Google Summer of Code 2014: Co-authorship social network App

Short Description (from Cytoscape GSoc wiki)

Goal
Create a visual summary of how individuals are connected

Description

Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution?

Goal:An existing App currently queries PubMed directly or takes in a file with a set of publications (from scopus or incites) and builds a co-publication network where nodes are authors and edges the number of publications two authors share. Different sources have different depths of data, for instance PubMed, the most widely accessible of the three main sources, has citation counts but they are limited to only those articles cited in pubmed central and its institution data is limited to the first author. Given that PubMed is the most accessible source we want to expand its functionality to include computed institution data as well as better citation count approximations, and H-index calculation for individuals or subsets of papers.

This functionality can be applied to several data types outside academia, whenever relationships between people is of interest. An example is professional social networks (e.g. linked-in), where individuals are connected by who they have worked with in the past or the twitter-verse where individuals are connected when they each reference the same (#) hash tag. This project will start with support for co-publication networks and extend to other networks like twitter and linked-in as time permits. Additionally, we want to expand our co-authorship cytoscape App to include generic file formats to easily create the above networks.

Links:
Existing code - https://github.com/BaderLab/SocialNetworkApp
Existing userguide - http://baderlab.org/UserguideSocialNetworkApp

Language and Skills
Java, XML, PubMed e-utils

Example input file

Three different ways to create the same network:

  1. Use the app internal capability to search pubmed and search for "Bader GD"

  2. Example incites data file - incites_example_gdb.xlsx

    Authors Title Year Source title Volume Issue Art. No. Page start Page end Page count Cited by Link Affiliations Authors with affiliations Abstract Author Keywords Index Keywords Molecular Sequence Numbers Chemicals/CAS Tradenames Manufacturers Funding Details References Correspondence Address Editors Sponsors Publisher Conference name Conference date Conference location Conference code ISSN ISBN CODEN DOI PubMed ID Language of Original Document Abbreviated Source Title Document Type Source
    "Lotia S. Montojo J. Dong Y. Bader G.D. Pico A.R." "Cytoscape app store" 2013 "Bioinformatics" 29 10 1350 1351 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84877944199&partnerID=40&md5=89bf09cc5d48de81cb8eddae655b9eb9" "Gladstone Institutes San Francisco CA 94158 United States; Donnelly Centre University of Toronto Toronto ON M5S 3E1 Canada" "Lotia S. Gladstone Institutes San Francisco CA 94158 United States; Montojo J. Donnelly Centre University of Toronto Toronto ON M5S 3E1 Canada; Dong Y. Donnelly Centre University of Toronto Toronto
    "Xin X. Gfeller D. Cheng J. Tonikian R. Sun L. Guo A. Lopez L. Pavlenco A. Akintobi A. Zhang Y. Rual J.-F. Currell B. Seshagiri S. Hao T. Yang X. Shen Y.A. Salehi-Ashtiani K. Li J. Cheng A.T. Bouamalay D. Lugari A. Hill D.E. Grimes M.L. Drubin D.G. Grant B.D. Vidal M. Boone C. Sidhu S.S. Bader G.D." "SH3 interactome conserves general function over specific form" 2013 "Molecular Systems Biology" 9 652 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84876580944&partnerID=40&md5=e77f23f0ed5102ca6c723f9ab976c0d9"
    "Antoniotti M. Bader G.D. Caravagna G. Crippa S. Graudenzi A. Mauri G." "GeStoDifferent: A Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process" 2013 "Bioinformatics" 29 4 513 514 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84874340854&partnerID=40&md5=da78832b54934c1792880f50c78c8358" "Department of Informatics Systems and Communication University of Milan Bicocca Viale Sarca 336 20126 Milano Italy; Bader Lab Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Department of Molecular Genetics Department of Computer Science University of Toronto Toronto ON Canada" "Antoniotti M. Department of Informatics Systems and Communication University of Milan Bicocca Viale Sarca 336 20126
    "Reimand J. Bader G.D." "Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers" 2013 "Molecular Systems Biology" 9 637 2 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84873802661&partnerID=40&md5=fcc8fd8eb80b3892d3947ff6f8c4b20f" "Donnelly Centre University of Toronto 160 College Street Toronto M5S 3E1 Canada" "Reimand J. Donnelly Centre University of Toronto 160 College Street Toronto M5S 3E1 Canada; Bader G.D. Donnelly Centre University of Toronto 160 College Street Toronto M5S 3E1 Canada" "Large-scale cancer genome sequencing has uncovered thousands of gene mutations but distinguishing tumor driver genes from functionally neutral passenger mutations is a major challenge. We analyzed 800 cancer genomes of eight types to find single-nucleotide variants (SNVs) that precisely target phosphorylation machinery important in cancer development and drug targeting. Assuming that cancer-related biological systems involve unexpectedly frequent mutations we used novel algorithms to identify genes with significant phosphorylation-associated SNVs (pSNVs) phospho-mutated pathways kinase networks
    "Aebersold R. Bader G.D. Edwards A.M. Van Eyk J.E. Kussmann M. Qin J. Omenn G.S." "The biology/disease-driven human proteome project (B/D-HPP): Enabling protein research for the life sciences community" 2013 "Journal of Proteome Research" 12 1 23 27 1 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84874074018&partnerID=40&md5=41bf64e86ae2957896407e1fcb168542" "Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland; Faculty of Science University of Zurich Zurich Switzerland; Donnelly Centre Faculty of Medicine University of Toronto Toronto ON Canada; Molecular Genetics University of Toronto Toronto ON M5S 1A8 Canada; Division of Cancer Genomics and Proteomics Ontario Cancer Institute Toronto M5G 2M9 Canada; Department of Medicine School of Medicine Johns Hopkins University
    "Ammar R. Torti D. Tsui K. Gebbia M. Durbic T. Bader G.D. Giaever G. Nislow C." "Chromatin is an ancient innovation conserved between Archaea and Eukarya" 2012 "eLife" 2012 1 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84878965063&partnerID=40&md5=ebc41b6096a950cb369247ac47ebddc4" "Department of Molecular Genetics University of Toronto Toronto Canada; Donnelly Centre University of Toronto Toronto Canada; Department of Pharmaceutical Sciences University of Toronto Toronto Canada" "Ammar R. Department of Molecular Genetics University of Toronto Toronto Canada Donnelly Centre University of Toronto Toronto Canada; Torti D.
    "Lechman E.R. Gentner B. Van Galen P. Giustacchini A. Saini M. Boccalatte F.E. Hiramatsu H. Restuccia U. Bachi A. Voisin V. Bader G.D. Dick J.E. Naldini L." "Attenuation of miR-126 activity expands HSC in vivo without exhaustion" 2012 "Cell Stem Cell" 11 6 799 811 4 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84870894496&partnerID=40&md5=0a7339f0d300a83fb3a33b6fc4fd5a14" "Campbell Family Institute Princess Margaret Cancer Centre University Health Network Toronto ON M5G 1L7 Canada; Department of Molecular Genetics University of Toronto Toronto ON M5G 1L7 Canada; Donnelly Centre University of Toronto Toronto ON M5S 3E1 Canada; Division of Regenerative Medicine San Raffaele Telethon Institute for Gene Therapy Milano 20132
    "Saito R. Smoot M.E. Ono K. Ruscheinski J. Wang P.-L. Lotia S. Pico A.R. Bader G.D. Ideker T." "A travel guide to Cytoscape plugins" 2012 "Nature Methods" 9 11 1069 1076 3 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84869054051&partnerID=40&md5=193093add4188a039d00560bece8ede3" "Department of Medicine University of California San Diego CA United States; Department of Bioengineering University of California San Diego CA United States; Gladstone Institutes San Francisco CA United States; Donnelly Centre Faculty of Medicine University of Toronto Toronto ON Canada" "Saito R. Department of Medicine
    "Alshalalfa M. Bader G.D. Goldenberg A. Morris Q. Alhajj R." "Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study" 2012 "BMC Systems Biology" 6 112 1 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84865322800&partnerID=40&md5=b6b50aa537dd5a27b15d2ef088803df6" "Department of Computer Science University of Calgary Calgary AB Canada; The Donnelly Centre University of Toronto The Department of Molecular Genetics University of Toronto Toronto ON Canada; Genetics and Genome Biology Toronto Canada; Biotechnology Research Centre Palestine Polytechnic University Hebron Palestine" "Alshalalfa M. Department of Computer Science University of Calgary Calgary AB Canada Biotechnology Research Centre
    "Reimand J. Hui S. Jain S. Law B. Bader G.D." "Domain-mediated protein interaction prediction: From genome to network" 2012 "FEBS Letters" 586 17 2751 2763 4 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84864579478&partnerID=40&md5=de15bc47f18f814f348c32268c7734a9" "Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Department of Molecular Genetics University of Toronto 1 King's College Circle Toronto ON M5S 1A8 Canada; Department of Computer Science University of Toronto 10 King's College Circle Toronto ON M5S 3G4 Canada" "Reimand J. Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
    "Northcott P.A. Shih D.J.H. Peacock J. Garzia L. Sorana Morrissy A. Zichner T. Stutz A.M. Korshunov A. Reimand J. Schumacher S.E. Beroukhim R. Ellison D.W. Marshall C.R. Lionel A.C. MacK S. Dubuc A. Yao Y. Ramaswamy V. Luu B. Rolider A. Cavalli F.M.G. Wang X. Remke M. Wu X. Chiu R.Y.B. Chu A. Chuah E. Corbett R.D. Hoad G.R. Jackman S.D. Li Y. Lo A. Mungall K.L. Ming Nip K. Qian J.Q. Raymond A.G.J. Thiessen N. Varhol R.J. Birol I. Moore R.A.
    "Labbe R.M. Irimia M. Currie K.W. Lin A. Zhu S.J. Brown D.D.R. Ross E.J. Voisin V. Bader G.D. Blencowe B.J. Pearson B.J." "A Comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals" 2012 "Stem Cells" 30 8 1734 1745 11 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84864376995&partnerID=40&md5=f44a304f5f9f5f26beabf1b3737944d1" "Hospital for Sick Children Program in Developmental and Stem Cell Biology University of Toronto Toronto ON Canada; Donnelly Centre University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada; Ontario Institute for Cancer Research Toronto ON Canada; Stowers Institute for Medical Research Kansas City
    "Michaut M. Bader G.D." "Multiple genetic interaction experiments provide complementary information useful for gene function prediction" 2012 "PLoS Computational Biology" 8 6 e1002559 2 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84864046645&partnerID=40&md5=b1d2f2d64e31686bcbbc2f3e7c0fc68c" "The Donnelly Centre University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada; Department of Computer Science University of Toronto Toronto ON Canada; Bioinformatics and Statistics Group Netherlands Cancer Institute Amsterdam Netherlands" "Michaut M. The Donnelly Centre University of Toronto Toronto ON Canada Bioinformatics and Statistics Group Netherlands Cancer Institute Amsterdam Netherlands; Bader
    "Liu J.C. Voisin V. Bader G.D. Deng T. Pusztai L. Symmans W.F. Esteva F.J. Egan S.E. Zacksenhaus E." "Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2 +:ERα - breast cancer" 2012 "Proceedings of the National Academy of Sciences of the United States of America" 109 15 5832 5837 6 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84859567448&partnerID=40&md5=84ad5e38e1844457e1df8fb3a902c3a4" "Division of Cell and Molecular Biology Toronto General Research Institute University Health Network Toronto ON M5G 2M9 Canada; Donnelly Centre University of Toronto Toronto ON M5S 3E1 Canada; Department of Molecular Genetics University of Toronto Toronto ON M5S 1A8 Canada; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON M5S 1A8 Canada; Department of Breast Medical Oncology MD Anderson Cancer Center Houston
    "Demir E. Cary M.P. 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 A.C. 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.
    "Tan C.S.H. Bader G.D." "Phosphorylation sites of higher stoichiometry are more conserved" 2012 "Nature Methods" 9 4 317 4 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84859165797&partnerID=40&md5=461e7178a3971baca606e2089cddd12b" "Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto Canada; Department of Molecular Genetics University of Toronto Toronto Canada; Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Canada; Research Center for Molecular Medicine Austrian Academy of Sciences Vienna Austria" "Tan C.S.H. Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto Canada Department of Molecular Genetics University of Toronto Toronto Canada Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Canada
    "Diezmann S. Michaut M. Shapiro R.S. Bader G.D. Cowen L.E." "Mapping the Hsp90 genetic interaction network in candida albicans reveals environmental contingency and rewired circuitry" 2012 "PLoS Genetics" 8 3 e1002562 8 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84859223051&partnerID=40&md5=bdff15af04585c719236a7e2d923bc98" "Department of Molecular Genetics University of Toronto Toronto Canada; The Donnelly Centre University of Toronto Toronto Canada" "Diezmann S. Department of Molecular Genetics University of Toronto Toronto Canada; Michaut M. The Donnelly Centre University of Toronto Toronto Canada; Shapiro R.S. Department of Molecular Genetics University of Toronto Toronto Canada; Bader G.D.
    "Kim T. Tyndel M.S. Huang H. Sidhu S.S. Bader G.D. Gfeller D. Kim P.M." "MUSI: An integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets" 2012 "Nucleic Acids Research" 40 6 6 "http://www.scopus.com/inward/record.url?eid=2-s2.0-84859303311&partnerID=40&md5=f41da226d0ddd7a801ef0aa1f6426ce7" "Donnelly Centre University of Toronto Toronto ON M5S 3E1 Canada; Banting and Best Department of Medical Research University of Toronto Toronto ON M5S 3E1 Canada; Department of Computer Science University of Toronto Toronto ON M5S 3E1 Canada; Edward S. Rogers Sr Department of Electrical and Computer Engineering University of Toronto ON M5S 3G4 Canada; Department of Molecular Genetics University of Toronto Toronto ON M5S 1A4 Canada; Swiss Institute of Bioinformatics Molecular Modeling Génopode
    "le Novere N. Hucka M. Anwar N. Bader G.D. Demir E. Moodie S. Sorokin A." "Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)" 2011 "Standards in Genomic Sciences" 5 2 230 242 "http://www.scopus.com/inward/record.url?eid=2-s2.0-83255181846&partnerID=40&md5=23b05695a042b6fdc8d8d9aa2d3ba3c6" "EMBL-EBI Hinxton CB10 1SD United Kingdom; Division of Engineering and Applied Science California Institute of Technology Pasadena CA United States; General Bioinformatics Limited Reading United Kingdom; The Donnelly Centre University of Toronto Toronto ON M5S Canada; MSKCC - Computational Biology Center New York NY United States; Eight Pillars Ltd 19 Redford Walk Edinburgh United Kingdom; School of Informatics University of Edinburgh Edinburgh
    "Raju R. Balakrishnan L. Nanjappa V. Bhattacharjee M. Getnet D. Muthusamy B. Thomas J.K. Sharma J. Rahiman B.A. Harsha H.C. Shankar S. Prasad T.S.K. Mohan S.S. Bader G.D. Wani M.R. Pandey A." "A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway" 2011 "Database" 2011 bar021 4 "http://www.scopus.com/inward/record.url?eid=2-s2.0-80052901014&partnerID=40&md5=848d02c998b5577f49667b79c92cd2b1" "Institute of Bioinformatics International Technology Park Bangalore 560066 India; Department of Biotechnology Kuvempu University Shankaraghatta 577451 India; School of Biotechnology Amrita Vishwa Vidyapeetham Kollam 690525 India; National Center for Cell Science University of Pune Campus Pune 411007 India; Bioinformatics Centre
    "Raju R. Nanjappa V. Balakrishnan L. Radhakrishnan A. Thomas J.K. Sharma J. Tian M. Palapetta S.M. Subbannayya T. Sekhar N.R. Muthusamy B. Goel R. Subbannayya Y. Telikicherla D. Bhattacharjee M. Pinto S.M. Syed N. Srikanth M.S. Sathe G.J. Ahmad S. Chavan S.N. Kumar G.S.S. Marimuthu A. Prasad T.S.K. Harsha H.C. Rahiman B.A. Ohara O. Bader G.D. Mohan S.S. Schiemann W.P. Pandey A." "NetSlim: High-confidence curated signaling maps" 2011 "Database" 2011 bar032
    "Morris J.H. Apeltsin L. Newman A.M. Baumbach J. Wittkop T. Su G. Bader G.D. Ferrin T.E." "ClusterMaker: A multi-algorithm clustering plugin for Cytoscape" 2011 "BMC Bioinformatics" 12 436 14 "http://www.scopus.com/inward/record.url?eid=2-s2.0-80655132169&partnerID=40&md5=30b32c8c6d3e77d78335c13f1107fd38" "Department of Pharmaceutical Chemistry University of California San Francisco San Francisco CA United States; Institute for Stem Cell Biology and Regenerative Medicine Stanford University School of Medicine Stanford CA United States; Max Planck Institute for Informatics Saarbrücken Germany; Buck Institute for Age Research Novato CA United States; Bioinformatics Program University of Michigan Ann Arbor MI United States; National Center for Integrative Biomedical Informatics University of Michigan Ann Arbor MI
    "Wallace I.M. Urbanus M.L. Luciani G.M. Burns A.R. Han M.K.L. Wang H. Arora K. Heisler L.E. Proctor M. St. Onge R.P. Roemer T. Roy P.J. Cummins C.L. Bader G.D. Nislow C. Giaever G." "Compound prioritization methods increase rates of chemical probe discovery in model organisms" 2011 "Chemistry and Biology" 18 10 1273 1283 7 "http://www.scopus.com/inward/record.url?eid=2-s2.0-80055075327&partnerID=40&md5=2b4009727ba1fe7f1d445932c7588df4" "Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON M5S 3E1 Canada; Banting and Best Department of Medical Research University of Toronto Toronto ON M5G 1L6 Canada; Department of Pharmaceutical Sciences University of Toronto Toronto ON M5S 3M2 Canada; Department of Molecular Genetics
    "Wallace I.M. Bader G.D. Giaever G. Nislow C." "Displaying chemical information on a biological network using cytoscape" 2011 "Methods in Molecular Biology" 781 363 376 "http://www.scopus.com/inward/record.url?eid=2-s2.0-80054741187&partnerID=40&md5=418638a84dcb9a912611f45142bc778b" "Department of Molecular Genetics University of Toronto Toronto ON Canada; Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON Canada; Department of Pharmaceutical Sciences University of Toronto Toronto ON Canada; Banting and Best Department of Medical Research Centre for Cellular and Biomolecular Research (CCBR) Toronto ON Canada" "Wallace I.M. Department of Molecular Genetics University of Toronto Toronto ON Canada Donnelly Centre for Cellular and Biomolecular Research
    "Merico D. Isserlin R. Bader G.D." "Visualizing gene-set enrichment results using the cytoscape plug-in enrichment map" 2011 "Methods in Molecular Biology" 781 257 277 1 "http://www.scopus.com/inward/record.url?eid=2-s2.0-80054761009&partnerID=40&md5=5dc2e93ae657d34c3c7987f2b756ba7c" "Banting and Best Department Medical Research Centre for Cellular and Biomolecular Research (CCBR) Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada" "Merico D. Banting and Best Department Medical Research Centre for Cellular and Biomolecular Research (CCBR) Toronto ON Canada Department of Molecular Genetics University of Toronto Toronto ON Canada; Isserlin R. Banting and Best Department Medical Research
    "Aranda B. Blankenburg H. Kerrien S. Brinkman F.S.L. Ceol A. Chautard E. Dana J.M. De Las Rivas J. Dumousseau M. Galeota E. Gaulton A. Goll J. Hancock R.E.W. Isserlin R. Jimenez R.C. Kerssemakers J. Khadake J. Lynn D.J. 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 G.D. Cesareni G. Donaldson I.M. Eisenberg D. Kleywegt G.J. Overington J. Ricard-Blum S. Tyers M. Albrecht M. Hermjakob H."
    "Tan C.S.H. Schoof E.M. Creixell P. Pasculescu A. Lim W.A. Pawson T. Bader G.D. Linding R." "Response to comment on ""positive selection of tyrosine loss in metazoan evolution""" 2011 "Science" 332 6032 917 b 2 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79956315380&partnerID=40&md5=3e0949e75c604308b5c45cdc983cbe15" "Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada; Donnelly Centre University of Toronto Toronto ON Canada; Institute of Cancer Research (ICR) London United Kingdom; Center for Biological Sequence Analysis (CBS) Department of Systems Biology Technical University of Denmark (DTU) DK-2800 Lyngby Denmark; Howard Hughes Medical Institute Department of Cellular and Molecular Pharmacology University of California
    "Gfeller D. Butty F. Wierzbicka M. Verschueren E. Vanhee P. Huang H. Ernst A. Dar N. Stagljar I. Serrano L. Sidhu S.S. Bader G.D. Kim P.M." "The multiple-specificity landscape of modular peptide recognition domains" 2011 "Molecular Systems Biology" 7 484 21 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79955569676&partnerID=40&md5=524626033dc34f3d0604def118d3de02" "Banting and Best Department of Medical Research Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Department of Biochemistry University of Toronto Toronto ON Canada; EMBL-CRG Systems Biology Unit CRG-Centre de Regulacio Genomica Barcelona Spain; Department of Molecular Genetics University of Toronto Toronto
    "Oesper L. Merico D. Isserlin R. Bader G.D." "WordCloud: A Cytoscape plugin to create a visual semantic summary of networks" 2011 "Source Code for Biology and Medicine" 6 7 3 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79953729967&partnerID=40&md5=c6ba00232fe9a23e3c3df1aa1c51d177" "Department of Computer Science Brown University Providence RI United States; The Donnelly Centre University of Toronto Toronto ON Canada; Banting and Best Department of Medical Research University of Toronto Toronto ON Canada" "Oesper L. Department of Computer Science Brown University Providence RI United States; Merico D. The Donnelly Centre University of Toronto Toronto ON
    "Bellay J. Han S. Michaut M. Kim T. Costanzo M. Andrews B.J. Boone C. Bader G.D. Myers C.L. Kim P.M." "Bringing order to protein disorder through comparative genomics and genetic interactions" 2011 "Genome Biology" 12 2 R14 21 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79851508882&partnerID=40&md5=dd510631dd19f2f2c2a739f8c130e2f3" "Department of Computer Science and Engineering University of Minnesota 200 Union Street SE Minneapolis MN 55455 United States; The Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Banting and Best Department of Medical Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Department of Molecular Genetics University of Toronto 160 College Street Toronto
    "Edwards A.M. Isserlin R. Bader G.D. Frye S.V. Willson T.M. Yu F.H." "Too many roads not taken" 2011 "Nature" 470 7333 163 165 47 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79951499644&partnerID=40&md5=b3d2e1332d70855c67650e6623a826ba" "University of Toronto Toronto ON M5G 1L7 Canada; Donnelly Centre University of Toronto Toronto ON M5S 3E1 Canada; Center for Integrative Chemical Biology and Drug Discovery Eshelman School of Pharmacy University of North Carolina at Chapel Hill Chapel Hill NC 27599 United States; GlaxoSmithKline Research Triangle Park NC 27709 United States; Program in Neurobiology School of Dentistry Seoul National University Seoul 110-749 South Korea" "Edwards A.M.
    "Michaut M. Baryshnikova A. Costanzo M. Myers C.L. Andrews B.J. Boone C. Bader G.D." "Protein complexes are central in the yeast genetic landscape" 2011 "PLoS Computational Biology" 7 2 e1001092 17 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79952474742&partnerID=40&md5=98ab53cc18a2e31f645026d7390734ba" "The Donnelly Centre University of Toronto Toronto ON Canada; Banting and Best Department of Medical Research University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada; Department of Computer Science University of Toronto Toronto ON Canada; Department of Computer Science and Engineering University of Minnesota Minneapolis MN United States" "Michaut
    "Shao X. Tan C.S.H. Voss C. Li S.S.C. Deng N. Bader G.D." "A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence" 2011 "Bioinformatics" 27 3 btq657 383 390 11 "http://www.scopus.com/inward/record.url?eid=2-s2.0-79551614773&partnerID=40&md5=1bae65cafc3fbf423ec03ca9df7d20c4" "Department of Applied Mathematics College of Science China Agricultural University Beijing 100083 China; Banting and Best Department of Medical Research University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto ON M5S 3E1 Canada; Department of Molecular Genetics University of Toronto Toronto ON M5S 3E1 Canada; Department of Biochemistry University of Western Ontario London ON N6A 5B8 Canada" "Shao X. Department of Applied Mathematics College of Science
    "Cerami E.G. Gross B.E. Demir E. Rodchenkov I. Babur O. Anwar N. Schultz N. Bader G.D. Sander C." "Pathway Commons a web resource for biological pathway data" 2011 "Nucleic Acids Research" 39 SUPPL. 1 D685 D690 83 "http://www.scopus.com/inward/record.url?eid=2-s2.0-78651332286&partnerID=40&md5=a958a96921a0a7105d326bdc76ac6607" "Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue Box 460 New York NY 10065 United States; Tri-Institutional Training Program in Computational Biology and Medicine New York United States; Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON M5S 3E1 Canada" "Cerami E.G. Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue
    "Oka T. Remue E. Meerschaert K. Vanloo B. Boucherie C. Gfeller D. Bader G.D. Sidhu S.S. Vandekerckhove J. Gettemans J. Sudol M." "Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent and regulate YAP2 nuclear localization and signalling" 2010 "Biochemical Journal" 432 3 461 472 19 "http://www.scopus.com/inward/record.url?eid=2-s2.0-78649892579&partnerID=40&md5=8d94c59599b888fd5244809dd58c2cd9" "Weis Center for Research 100 North Academy Avenue Danville PA 17822 United States; Department of Medical Protein Research VIB Ghent University B-9000 Ghent Belgium; Department of Biochemistry Faculty of Medicine and Health Sciences Ghent University Albert Baertsoenkaai 3 B-9000 Ghent Belgium; Terrence Donnelly Center for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto
    "Merico D. Isserlin R. Stueker O. Emili A. Bader G.D." "Enrichment map: A network-based method for gene-set enrichment visualization and interpretation" 2010 "PLoS ONE" 5 11 e13984 65 "http://www.scopus.com/inward/record.url?eid=2-s2.0-78649775562&partnerID=40&md5=2ed1ac05a31c6758b087c88214a1993a" "Department of Molecular Genetics Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto Ontario Canada" "Merico D. Department of Molecular Genetics Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto Ontario Canada; Isserlin R. Department of Molecular Genetics Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto Ontario Canada; Stueker O. Department of Molecular Genetics Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto Ontario Canada; Emili
    "Baryshnikova A. Costanzo M. Kim Y. Ding H. Koh J. Toufighi K. Youn J.-Y. Ou J. San Luis B.-J. Bandyopadhyay S. Hibbs M. Hess D. Gingras A.-C. Bader G.D. Troyanskaya O.G. Brown G.W. Andrews B. Boone C. Myers C.L." "Quantitative analysis of fitness and genetic interactions in yeast on a genome scale" 2010 "Nature Methods" 7 12 1017 1024 50 "http://www.scopus.com/inward/record.url?eid=2-s2.0-78649705725&partnerID=40&md5=3eb946d2d45b16713e43951bfb280f6c" "Banting and Best Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Canada; Department of Molecular Genetics Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Canada; Department of Computer Science and Engineering University of Minnesota-Twin Cities
    "Demir E. 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 A.C. 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.
    "Jain S. Bader G.D." "An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology" 2010 "BMC Bioinformatics" 11 562 22 "http://www.scopus.com/inward/record.url?eid=2-s2.0-78149449890&partnerID=40&md5=e9703707613f33764ea8bd28ea001b47" "Department of Computer Science University of Toronto 10 Kings College Road Toronto ON M5 S 3G4 Canada; Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College St Toronto ON M5 S 3E1 Canada" "Jain S. Department of Computer Science University of Toronto 10 Kings College Road Toronto ON M5 S 3G4 Canada Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College St Toronto ON M5 S 3E1 Canada; Bader
    "Montojo J. Zuberi K. Rodriguez H. Kazi F. Wright G. Donaldson S.L. Morris Q. Bader G.D." "GeneMANIA cytoscape plugin: Fast gene function predictions on the desktop" 2010 "Bioinformatics" 26 22 btq562 2927 2928 20 "http://www.scopus.com/inward/record.url?eid=2-s2.0-78149262301&partnerID=40&md5=5ba549251e0ed476753a70c990301356" "Banting and Best Department of Medical Research Departments of Molecular Genetics and Computer Science The Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada" "Montojo J. Banting and Best Department of Medical Research Departments of Molecular Genetics and Computer Science The Donnelly Centre University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Zuberi K.
    "Kirouac D.C. Ito C. Csaszar E. Roch A. Yu M. Sykes E.A. Bader G.D. Zandstra P.W." "Dynamic interaction networks in a hierarchically organized tissue" 2010 "Molecular Systems Biology" 6 417 38 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77957762129&partnerID=40&md5=cf507a8c2bbec1d665274032ad6c2c7a" "Institute for Biomaterials and Biomedical Engineering University of Toronto Toronto ON Canada; Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto ON Canada; Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland; Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON Canada; Banting and Best Department of Medical Research University of Toronto Toronto ON Canada; Department of Medical Genetics University of Toronto Toronto
    "Hui S. Bader G.D." "Proteome scanning to predict PDZ domain interactions using support vector machines" 2010 "BMC Bioinformatics" 11 507 18 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77957737014&partnerID=40&md5=1c0c2b0e539551ffafe050b523ddfb03" "Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada" "Hui S. Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto Toronto ON Canada Department of Molecular Genetics University of Toronto Toronto ON Canada; Bader G.D. Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto Toronto ON Canada Department of Molecular Genetics University of Toronto
    "Ernst A. Gfeller D. Kan Z. Seshagiri S. Kim P.M. Bader G.D. Sidhu S.S." "Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing" 2010 "Molecular BioSystems" 6 10 1782 1790 24 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77956544553&partnerID=40&md5=729680703c7eb445404c1975e3aefae7" "Department of Molecular Genetics Terrence Donnelly Center for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Department of Molecular Biology Genentech 1 DNA Way South San Francisco CA 94080 United States" "Ernst A. Department of Molecular Genetics Terrence Donnelly Center for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Gfeller D.
    "Demir E. Cary M.P. 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 A.C. 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.
    "Lopes C.T. Franz M. Kazi F. Donaldson S.L. Morris Q. Bader G.D." "Cytoscape web: An interactive web-based network browser" 2010 "Bioinformatics" 26 18 btq430 2347 2348 89 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77956548953&partnerID=40&md5=fa81dd2115800a7db7bda3af64d687da" "Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada" "Lopes C.T. Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Franz M. Banting and Best Department of Medical Research Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1
    "Pinto D. Pagnamenta A.T. Klei L. Anney R. Merico D. Regan R. Conroy J. Magalhaes T.R. Correia C. Abrahams B.S. Almeida J. Bacchelli E. Bader G.D. Bailey A.J. Baird G. Battaglia A. Berney T. Bolshakova N. Bolte S. Bolton P.F. Bourgeron T. Brennan S. Brian J. Bryson S.E. Carson A.R. Casallo G. Casey J. Chung B.H.Y. Cochrane L. Corsello C. Crawford E.L. Crossett A. Cytrynbaum C. Dawson G. De Jonge M. Delorme R. Drmic I. Duketis E. Duque F. Estes A.
    "Burns A.R. Wallace I.M. Wildenhain J. Tyers M. Giaever G. Bader G.D. Nislow C. Cutler S.R. Roy P.J." "A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans" 2010 "Nature Chemical Biology" 6 7 549 557 35 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77953805895&partnerID=40&md5=4f794763c9e8ecbc04e991aa8b935ee2" "Department of Molecular Genetics University of Toronto Toronto ON Canada; Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON Canada; Samuel Lunenfeld Research Institute Mount Sinai Hospital University of Toronto Toronto ON Canada; Wellcome Trust Centre for Cell Biology University of Edinburgh Edinburgh United Kingdom; Department of Pharmaceutical Sciences University of Toronto Toronto ON
    "Warde-Farley D. Donaldson S.L. Comes O. Zuberi K. Badrawi R. Chao P. Franz M. Grouios C. Kazi F. Lopes C.T. Maitland A. Mostafavi S. Montojo J. Shao Q. Wright G. Bader G.D. Morris Q." "The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function" 2010 "Nucleic Acids Research" 38 SUPPL. 2 gkq537 W214 W220 113 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77954269901&partnerID=40&md5=3510502728fb9496be38ff909f211d19" "Department of Computer Science University of Toronto Toronto ON Canada; Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON
    "Hudson T.J. Anderson W. Aretz A. Barker A.D. Bell C. Bernabe R.R. Bhan M.K. Calvo F. Eerola I. Gerhard D.S. Guttmacher A. Guyer M. Hemsley F.M. Jennings J.L. Kerr D. Klatt P. Kolar P. Kusuda J. Lane D.P. Laplace F. Lu Y. Nettekoven G. Ozenberger B. Peterson J. Rao T.S. Remacle J. Schafer A.J. Shibata T. Stratton M.R. Vockley J.G. Watanabe K. Yang H. Yuen M.M.F. Knoppers B.M. Bobrow M. Cambon-Thomsen A. Dressler L.G. Dyke S.O.M. Joly Y. Kato K.
    "Isserlin R. Merico D. Alikhani-Koupaei R. Gramolini A. Bader G.D. Emili A." "Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps" 2010 "Proteomics" 10 6 1316 1327 19 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77949701781&partnerID=40&md5=0323cae9b525b85280e36a72f5db8813" "Banting and Best Department of Medical Research University of Toronto Toronto ON Canada; Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON Canada; Department of Physiology University of Toronto Toronto ON Canada" "Isserlin R. Banting and Best Department of Medical Research University of Toronto Toronto ON Canada Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto
    "Costanzo M. Baryshnikova A. Bellay J. Kim Y. Spear E.D. Sevier C.S. Ding H. Koh J.L.Y. Toufighi K. Mostafavi S. Prinz J. St. Onge R.P. Vandersluis B. Makhnevych T. Vizeacoumar F.J. Alizadeh S. Bahr S. Brost R.L. Chen Y. Cokol M. Deshpande R. Li Z. Lin Z.-Y. Liang W. Marback M. Paw J. Luis B.-J.S. Shuteriqi E. Tong A.H.Y. Van Dyk N. Wallace I.M. Whitney J.A. Weirauch M.T. Zhong G. Zhu H. Houry W.A. Brudno M. Ragibizadeh S. Papp B. Pal C.
    "Kandasamy K. Sujatha Mohan S. Raju R. Keerthikumar S. Sameer Kumar G.S. Venugopal A.K. Telikicherla D. Navarro D.J. Mathivanan S. Pecquet C. Gollapudi S.K. Tattikota S.G. Mohan S. Padhukasahasram H. Subbannayya Y. Goel R. Jacob H.K. Zhong J. Sekhar R. Nanjappa V. Balakrishnan L. Subbaiah R. Ramachandra Y.L. Abdul Rahiman B. Keshava Prasad T.S. Lin J.-X. Houtman J.C. Desiderio S. Renauld J.-C. Constantinescu S. Ohara O. Hirano T. Kubo M. Singh S. Khatri P. Draghici S. Bader G.D. Sander C. Leonard W.J. Pandey A."
    "Koh J.L.Y. Ding H. Costanzo M. Baryshnikova A. Toufighi K. Bader G.D. Myers C.L. Andrews B.J. Boone C." "DRYGIN: A database of quantitative genetic interaction networks in yeast" 2010 "Nucleic Acids Research" 38 SUPPL.1 gkp820 D502 D507 27 "http://www.scopus.com/inward/record.url?eid=2-s2.0-75549091259&partnerID=40&md5=2002c423086ec89593c870fb0f729ba6" "Banting and Best Department of Medical Research and Department of Molecular Genetics The Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada; Department of Computer Science and Engineering University of Minnesota 4-192 EE/CS Building 200 Union Street SE Minneapolis MN 55455 United States" "Koh J.L.Y. Banting and Best Department of Medical Research and Department of Molecular Genetics The Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto
    "Tan C.S.H. Pasculescu A. Lim W.A. Pawson T. Bader G.D. Linding R." "Positive selection of tyrosine loss in metazoan evolution" 2009 "Science" 325 5948 1686 1688 40 "http://www.scopus.com/inward/record.url?eid=2-s2.0-70349518562&partnerID=40&md5=89d3ebfb0408bc684cfbdb39c7496289" "Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto MSG 1X5 Canada; Department of Molecular Genetics University of Toronto Toronto M5S 1A8 Canada; Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto MSS 3E1 Canada; Howard Hughes Medical Institute Department of Cellular and Molecular Pharmacology University of California San Francisco San Francisco CA 94158 United States; Cellular and Molecular Logic Team Section of Cell and Molecular Biology Institute of Cancer Research (ICR) London SW3 6JB United Kingdom" "Tan C.S.H.
    "Tonikian R. Xin X. Toret C.P. Gfeller D. Landgraf C. Panni S. Paoluzi S. Castagnoli L. Currell B. Seshagiri S. Yu H. Winsor B. Vidal M. Gerstein M.B. Bader G.D. Volkmer R. Cesareni G. Drubin D.G. Kim P.M. Sidhu S.S. Boone C." "Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins" 2009 "PLoS Biology" 7 10 e1000218 65 "http://www.scopus.com/inward/record.url?eid=2-s2.0-70350404403&partnerID=40&md5=f4f2efecf5e502aa643bb964a3d94e5b" "Terrence Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto
    "Merico D. Gfeller D. Bader G.D." "How to visually interpret biological data using networks" 2009 "Nature Biotechnology" 27 10 921 924 26 "http://www.scopus.com/inward/record.url?eid=2-s2.0-70349948795&partnerID=40&md5=a0d7cb756cd1a8e12667ba86f8a67f7f" "Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) University of Toronto Toronto ON Canada" "Merico D. Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) University of Toronto Toronto ON Canada; Gfeller D. Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) University of Toronto Toronto ON Canada; Bader G.D. Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR) University of Toronto Toronto
    "Ernst A. Sazinsky S.L. Hui S. Currell B. Dharsee M. Seshagiri S. Bader G.D. Sidhu S.S." "Rapid evolution of functional complexity in a domain family" 2009 "Science Signaling" 2 87 29 "http://www.scopus.com/inward/record.url?eid=2-s2.0-77949772254&partnerID=40&md5=4753a495166a1cf043ceba267d7932a5" "Department of Protein Engineering Genentech 1 DNA Way South San Francisco CA 94080 United States; Department of Biological Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue E19-563 Cambridge MA 02139 United States; Banting and Best Department of Medical Research University of Toronto Donnelly CCBR 160 College Street Toronto ON M5S E1 Canada; Department of Molecular Genetics University of Toronto Toronto ON
    "Tan C.S.H. Bodenmiller B. Pasculescu A. Jovanovic M. Hengartner M.O. Claus J. Bader G.D. Aebersold R. Pawson T. Linding R." "Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases" 2009 "Science Signaling" 2 81 83 "http://www.scopus.com/inward/record.url?eid=2-s2.0-70349526350&partnerID=40&md5=f2d184a10e6fe0ffaefd5885a25d39eb" "Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto ON M5G 1X5 Canada; Department of Molecular Genetics University of Toronto Toronto ON M5S 1A8 Canada; Institute of Molecular Systems Biology Eidgenössische Technische Hochschule (ETH) 8093 Zurich Switzerland; Institute of Molecular Biology University of Zurich 8057 Zurich Switzerland; Institute for Systems Biology Seattle WA 98103 United States; Competence Center for Systems Physiology and Metabolic Diseases ETH Zurich
    "Yeung N. Cline M.S. Kuchinsky A. Smoot M.E. Bader G.D." "Exploring biological networks with cytoscape software" 2008 "Current Protocols in Bioinformatics" SUPPL. 23 8.13.1 8.13.20 10 "http://www.scopus.com/inward/record.url?eid=2-s2.0-58749115239&partnerID=40&md5=fe7326372204a8776f3f3efd5e5d9e42" "University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto ON Canada; Department of Molecular Cell and Developmental Biology University of California Santa Cruz CA United States; Agilent Technologies Santa Clara CA United States; Department of Bioengineering University of California La Jolla CA United States" "Yeung N. University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto ON
    "Tonikian R. Zhang Y. Sazinsky S.L. Currell B. Yeh J.H. Reva B. Held H.A. Appleton B.A. Evangelista M. Wu Y. Xin X. Chan A.C. Seshagiri S. Lasky L.A. Sander C. Boone C. Bader G.D. Sidhu S.S." "A specificity map for the PDZ domain family." 2008 "PLoS biology" 6 9 68 "http://www.scopus.com/inward/record.url?eid=2-s2.0-55749111046&partnerID=40&md5=9280a21ee56fc9729f02045953303270" "Terrence Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto Toronto Ontario Canada." "Tonikian R. Terrence Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto
    "Yeung N. Cline M.S. Kuchinsky A. Smoot M.E. Bader G.D." "Exploring biological networks with Cytoscape software." 2008 "Current protocols in bioinformatics / editoral board Andreas D. Baxevanis ... [et al.]" Chapter 8 4 "http://www.scopus.com/inward/record.url?eid=2-s2.0-55249083549&partnerID=40&md5=c13f0ae27a31458440a27cc79a60ebcc" "University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto Ontario Canada." "Yeung N. University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto Ontario Canada.; Cline M.S. University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto Ontario Canada.; Kuchinsky A. University of Toronto Donnelly Centre for Cellular and Biomolecular Research Toronto Ontario
    "Tonikian R. Zhang Y. Sazinsky S.L. Currell B. Yeh J.-H. Reva B. Held H.A. Appleton B.A. Evangelista M. Wu Y. Xin X. Chan A.C. Seshagiri S. Lasky L.A. Sander C. Boone C. Bader G.D. Sidhu S.S." "A specificity map for the PDZ domain family" 2008 "PLoS Biology" 6 9 e239 2043 2059 80 "http://www.scopus.com/inward/record.url?eid=2-s2.0-54749086397&partnerID=40&md5=0ecb32128c66ec4667c877716155976f" "Terrence Donnelly Center for Cellular and Biomolecular Research Banting and Best Department of Medical Research University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada; Department of Protein Engineering Genentech
    "Ashkenazi M. Bader G.D. Kuchinsky A. Moshelion M. States D.J." "Cytoscape ESP: Simple search of complex biological networks" 2008 "Bioinformatics" 24 12 1465 1466 7 "http://www.scopus.com/inward/record.url?eid=2-s2.0-45449103076&partnerID=40&md5=3c692520f1deb3619c63b67df21752d8" "Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture Hebrew University of Jerusalem Rehovot Israel; Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON Canada; Agilent Technologies Santa Clara CA United States; Center for Computational Medicine and Biology University of Michigan Ann Arbor MI United States" "Ashkenazi M. Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture Hebrew University of Jerusalem Rehovot Israel; Bader G.D. Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto
    "Skrabanek L. Saini H.K. Bader G.D. Enright A.J." "Computational prediction of protein-protein interactions" 2008 "Molecular Biotechnology" 38 1 1 17 60 "http://www.scopus.com/inward/record.url?eid=2-s2.0-38949138554&partnerID=40&md5=9cec43b3b15f5eb79b24fc905537455c" "Department of Physiology and Biophysics Institute for Computational Biomedicine Weill Medical College of Cornell University 1300 York Avenue New York NY 10021 United States; Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA United Kingdom; Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College Street Toronto ON M5S 3E1 Canada" "Skrabanek L. Department of Physiology and Biophysics Institute for Computational Biomedicine Weill Medical College of Cornell University 1300 York Avenue New York NY 10021 United States; Saini
    "Cline M.S. 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 A.R. Vailaya A. Wang P.L. Adler A. Conklin B.R. Hood L. Kuiper M. Sander C. Schmulevich I. Schwikowski B. Warner G.J. Ideker T. Bader G.D." "Integration of biological networks and gene expression data using Cytoscape." 2007 "Nature protocols" 2 10 2366 2382
    "Zogopoulos G. Ha K.C.H. Naqib F. Moore S. Kim H. Montpetit A. Robidoux F. Laflamme P. Cotterchio M. Greenwood C. Scherer S.W. Zanke B. Hudson T.J. Bader G.D. Gallinger S." "Germ-line DNA copy number variation frequencies in a large North American population" 2007 "Human Genetics" 122 3-4 345 353 94 "http://www.scopus.com/inward/record.url?eid=2-s2.0-35448992970&partnerID=40&md5=67e64d2604763fb82c916b357909d209" "Sam Minuk Cancer Genetics and Biomarker Laboratories Fred Litwin Centre for Cancer Genetics Samuel Lunenfeld Research Institute Toronto ON Canada; Dr. Zane Cohen Digestive Diseases Clinical Research Centre Mount Sinai Hospital Toronto ON Canada; Banting and Best Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto ON
    "Kerrien S. Orchard S. Montecchi-Palazzi L. Aranda B. Quinn A.F. Vinod N. Bader G.D. Xenarios I. Wojcik J. Sherman D. Tyers M. Salama J.J. Moore S. Ceol A. Chatr-Aryamontri A. Oesterheld M. Stumpflen V. Salwinski L. Nerothin J. Cerami E. Cusick M.E. Vidal M. Gilson M. Armstrong J. Woollard P. Hogue C. Eisenberg D. Cesareni G. Apweiler R. Hermjakob H." "Broadening the horizon - Level 2.5 of the HUPO-PSI format for molecular interactions" 2007 "BMC Biology" 5 44 92
    "Orchard S. Salwinski L. Kerrien S. Montecchi-Palazzi L. Oesterheld M. Stumpflen V. Ceol A. Chatr-Aryamontri A. Armstrong J. Woollard P. Salama J.J. Moore S. Wojcik J. Bader G.D. Vidal M. Cusick M.E. Gerstein M. Gavin A.-C. Superti-Furga G. Greenblatt J. Bader J. Uetz P. Tyers M. Legrain P. Fields S. Mulder N. Gilson M. Niepmann M. Burgoon L. Rivas J.D.L. Prieto C. Perreau V.M. Hogue C. Mewes H.-W. Apweiler R. Xenarios I. Eisenberg D. Cesareni G. Hermjakob H." "The minimum information required for reporting a molecular interaction experiment (MIMIx)"
    "Ferro A. Giugno R. Pigola G. Pulvirenti A. Skripin D. Bader G.D. Shasha D." "NetMatch: A Cytoscape plugin for searching biological networks" 2007 "Bioinformatics" 23 7 910 912 28 "http://www.scopus.com/inward/record.url?eid=2-s2.0-34248576314&partnerID=40&md5=230cbd795c667b1d18fe65b51bda90b4" "Dipartimento di Matematica e Informatica Università di Catania Viale A. Doria 6 I-95125 Catania Italy; Banting and Best Department of Medical Research Department of Medical Genetics and Microbiology University of Toronto 160 College St Toronto ON M5S 3E1 Canada; Courant Institute of Mathematical Sciences New York University 251 Mercer Street New York NY 10012 United States" "Ferro A. Dipartimento di Matematica e Informatica Università di Catania Viale A. Doria 6 I-95125 Catania
    "Mathew J.P. Taylor B.S. Bader G.D. Pyarajan S. Antoniotti M. Chinnaiyan A.M. Sander C. Burakoff S.J. Mishra B." "From bytes to bedside: Data integration and computational biology for translational cancer research" 2007 "PLoS Computational Biology" 3 2 0153 0163 19 "http://www.scopus.com/inward/record.url?eid=2-s2.0-33847253388&partnerID=40&md5=dea966d5577e3b2cc06b463f0a901c5b" "Dana-Farber Cancer Institute Boston MA United States; Department of Physiology and Biophysics Weill Medical College Cornell University New York NY United States; Computational Biology Center Memorial Sloan-Kettering Cancer Center New York NY United States; Banting and Best Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Toronto Ont. Canada; Skirball Institute of Biomolecular Medicine New York University Cancer Institute New York
    "Cerami E.G. Bader G.D. Gross B.E. Sander C." "cPath: Open source software for collecting storing and querying biological pathways" 2006 "BMC Bioinformatics" 7 497 53 "http://www.scopus.com/inward/record.url?eid=2-s2.0-33751435209&partnerID=40&md5=94f6c8e36c8cbfa869a352740aca9fc1" "Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue New York NY 10021 United States; Banting and Best Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto 160 College St. Toronto ON M5S 3E1 Canada" "Cerami E.G. Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue New York NY 10021 United States; Bader G.D. Banting and Best Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research
    "Bader G.D. Cary M.P. Sander C." "Pathguide: a pathway resource list." 2006 "Nucleic acids research." 34 Database issue D504 506 121 "http://www.scopus.com/inward/record.url?eid=2-s2.0-33644873677&partnerID=40&md5=876a29f8533304dec87ca4bbd6dc13f1" "Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue Box 460 New York NY 10021 USA." "Bader G.D. Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue Box 460 New York NY 10021 USA.; Cary M.P. Computational Biology Center Memorial Sloan-Kettering Cancer Center 1275 York Avenue Box 460 New York NY 10021 USA.; Sander C. Computational Biology Center
    "Cary M.P. Bader G.D. Sander C." "Pathway information for systems biology" 2005 "FEBS Letters" 579 8 1815 1820 60 "http://www.scopus.com/inward/record.url?eid=2-s2.0-14844332708&partnerID=40&md5=7e5050af75333cc3aadf2a6c5577cf92" "Computational Biology Center Mem. Sloan-Kettering Cancer Center Box 460 1275 York Avenue New York NY 10021 United States" "Cary M.P. Computational Biology Center Mem. Sloan-Kettering Cancer Center Box 460 1275 York Avenue New York NY 10021 United States; Bader G.D. Computational Biology Center Mem. Sloan-Kettering Cancer Center Box 460 1275 York Avenue New York NY 10021 United States; Sander C. Computational Biology Center
    "Tong A.H.Y. Lesage G. Bader G.D. Ding H. Xu H. Xin X. Young J. Berriz G.F. Brost R.L. Chang M. Chen Y. Cheng X. Chua G. Friesen H. Goldberg D.S. Haynes J. Humphries C. He G. Hussein S. Ke L. Krogan N. Li Z. Levinson J.N. Lu H. Menard P. Munyana C. Parsons A.B. Ryan O. Tonikian R. Roberts T. Sdicu A.-M. Shapiro J. Sheikh B. Suter B. Wong S.L. Zhang L.V. Zhu H. Burd C.G. Munro S. Sander C.
    "Andrews B.J. Bader G.D. Boone C." "Playing tag with the yeast proteome" 2003 "Nature Biotechnology" 21 11 1297 1299 5 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0242290928&partnerID=40&md5=38b82f4e6cce198ef9c0a9813b10eee7" "Dept. of Med. Genet. and Microbiol. University of Toronto Toronto Ont. M5S IA8 Canada; Dept. of Med. Genet. and Microbiol. Banting and Best Dept. of Med. Res. University of Toronto Toronto Ont. M5S IA8 Canada; Computational Biology Center Mem. Sloan-Kettering Cancer Center Box 460 1275 York Ave. New York NY 10021 United States" "Andrews B.J. Dept. of Med. Genet. and Microbiol. University of Toronto Toronto Ont. M5S IA8 Canada; Bader G.D. Computational Biology Center Mem. Sloan-Kettering Cancer Center
    "Bader G.D. Heilbut A. Andrews B. Tyers M. Hughes T. Boone C." "Functional genomics and proteomics: Charting a multidimensional map of the yeast cell" 2003 "Trends in Cell Biology" 13 7 344 356 70 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0037756723&partnerID=40&md5=ff8c1ceae48fc5b6b6bcca7c777aac9c" "Computational Biology Center Mem. Sloan-Kettering Cancer Center Box 460 1275 York Avenue New York NY 10021 United States; MDS Proteomics 251 Attwell Drive Toronto Ont. M9W 7H4 Canada; Dept. of Med. Genet./Microbiology University of Toronto 1 Kings College Circle Toronto Ont. M5S 1A8 Canada; Samuel Lunenfeld Research Institute Mount Sinai Hospital University Avenue Toronto Ont. M5G 1X5 Canada; Banting/Best Dept. of Med. Research University of Toronto 112 College St.
    "Donaldson I. Martin J. de Bruijn B. Wolting C. Lay V. Tuekam B. Zhang S. Baskin B. Bader G.D. Michalickova K. Pawson T. Hogue C.W.V." "PreBIND and textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine" 2003 "BMC Bioinformatics" 4 11 13 81 "http://www.scopus.com/inward/record.url?eid=2-s2.0-2942549190&partnerID=40&md5=3fa219bc0529acb3c926aff9480c1519" "Samuel Lunenfeld Research Institute Toronto Ont. M4G 1X5 Canada; Institute for Information Technology National Research Council of Canada Ottawa Ont. K1A 0R6 Canada; MDS Proteomics Inc. Toronto Ont. M9W 7H4 Canada; Dept. of Biochemistry University of Toronto Toronto Ont. Canada; Computational Biology Center Memorial Sloan-Kettering Cancer 1275 York Avenue
    "Donaldson I. Martin J. de Bruijn B. Wolting C. Lay V. Tuekam B. Zhang S. Baskin B. Bader G.D. Michalickova K. Pawson T. Hogue C.W." "PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine." 2003 "BMC bioinformatics [electronic resource]" 4 1 11 80 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0642371101&partnerID=40&md5=6f25a104665f09588bcdcf4e6e80e0e0" "Samuel Lunenfeld Research Institute Toronto M5G 1X5 Canada." "Donaldson I. Samuel Lunenfeld Research Institute Toronto M5G 1X5 Canada.; Martin J. Samuel Lunenfeld Research Institute Toronto M5G 1X5 Canada.; de Bruijn B. Samuel Lunenfeld Research Institute
    "Sidhu S.S. Bader G.D. Boone C." "Functional genomics of intracellular peptide recognition domains with combinatorial biology methods" 2003 "Current Opinion in Chemical Biology" 7 1 97 102 15 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0037305940&partnerID=40&md5=0f40c0987dce8b32f5a7bcd7de4b509b" "Department of Protein Engineering Genentech Inc. 1 DNA Way South San Francisco CA 94080 United States; Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Avenue Toronto Ont. M5S 1A8 Canada; Computational Biology Center Mem. Sloan-Kattering Cancer Center 1275 York Avenue New York NY 10021 United States" "Sidhu S.S. Department of Protein Engineering Genentech Inc. 1 DNA Way South San Francisco CA 94080 United States; Bader
    "Bader G.D. Hogue C.W.V." "An automated method for finding molecular complexes in large protein interaction networks" 2003 "BMC Bioinformatics" 4 2 27 186 "http://www.scopus.com/inward/record.url?eid=2-s2.0-2942552459&partnerID=40&md5=79fe27abb7ff1291201e2c9da03829ba" "Samuel Lunenfeld Research Institute Mt. Sinai Hospital Toronto Ont. M5G 1X5 Canada; Memorial Sloan-Kettering Cancer Ctr. 1275 York Avenue New York NY 10021 United States; Dept. of Biochemistry University of Toronto Toronto Ont. M5S 1A8 Canada" "Bader G.D. Samuel Lunenfeld Research Institute Mt. Sinai Hospital Toronto Ont. M5G 1X5 Canada Memorial Sloan-Kettering Cancer Ctr. 1275 York Avenue New York NY 10021 United States Dept. of Biochemistry University of Toronto
    "Bader G.D. Hogue C.W." "An automated method for finding molecular complexes in large protein interaction networks." 2003 "BMC bioinformatics [electronic resource]" 4 1 2 496 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0037566556&partnerID=40&md5=95c65367b5dfd3421c441c38ff34a955" "Samuel Lunenfeld Research Institute Mt Sinai Hospital Toronto ON Canada M5G 1X5 Dept of Biochemistry University of Toronto Toronto ON Canada M5S 1A8." "Bader G.D. Samuel Lunenfeld Research Institute Mt Sinai Hospital Toronto ON Canada M5G 1X5 Dept of Biochemistry University of Toronto Toronto ON Canada M5S 1A8.; Hogue C.W. Samuel Lunenfeld Research Institute Mt Sinai Hospital Toronto ON Canada M5G 1X5 Dept of Biochemistry University of Toronto Toronto ON Canada M5S 1A8."
    "Bader G.D. Betel D. Hogue C.W.V." "BIND: The Biomolecular Interaction Network Database" 2003 "Nucleic Acids Research" 31 1 248 250 567 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0037245913&partnerID=40&md5=88ac074107b4901734ce9f07c4c687e5" "Department of Biochemistry Samuel Lunenfeld Research Inst. University of Toronto Toronto Ont. M5G 1X5 Canada" "Bader G.D. Department of Biochemistry Samuel Lunenfeld Research Inst. University of Toronto Toronto Ont. M5G 1X5 Canada; Betel D. Department of Biochemistry Samuel Lunenfeld Research Inst. University of Toronto Toronto Ont. M5G 1X5 Canada; Hogue C.W.V. Department of Biochemistry Samuel Lunenfeld Research Inst. University of Toronto Toronto
    "Michalickova K. Bader G.D. Dumontier M. Lieu H. Betel D. Isserlin R. Hogue C.W.V." "SeqHound: Biological sequence and structure database as a platform for bioinformatics research" 2002 "BMC Bioinformatics" 3 32 13 37 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0012787398&partnerID=40&md5=37e69a1b13692929f9452e56b952aad3" "Department of Biochemistry University of Toronto Toronto Ont. M5S 1A8 Canada; Samuel Lunenfeld Research Institute 600 University Avenue Toronto Ont. M5G 1X5 Canada" "Michalickova K. Department of Biochemistry University of Toronto Toronto Ont. M5S 1A8 Canada Samuel Lunenfeld Research Institute 600 University Avenue Toronto Ont. M5G 1X5 Canada; Bader G.D.
    "Bader G.D. Hogue C.W.V." "Analyzing yeast protein-protein interaction data obtained from different sources" 2002 "Nature Biotechnology" 20 10 991 997 318 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0036789265&partnerID=40&md5=ae3c9cbcba4019239ba41b2d4892c98d" "Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto Ont. MSG 1X5 Canada" "Bader G.D. Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto Ont. MSG 1X5 Canada; Hogue C.W.V. Samuel Lunenfeld Research Institute Mount Sinai Hospital Toronto Ont. MSG 1X5 Canada" "High-throughput methods for detecting protein interactions such as mass spectrometry and yeast two-hybrid assays continue to produce vast amounts of data that may be exploited to infer protein function and regulation. As this article went to press the pool of all published interaction information on Saccharomyces cerevisiae was 15 143 interactions among 4 825 proteins and power-law scaling supports an estimate of 20 000 specific protein interactions. To investigate the biases overlaps
    "Tong A.H.Y. Drees B. Nardelli G. Bader G.D. Brannetti B. Castagnoli L. Evangelista M. Ferracuti S. Nelson B. Paoluzi S. Quondam M. Zucconi A. Hogue C.W.V. Fields S. Boone C. Cesareni G." "A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules" 2002 "Science" 295 5553 321 324 409 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0037059461&partnerID=40&md5=18dd0e47d9d987d66fb9cb38860bffe5" "Department of Genome Sciences University of Washington Box 357730 Seattle WA 98195 United States" "Tong A.H.Y. Department of Genome Sciences University of Washington Box 357730 Seattle WA 98195
    "Ho Y. Gruhler A. Heilbut A. Bader G.D. Moore L. Adams S.-L. 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 A.R. Sassi H. Nielsen P.A. Rasmussen K.J. Andersen J.R. Johansen L.E. Hansen L.H. Jespersen H. Podtelejnikov A. Nielsen E. Crawford J. Poulsen V. Sorensen B.D. Matthiesen J. Hendrickson R.C. Gleeson F. Pawson T.
    "Tong A.H.Y. Evangelista M. Parsons A.B. Xu H. Bader G.D. Page N. Robinson M. Raghibizadeh S. Hogue C.W.V. Bussey H. Andrews B. Tyers M. Boone C." "Systematic genetic analysis with ordered arrays of yeast deletion mutants" 2001 "Science" 294 5550 2364 2368 987 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0035861532&partnerID=40&md5=657ee95d11c5632631929ebff81208b5" "Department of Medical Genetics University of Toronto Toronto Ont. M5S 1A8 Canada" "Tong A.H.Y. Department of Medical Genetics University of Toronto Toronto Ont. M5S 1A8 Canada; Evangelista M. Department of Medical Genetics University of Toronto Toronto
    "Bader G.D. Donaldson I. Wolting C. Ouellette B.F.F. Pawson T. Hogue C.W.V." "BIND - The Biomolecular Interaction Network Database" 2001 "Nucleic Acids Research" 29 1 242 245 319 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0035171884&partnerID=40&md5=4aea202e18d48475fa5b9ee9956ecc17" "Department of Biochemistry University of Toronto Toronto Ont. Canada; Samuel Lunenfeld Research Institute Toronto Ont. M5G 1X5 Canada; Centre for Molecular Medicine and Therapeutics Children's and Women's Health Centre of British Columbia University of British Columbia Vancouver BC V5Z 4H4 Canada; Department of Molecular and Medical Genetics University of Toronto Toronto Ont. Canada; Samuel Lunenfeld Research Institute 600 University Avenue Toronto Ont. M5G 1X5 Canada" "Bader G.D.
    "Bader G.D. Hogue C.W.V." "BIND - A data specification for storing and describing biomolecular interactions molecular complexes and pathways" 2000 "Bioinformatics" 16 5 465 477 109 "http://www.scopus.com/inward/record.url?eid=2-s2.0-0033930882&partnerID=40&md5=18d2f22f5827f610215e946abeba244b" "Department of Biochemistry University of Toronto Samuel Lunenfeld Research Institute Toronto Ont. M5G 1X5 Canada; Samuel Lunenfeld Research Institute Toronto Ont. M5G 1X5 Canada" "Bader G.D. Department of Biochemistry University of Toronto Samuel Lunenfeld Research Institute Toronto Ont. M5G 1X5 Canada; Hogue C.W.V. Samuel Lunenfeld Research Institute Toronto Ont. M5G 1X5 Canada" "Motivation: Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins protein domains and protein interactions in a cell and will eventually create more recorded biological information than the Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any database or tool for managing and analysing this information. Results: We have defined a complete data specification in ASN.1 that can describe information about biomolecular interactions complexes and pathways. Our group is using this data specification in our database the Biomolecular Interaction Network Database (BIND). An interaction record is based on the interaction between two objects. An object can be a protein

  3. Example scopus data file - scopus_example_gdb.csv

Going Beyond Simple Solutions

We would like applicants to be creative, and come up with new or different ways to generalize their proposed app so that it is applicable for more than just publications.

About

Potential members:

We are part of Gary Bader's lab at University of Toronto - CCBR (Toronto, ON Canada). Our lab is strongly engaged in biological network research. Feel free to have a look at our home page for more details on the lab research areas, and at our home-pages for our own research interests.

GSoC2014_SocialNetworkApp (last edited 2014-02-27 20:28:37 by RuthIsserlin)

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