALYSIS OF ARCHAEAL CHROMATIN'''

 1. '''Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion'''<<BR>>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<<BR>> [[http://www.sciencedirect.com/science/article/pii/S1934590912005371|Cell Stem Cell. 2012 Nov 7. doi:pii: S1934-5909(12)00537-1. 10.1016/j.stem.2012.09.001]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23142521|PubMed Abstract]] [[attachment:2012_mir126andHSC.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''A travel guide to Cytoscape plugins'''<<BR>>Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, '''Bader GD''', Ideker T<<BR>> [[http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2212.html|Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23132118|PubMed Abstract]] [[attachment:2012_CytoscapePluginTravelGuide.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study'''<<BR>>'''Alshalalfa M''', '''Bader GD''', Goldenberg A, Morris Q, Alhajj R<<BR>> [[http://www.biomedcentral.com/1752-0509/6/112|BMC Syst Biol. 2012 Aug 28;6:112. doi: 10.1186/1752-0509-6-112]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/22929553|PubMed Abstract]] [[attachment:2012_microRNAinfluence.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice'''<<BR>>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<<BR>> [[http://www.nature.com/oncsis/journal/v1/n9/full/oncsis201228a.html|Oncogenesis (2012) 1, e26; doi:10.1038/oncsis.2012.28]] <<BR>>[[attachment:2012_Xiong_ABI1_Oncogenesis.pdf|PDF]]<<BR>>'''CANCER GENOMICS'''

 1. '''Subgroup-specific structural variation across 1,000 medulloblastoma genomes'''<<BR>>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<<BR>> [[http://www.nature.com/nature/journal/v488/n7409/full/nature11327.html|Nature. 2012 Aug 2;488(7409):49-56]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/22832581|PubMed Abstract]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals'''<<BR>>Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, '''Voisin V, Bader GD''', Blencowe BJ, Pearson BJ<<BR>> [[http://onlinelibrary.wiley.com/doi/10.1002/stem.1144/abstract|Stem Cells. 2012 Jun 13 doi: 10.1002/stem.1144]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/22696458|PubMed Abstract]] [[attachment:PlanariaStemCells.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction'''<<BR>>'''Michaut M, Bader GD'''<<BR>> [[http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002559|PLoS Comput Biol 8(6): e1002559]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/22737063|PubMed Abstract]] [[attachment:MultipleGeneticInteractions.pdf|PDF]]<<BR>>'''GENETIC INTERACTIONS'''

 1. '''Domain-mediated protein interaction prediction: From genome to network'''<<BR>>'''Reimand J, Hui S, Jain S, Law B, Bader GD'''<<BR>> [[http://www.sciencedirect.com/science/article/pii/S001457931200316X|FEBS Lett. 2012 May 3]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/22561014|PubMed Abstract]] [[attachment:Genome2NetworkReview.pdf|PDF]]<<BR>>'''PROTEIN INTERACTIONS'''

 1. '''Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer'''<<BR>>Liu JC, '''Voisin V''', '''Bader GD''', Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E<<BR>>[[http://www.pnas.org/content/early/2012/03/27/1201105109.abstract|Proc Natl Acad Sci U S A. 2012 Mar 28]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22460789|PubMed Abstract]] -[[attachment:breastcancer-2012.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Phosphorylation sites of higher stoichiometry are more conserved'''<<BR>>'''Tan CS''', '''Bader GD'''<<BR>>[[http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1941.html|Nat Methods. 2012 Mar 27;9(4):317]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22453906|PubMed Abstract]] -[[attachment:phospholetter-2012.pdf|PDF]]<<BR>>'''PHOSPHOPROTEOMICS'''

 1. '''Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry'''<<BR>>Diezmann S, '''Michaut M''', Shapiro RS, '''Bader GD''', Cowen LE<<BR>>[[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002562|PLoS Genet. 2012 Mar;8(3):e1002562]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22438817|PubMed Abstract]] -[[attachment:candida2012.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

== 2011 ==
 1. '''MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets'''<<BR>>Kim T, Tyndel MS, Huang H, Sidhu SS, '''Bader GD''', '''Gfeller D''', Kim PM<<BR>>[[http://nar.oxfordjournals.org/content/early/2011/12/30/nar.gkr1294.long|Nucleic Acids Res. 2011 Dec 30]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22210894|PubMed Abstract]] -[[attachment:musi-2011.pdf|PDF]]<<BR>>'''DOMAIN SPECIFICITY SOFTWARE'''

 1. '''Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)'''<<BR>>Le Novère N, Hucka M, Anwar N, '''Bader GD''', Demir E, Moodie S, Sorokin A<<BR>>[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235518/?tool=pubmed|Stand Genomic Sci. 2011 Nov 30;5(2):230-42]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22180826|PubMed Abstract]] -[[attachment:combine-report-2011.pdf|PDF]]<<BR>>'''DATA STANDARD'''

 1. '''clusterMaker: a multi-algorithm clustering plugin for Cytoscape'''<<BR>>Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, '''Bader GD''', Ferrin TE<<BR>>[[http://www.biomedcentral.com/1471-2105/12/436|BMC Bioinformatics. 2011 Nov 9;12(1):436]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22070249|PubMed Abstract]] -[[attachment:clustermaker.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms'''<<BR>> '''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 <<BR>> [[http://www.cell.com/chemistry-biology/abstract/S1074-5521(11)00276-6|Cell Chemistry & Biology 2011 18, 1273–1283]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/22035796|PubMed Abstract]] - [[attachment:yactives.pdf|PDF]]<<BR>> [[http://www.cell.com/chemistry-biology/abstract/S1074-5521(11)00364-4|Chemistry & Biology 2011 18:10, 1204-1205]] [[attachment:commentary_yactives.pdf|Commentary on paper]]<<BR>>'''CHEMICAL GENOMICS'''

 1. '''!NetSlim: high-confidence curated signaling maps'''<<BR>> 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 <<BR>> [[http://database.oxfordjournals.org/content/2011/bar032.long|Database (Oxford). 2011 Sep 29;2011(0):bar032]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21959865|PubMed Abstract]] - [[attachment:netslim.pdf|PDF]]<<BR>>'''PATHWAY DATABASE'''

 1. '''Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma'''<<BR>> 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 <<BR>> [[http://www.sciencedirect.com/science/article/pii/S1535610811002625|Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21840481|PubMed Abstract]] - [[attachment:ependymoma.pdf|PDF]]<<BR>>'''PATHWAY ANALYSIS'''

 1. '''A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway'''<<BR>>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 <<BR>>[[http://database.oxfordjournals.org/content/2011/bar021.long|Database (Oxford). 2011 Jul 8;2011]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21742767|PubMed Abstract]] -[[attachment:2011_Raju-RANKL_Database.pdf|PDF]]<<BR>>'''PATHWAY DATABASE'''

 1. '''PSICQUIC and PSISCORE: accessing and scoring molecular interactions'''<<BR>>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<<BR>> [[http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1637.html|Nature Methods 2011 Jun 29;8(7):528-9]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/21716279|Pubmed Abstract]] [[attachment:psicquic.pdf|PDF]]<<BR>>'''PROTEIN INTERACTIONS'''

 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>>[[attachment:Science-2011-tan-917.pdf|PDF]]<<BR>>'''NETWORK EVOLUTION'''

 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 SS, '''Bader GD''', Kim PM<<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 GD'''<<BR>>[[http://www.scfbm.org/content/6/1/7/abstract|Source Code for Biology and Medicine 2011, 6:7, 7 April 2011]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/21473782|PubMed Abstract]] -[[attachment:wordcloud.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Protein Complexes are Central in the Yeast Genetic Landscape'''<<BR>>'''Michaut M''', Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, '''Bader GD'''<<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>> [[http://www.ncbi.nlm.nih.gov/pubmed/21390331|PubMed Abstract]] - [[attachment:2011_Michaut_Mono.pdf|PDF]] <<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]] - [[attachment:2011_Michaut_Diso.pdf|PDF]]<<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'''

== 2010 ==
 1. '''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'''

 1. '''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'''

 1. '''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'''

 1. '''DRYGIN: a database of quantitative genetic interaction networks in yeast'''<<BR>>Koh JL, Ding H, Costanzo M, '''Baryshnikova A''', Toufighi K, '''Bader GD''', Myers CL, Andrews BJ, Boone C<<BR>>[[http://nar.oxfordjournals.org/cgi/content/full/38/suppl_1/D502|Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. Epub 2009 Oct 30]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19880385|PubMed Abstract]] - [[attachment:2009_Koh_Drygin_NAR_Oct.pdf|PDF]]<<BR>>'''GENETIC INTERACTION NETWORK DATABASE'''

== 2009 ==
 1. '''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'''

 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 <<BR>> '''NETWORK PRIMER'''

 1. '''Rapid evolution of functional complexity in a domain family'''<<BR>>Ernst A, Sazinsky SL, '''Hui S''', Currell B, '''Dharsee M''', Seshagiri S, '''Bader GD''', Sidhu SS<<BR>>[[http://stke.sciencemag.org/cgi/content/full/sigtrans;2/87/ra50|Science Signaling 2009 Sep 8;2(87):ra50]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19738200|PubMed Abstract]] - [[attachment:2009_Ernst_PDZEvolution_ScienceSignaling_Sep.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK EVOLUTION'''

 1. '''Positive Selection of Tyrosine Loss in Metazoan Evolution'''<<BR>>'''Tan CS''', Pasculescu A, Lim WA, Pawson T, '''Bader GD''', Linding R<<BR>>[[http://www.sciencemag.org/cgi/content/abstract/1174301v2|Science. Sep 25;325(5948):1686-8. Epub 2009 Jul 9]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19589966|PubMed Abstract]] - [[attachment:2009_Tan_TyrosineLoss_Science.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK EVOLUTION'''

 1. '''Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases'''<<BR>>'''Tan CS''', Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, '''Bader GD''', Aebersold R, Pawson T, Linding R<<BR>>[[http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2/81/ra39|Science Signaling 2(81):r39 (2009)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/19638616|PubMed Abstract]] - [[attachment:2009_Tan_ComparativePhosphoProteomics_ScienceSignaling_Jul.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK EVOLUTION'''

== 2008 ==
 1. '''A Specificity Map for the PDZ Domain Family'''<<BR>>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<<BR>>[[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060239|PLoS Biology Vol. 6, No. 9, e239]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18828675|PubMed Abstract]] - [[attachment:2008_Tonikian_PDZSpecificityMap_PlosBiology.pdf|PDF]]<<BR>>'''PROTEIN-PROTEIN INTERACTION ANALYSIS'''

 1. '''Cytoscape ESP: simple search of complex biological networks'''<<BR>>Ashkenazi M, '''Bader GD''', Kuchinsky A, Moshelion M, States DJ<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn208v1|Bioinformatics 2008 Jun 15;24(12):1465-6]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18445605|PubMed Abstract]] - [[attachment:2008_Ashkenazi_CytoscapeESP_Bioinformatics.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Computational prediction of protein-protein interactions'''<<BR>>Skrabanek L, Saini HK, '''Bader GD''', Enright AJ<<BR>>[[http://humanapress.com/index.php?option=com_journalshome&task=articledetails&category=journals&article_code=MB:38:1:1|Molecular Biotechnology 2008 Jan;38(1):1-17]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/18095187|PubMed Abstract]] - [[attachment:2008_Skrabanek_MolBiotech_PPI.pdf|PDF]]<<BR>>'''REVIEW'''
-Line 4:
+Line 167:
-. '''!NetMatch: a Cytoscape Plugin for Searching Biological Networks.'''[[BR]]Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, '''Bader GD''', Shasha D[[BR]][http://bioinformatics.oxfordjournals.org/cgi/reprint/btm032v1 Bioinformatics. 2007 Feb 3;][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17277332 PubMed Abstract][[BR]][:Software/NetMatch:Download software][[BR]]'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Computational prediction of cancer-gene function'''[[BR]]Hu P, '''Bader G''', Wigle DA, Emili A[[BR]][http://www.nature.com/nrc/journal/v7/n1/abs/nrc2036.html Nature Reviews Cancer 2007 Jan;7(1):23-34. Epub 2006 Dec 14][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17167517 PubMed Abstract] - [attachment:2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf PDF][[BR]]'''CANCER REVIEW'''
+. '''Integration of biological networks and gene expression data using Cytoscape'''<<BR>>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'''<<BR>>[[http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html|Nature Protocols 2007;2(10):2366-82]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17947979|PubMed Abstract]] - [[attachment:2007_Cytoscape_Cline_NatureProtocols_Oct.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions'''<<BR>>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<<BR>>[[http://www.biomedcentral.com/1741-7007/5/44/abstract|BMC Biology 2007 Oct 9;5(1):44]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17925023|PubMed Abstract]] - [[attachment:2007_Kerrien_PSIMI_BMCBiology.pdf|PDF]]<<BR>>'''DATA STANDARD'''

 1. '''The minimum information required for reporting a molecular interaction experiment (MIMIx)'''<<BR>>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<<BR>>[[http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html|Nat Biotechnol. 2007 Aug;25(8):894-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17687370|PubMed Abstract]] - [[attachment:2007_MIMIx_OrchardEtAl_NatBiotech_August.pdf|PDF]]<<BR>>'''DATA STANDARD'''

 1. '''Germ-line DNA copy number variation frequencies in a large North American population'''<<BR>>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<<BR>>[[http://www.springerlink.com/content/f57t61764r0t21mv/|Hum Genet. 2007 Jul 19]]<<BR>>[[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17638019|PubMed Abstract]] - [[attachment:2007_Germ-lineDNACopyNumberVariationFrequenciesInALargeNorthAmericanPopulation_Zogopoulos_Bader_Gallinder_HumanGenetics.pdf|PDF]]<<BR>>'''GENOMICS'''

 1. '''From bytes to bedside: data integration and computational biology for translational cancer research'''<<BR>>Mathew JP, Taylor BS, '''Bader GD''', Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B<<BR>>[[http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030012|PLoS Comput Biol. 2007 Feb 23;3(2):e12]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17319736|PubMed Abstract]] - [[attachment:2007_MatthewTaylorBader_TranslationalReview_PLoSCompBio_Feb.pdf|PDF]]<<BR>>'''CANCER REVIEW'''

 1. '''!NetMatch: a Cytoscape Plugin for Searching Biological Networks'''<<BR>>Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, '''Bader GD''', Shasha D<<BR>>[[http://bioinformatics.oxfordjournals.org/cgi/reprint/btm032v1|Bioinformatics 2007 Apr 1;23(7):910-2]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17277332|PubMed Abstract]] - [[attachment:2007_NetMatch-ACytoscapePluginForSearchingBiologicalNetworks_Ferro_Guigno_Bader_Shasha_Apr.pdf|PDF]]<<BR>>[[Software/NetMatch|Download software]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Computational prediction of cancer-gene function'''<<BR>>Hu P, '''Bader G''', Wigle DA, Emili A<<BR>>[[http://www.nature.com/nrc/journal/v7/n1/abs/nrc2036.html|Nature Reviews Cancer 2007 Jan;7(1):23-34. Epub 2006 Dec 14]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17167517|PubMed Abstract]] - [[attachment:2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf|PDF]]<<BR>>'''CANCER REVIEW'''
-Line 10:
+Line 182:
-. '''cPath: open source software for collecting, storing, and querying biological pathways'''[[BR]]Cerami EG, '''Bader GD''', Gross BE, Sander C[[BR]][http://www.biomedcentral.com/1471-2105/7/497/abstract BMC Bioinformatics 2006, 7:497][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17101041 PubMed Abstract] - [attachment:2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf PDF][[BR]]'''PATHWAY SOFTWARE'''

 1. '''Pathguide: a Pathway Resource List'''[[BR]]'''Bader GD''', Cary MP, Sander C[[BR]][http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D504 Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16381921&query_hl=14&itool=pubmed_docsum PubMed Abstract] - [attachment:2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf PDF][[BR]]'''PATHWAY WEBSITE'''
+. '''cPath: open source software for collecting, storing, and querying biological pathways'''<<BR>>Cerami EG, '''Bader GD''', Gross BE, Sander C<<BR>>[[http://www.biomedcentral.com/1471-2105/7/497/abstract|BMC Bioinformatics 2006, 7:497]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17101041|PubMed Abstract]] - [[attachment:2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf|PDF]]<<BR>>'''PATHWAY SOFTWARE'''

 1. '''Pathguide: a Pathway Resource List'''<<BR>>'''Bader GD''', Cary MP, Sander C<<BR>>[[http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D504|Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16381921&query_hl=14&itool=pubmed_docsum|PubMed Abstract]] - [[attachment:2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf|PDF]]<<BR>>'''PATHWAY WEBSITE'''
-Line 16:
+Line 187:
-. '''Pathway information for systems biology'''[[BR]]Cary MP, '''Bader GD''', Sander C[[BR]][http://www.febsletters.org/retrieve/pii/S0014579305001705 FEBS Lett. 2005 Mar 21;579(8):1815-20][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15763557&query_hl=14&itool=pubmed_docsum PubMed Abstract] - [attachment:2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf PDF][[BR]]'''PATHWAY REVIEW'''
+. '''Pathway information for systems biology'''<<BR>>Cary MP, '''Bader GD''', Sander C<<BR>>[[http://www.febsletters.org/retrieve/pii/S0014579305001705|FEBS Lett. 2005 Mar 21;579(8):1815-20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15763557&query_hl=14&itool=pubmed_docsum|PubMed Abstract]] - [[attachment:2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf|PDF]]<<BR>>'''PATHWAY REVIEW'''
-Line 20:
+Line 190:
-. '''Global Mapping of the Yeast Genetic Interaction Network'''[[BR]]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[[BR]][http://www.sciencemag.org/cgi/content/full/303/5659/808 Science 2004 Feb 6;303(5659):808-813][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870 PubMed Abstract] - [attachment:2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf PDF][[BR]][attachment:2004_SGA_Hartwell_comment.pdf Science Perspective PDF][[BR]]'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data'''[[BR]]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[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 Nature Biotechnology 2004 Feb;22(2):177-83][[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147 PubMed Abstract] - [attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf PDF][[BR]]'''DATA STANDARD'''
+. '''Global Mapping of the Yeast Genetic Interaction Network'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/full/303/5659/808|Science 2004 Feb 6;303(5659):808-813]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870|PubMed Abstract]] - [[attachment:2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf|PDF]]<<BR>>[[attachment:2004_SGA_Hartwell_comment.pdf|Science Perspective PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data'''<<BR>>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<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147|Nature Biotechnology 2004 Feb;22(2):177-83]]<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147|PubMed Abstract]] - [[attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf|PDF]]<<BR>>'''DATA STANDARD'''
-Line 26:
+Line 195:
-. '''Playing tag with the yeast proteome'''[[BR]]Andrews BJ, '''Bader GD''', Boone C[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v21/n11/full/nbt1103-1297.html Nature Biotechnology Nov;21(11):1297-1299][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14595360 PubMed Abstract] - [attachment:2003_OsheaWeissmanReview_NatureBiotech.pdf PDF][[BR]]'''REVIEW'''

 1. '''Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell'''[[BR]]'''Bader GD''', Heilbut A, Andrews B, Tyers M, Hughes T, Boone C[[BR]][http://linkinghub.elsevier.com/retrieve/pii/S0962892403001272 Trends in Cell Biology Jul, 2003 13(7):344-56][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12837605&dopt=Abstract PubMed Abstract] - [attachment:2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf PDF][[BR]]'''REVIEW'''

 1. '''PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine'''[[BR]]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[[BR]][http://www.biomedcentral.com/1471-2105/4/11 BMC Bioinformatics Mar 27, 2003 4(1):11][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12689350&dopt=Abstract PubMed Abstract] - [attachment:PreBIND_BMC2003.pdf PDF][[BR]]'''TEXT MINING SOFTWARE'''

 1. '''Functional genomics of intracellular peptide recognition domains with combinatorial biology methods'''[[BR]]Sidhu SS, '''Bader GD''', Boone C[[BR]][http://linkinghub.elsevier.com/retrieve/pii/S136759310200011X Current Opinion in Chemical Biology 2003 Feb;7(1):97-102][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12547433&dopt=Abstract PubMed Abstract] - [attachment:2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf PDF][[BR]]'''REVIEW'''

 1. '''An automated method for finding molecular complexes in large protein interaction networks'''[[BR]]'''Bader GD''', Hogue CWV[[BR]][http://www.biomedcentral.com/1471-2105/4/2 BMC Bioinformatics 2003 Jan 13;4(1):2][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract PubMed Abstract] - [attachment:2003_BaderHogue_MCODE.pdf PDF][[BR]]'''ALGORITHM'''

 1. '''BIND-The Biomolecular Interaction Network Database'''[[BR]]'''Bader GD''', Betel D, Hogue CWV[[BR]][http://nar.oupjournals.org/cgi/content/abstract/31/1/248 Nucleic Acids Research Jan 1, 2003 31(1):248-250][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519993&dopt=Abstract PubMed Abstract] - [attachment:2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf PDF][[BR]]'''INTERACTION DATABASE'''
+. '''Playing tag with the yeast proteome'''<<BR>>Andrews BJ, '''Bader GD''', Boone C<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v21/n11/full/nbt1103-1297.html|Nature Biotechnology Nov;21(11):1297-1299]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14595360|PubMed Abstract]] - [[attachment:2003_OsheaWeissmanReview_NatureBiotech.pdf|PDF]]<<BR>>'''REVIEW'''

 1. '''Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell'''<<BR>>'''Bader GD''', Heilbut A, Andrews B, Tyers M, Hughes T, Boone C<<BR>>[[http://linkinghub.elsevier.com/retrieve/pii/S0962892403001272|Trends in Cell Biology Jul, 2003 13(7):344-56]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12837605&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf|PDF]]<<BR>>'''REVIEW'''

 1. '''PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine'''<<BR>>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<<BR>>[[http://www.biomedcentral.com/1471-2105/4/11|BMC Bioinformatics Mar 27, 2003 4(1):11]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12689350&dopt=Abstract|PubMed Abstract]] - [[attachment:PreBIND_BMC2003.pdf|PDF]]<<BR>>'''TEXT MINING SOFTWARE'''

 1. '''Functional genomics of intracellular peptide recognition domains with combinatorial biology methods'''<<BR>>Sidhu SS, '''Bader GD''', Boone C<<BR>>[[http://linkinghub.elsevier.com/retrieve/pii/S136759310200011X|Current Opinion in Chemical Biology 2003 Feb;7(1):97-102]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12547433&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf|PDF]]<<BR>>'''REVIEW'''

 1. '''An automated method for finding molecular complexes in large protein interaction networks'''<<BR>>'''Bader GD''', Hogue CWV<<BR>>[[http://www.biomedcentral.com/1471-2105/4/2|BMC Bioinformatics 2003 Jan 13;4(1):2]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_BaderHogue_MCODE.pdf|PDF]]<<BR>>'''ALGORITHM'''

 1. '''BIND-The Biomolecular Interaction Network Database'''<<BR>>'''Bader GD''', Betel D, Hogue CWV<<BR>>[[http://nar.oupjournals.org/cgi/content/abstract/31/1/248|Nucleic Acids Research Jan 1, 2003 31(1):248-250]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519993&dopt=Abstract|PubMed Abstract]] - [[attachment:2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf|PDF]]<<BR>>'''INTERACTION DATABASE'''
-Line 40:
+Line 208:
-. '''!SeqHound: biological sequence and structure database as a platform for bioinformatics research'''[[BR]]Michalickova K, '''Bader GD''', Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW[[BR]][http://www.biomedcentral.com/1471-2105/3/32 BMC Bioinformatics 2002, 3:32 (25 October 2002)][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract PubMed Abstract] - [attachment:2002_SeqHound_BMCBioinfo.pdf PDF][[BR]]'''PROTEIN DATABASE'''

 1. '''Analyzing yeast protein–protein interaction data obtained from different sources'''[[BR]]'''Bader GD''', Hogue CW[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v20/n10/abs/nbt1002-991.html&dynoptions=doi1040752166 Nature Biotechnology 2002 Oct;20(10):991-997][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12355115&dopt=Abstract PubMed Abstract] - [attachment:BaderHogueNBT2002.pdf PDF][[BR]]'''META-ANALYSIS'''

 1. '''A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules'''[[BR]]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[[BR]][http://www.sciencemag.org/cgi/content/abstract/295/5553/321 Science 2002 Jan 11;295(5553):321-324][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743162&dopt=Abstract PubMed Abstract] - [attachment:SH3ScienceJan11_2002.pdf PDF][[BR]][attachment:Perspective_ScienceJan11_2002.pdf Science Perspective PDF][[BR]]'''PROTEIN INTERACTION PREDICTION'''

 1. '''Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry'''[[BR]]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[[BR]][http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v415/n6868/abs/415180a_fs.html Nature 2002 Jan 10;415(6868): 180-183][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11805837&dopt=Abstract PubMed Abstract] - [attachment:HMS-PCI-Nature-Jan10_2002.pdf PDF][[BR]][attachment:HMS-PCINewsAndViews-NatureJan10_2002.pdf Nature News and Views PDF][[BR]]'''PROTEIN INTERACTION NETWORK ANALYSIS'''
+. '''!SeqHound: biological sequence and structure database as a platform for bioinformatics research'''<<BR>>Michalickova K, '''Bader GD''', Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW<<BR>>[[http://www.biomedcentral.com/1471-2105/3/32|BMC Bioinformatics 2002, 3:32 (25 October 2002)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract|PubMed Abstract]] - [[attachment:2002_SeqHound_BMCBioinfo.pdf|PDF]]<<BR>>'''PROTEIN DATABASE'''

 1. '''Analyzing yeast protein–protein interaction data obtained from different sources'''<<BR>>'''Bader GD''', Hogue CW<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v20/n10/abs/nbt1002-991.html&dynoptions=doi1040752166|Nature Biotechnology 2002 Oct;20(10):991-997]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12355115&dopt=Abstract|PubMed Abstract]] - [[attachment:BaderHogueNBT2002.pdf|PDF]]<<BR>>'''META-ANALYSIS'''

 1. '''A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/abstract/295/5553/321|Science 2002 Jan 11;295(5553):321-324]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743162&dopt=Abstract|PubMed Abstract]] - [[attachment:SH3ScienceJan11_2002.pdf|PDF]]<<BR>>[[attachment:Perspective_ScienceJan11_2002.pdf|Science Perspective PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''

 1. '''Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry'''<<BR>>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<<BR>>[[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v415/n6868/abs/415180a_fs.html|Nature 2002 Jan 10;415(6868): 180-183]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11805837&dopt=Abstract|PubMed Abstract]] - [[attachment:HMS-PCI-Nature-Jan10_2002.pdf|PDF]]<<BR>>[[attachment:HMS-PCINewsAndViews-NatureJan10_2002.pdf|Nature News and Views PDF]]<<BR>>'''PROTEIN INTERACTION NETWORK ANALYSIS'''
-Line 50:
+Line 217:
-. '''Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants'''[[BR]]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[[BR]][http://www.sciencemag.org/cgi/content/abstract/294/5550/2364 Science 2001 Dec 14;294(5550):2364-8][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743205&dopt=Abstract PubMed Abstract] - [attachment:SGA_ScienceVol294-2001.pdf PDF][[BR]]'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''BIND - The Biomolecular Interaction Network Database'''[[BR]]'''Bader GD''', Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW[[BR]][http://nar.oupjournals.org/cgi/content/abstract/29/1/242 Nucleic Acids Research Jan 1, 2001 29(1):242-245][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11125103&dopt=Abstract PubMed Abstract] - [attachment:BIND_NAR_2001.pdf PDF][[BR]]'''INTERACTION DATABASE'''
+. '''Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants'''<<BR>>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<<BR>>[[http://www.sciencemag.org/cgi/content/abstract/294/5550/2364|Science 2001 Dec 14;294(5550):2364-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743205&dopt=Abstract|PubMed Abstract]] - [[attachment:SGA_ScienceVol294-2001.pdf|PDF]]<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''

 1. '''BIND - The Biomolecular Interaction Network Database'''<<BR>>'''Bader GD''', Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW<<BR>>[[http://nar.oupjournals.org/cgi/content/abstract/29/1/242|Nucleic Acids Research Jan 1, 2001 29(1):242-245]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11125103&dopt=Abstract|PubMed Abstract]] - [[attachment:BIND_NAR_2001.pdf|PDF]]<<BR>>'''INTERACTION DATABASE'''
-Line 56:
+Line 222:
-. '''BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways'''[[BR]]'''Bader GD''', Hogue CW[[BR]][http://bioinformatics.oupjournals.org/cgi/content/abstract/16/5/465 Bioinformatics. 2000 May;16(5):465-77][[BR]][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10871269&dopt=Abstract PubMed Abstract] - [attachment:BIND_Spec_2000.pdf PDF][[BR]]'''INTERACTION DATABASE'''
+. '''BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways'''<<BR>>'''Bader GD''', Hogue CW<<BR>>[[http://bioinformatics.oupjournals.org/cgi/content/abstract/16/5/465|Bioinformatics. 2000 May;16(5):465-77]]<<BR>>[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10871269&dopt=Abstract|PubMed Abstract]] - [[attachment:BIND_Spec_2000.pdf|PDF]]<<BR>>'''INTERACTION DATABASE'''
-Line 60:
+Line 225:
+== 2011 ==
 1. '''Displaying chemical information on a biological network using cytoscape'''<<BR>>'''Wallace IM''', '''Bader GD''', Giaever G, Nislow C<<BR>>[[http://www.springerlink.com/content/q321h06847668r94/#section=953422&page=1|Methods Mol Biol. 2011;781:363-76]] - [[http://www.ncbi.nlm.nih.gov/pubmed/21877291|PubMed Abstract]] - [[attachment:ChemicalInformationCytoscape_Wallace2011.pdf|PDF]] [[http://baderlab.org/VisualizingChemicalInformation|Supplemental Website]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map'''<<BR>>'''Merico D''', '''Isserlin R''', '''Bader GD'''<<BR>>[[http://www.springerlink.com/content/hq415338j6u8k124/#section=953415&page=1|Methods Mol Biol. 2011;781:257-77]] - [[http://www.ncbi.nlm.nih.gov/pubmed/21877285|PubMed Abstract]] - [[attachment:EnrichmentMapsCytoscape_MericoIsserlin2011.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

== 2008 ==
 1. '''Exploring Biological Networks with Cytoscape Software'''<<BR>>'''Natalie Yeung''', Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and '''Gary D. Bader'''<<BR>>[[http://mrw.interscience.wiley.com/emrw/9780471250951/cp/cpbi/article/bi0813/current/abstract|Current Protocols in Bioinformatics]] - [[http://www.ncbi.nlm.nih.gov/pubmed/18819078|PubMed Abstract]] - [[attachment:CytoscapeCurrProtocolsProof-YeungBader_Sep2008.pdf|PDF]]<<BR>>John Wiley & Sons, Inc.<<BR>>'''NETWORK ANALYSIS SOFTWARE'''
-Line 62:
+Line 234:
-. '''BioPAX - Biological Pathway Data Exchange Format'''[[BR]]'''Gary D. Bader''', Michael Cary, Chris Sander[[BR]][http://www.mrw.interscience.wiley.com/ggpb/articles/g408117/frame.html Encyclopedia of Genomics, Proteomics and Bioinformatics][[BR]]Humana Press, New Jersey[[BR]]'''DATA STANDARD'''
+. '''BioPAX - Biological Pathway Data Exchange Format'''<<BR>>'''Gary D. Bader''', Michael Cary, Chris Sander<<BR>>[[http://www.mrw.interscience.wiley.com/ggpb/articles/g408117/frame.html|Encyclopedia of Genomics, Proteomics and Bioinformatics]]<<BR>>Humana Press, New Jersey<<BR>>'''DATA STANDARD'''
-Line 66:
+Line 237:
-. '''Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks'''[[BR]]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[[BR]][http://educationbook.aacrjournals.org/cgi/content/full/2005/1/12 Am Assoc Cancer Res Educ Book 2005: 12-16][[BR]]'''NETWORK ANALYSIS SOFTWARE'''


 1. '''Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes'''[[BR]]'''Gary D. Bader''', Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone[[BR]]in [http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155 Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.][[BR]]Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA[[BR]]'''GENETIC INTERACTION NETWORK ANALYSIS'''
+. '''Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks'''<<BR>>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<<BR>>[[http://educationbook.aacrjournals.org/cgi/content/full/2005/1/12|Am Assoc Cancer Res Educ Book 2005: 12-16]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

 1. '''Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes'''<<BR>>'''Gary D. Bader''', Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone<<BR>>in [[http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155|Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition.]]<<BR>>Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA<<BR>>'''GENETIC INTERACTION NETWORK ANALYSIS'''
-Line 73:
+Line 242:
-. '''Interaction Databases, in Genomics and Bioinformatics, 2nd Edition'''[[BR]]'''Gary D. Bader''', Christopher W.V. Hogue[[BR]]in [http://www.wiley-vch.de/books/biotech/con_v05b.html Volume 5B of the Series: Biotechnology, 2nd Edition.][[BR]]Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany[[BR]]'''INTERACTION DATABASE'''

 1. '''Intermolecular Interactions and Biological Pathways'''[[BR]]'''Gary D. Bader''', Anton J. Enright[[BR]]in [http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey][[BR]]'''INTERACTION DATABASE'''

 1. '''Computational Prediction of Protein-Protein Interactions'''[[BR]]Anton J. Enright, Lucy Skrabanek, '''Gary D. Bader'''[[BR]]in [http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1 The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)][[BR]]'''PROTEIN INTERACTION PREDICTION'''
+. '''Interaction Databases, in Genomics and Bioinformatics, 2nd Edition'''<<BR>>'''Gary D. Bader''', Christopher W.V. Hogue<<BR>>in [[http://www.wiley-vch.de/books/biotech/con_v05b.html|Volume 5B of the Series: Biotechnology, 2nd Edition.]]<<BR>>Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany<<BR>>'''INTERACTION DATABASE'''

 1. '''Intermolecular Interactions and Biological Pathways'''<<BR>>'''Gary D. Bader''', Anton J. Enright<<BR>>in [[http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html|Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey]]<<BR>>'''INTERACTION DATABASE'''

 1. '''Computational Prediction of Protein-Protein Interactions'''<<BR>>Anton J. Enright, Lucy Skrabanek, '''Gary D. Bader'''<<BR>>in [[http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1|The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''
-Line 81:
+Line 249:
-. '''Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions'''[[BR]]'''Gary D. Bader''', Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone[[BR]]in [http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462 Handbook of Cell Signaling][[BR]]Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)[[BR]]'''PROTEIN INTERACTION PREDICTION'''
+. '''Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions'''<<BR>>'''Gary D. Bader''', Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone<<BR>>in [[http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462|Handbook of Cell Signaling]]<<BR>>Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)<<BR>>[[attachment:2003_PeptideRecognitionModuleNetworks.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''
-Line 86:
+Line 252:
-. '''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'''
+. '''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. 2013 '''Shirley Hui''' - Computational Prediction of PDZ Mediated Protein-Protein Interactions - [[attachment:Hui_Shirley_201311_PhD_thesis,pdf|PDF]], University of Toronto, Department of Molecular Genetics  
 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