#acl All:read
<<TableOfContents(1)>>

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= Peer-reviewed Articles =

== 2015 ==
 1. '''Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action.'''<<BR>>Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, '''Isserlin R''', '''Bader GD''', Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G.<<BR>>  [[http://www.biochemj.org/bj/imps/abs/BJ20141455.htm|Biochem J. 2015 Apr 27.]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25915851|Pubmed]] - [[attachment:BiochemApr2015.pdf|PDF]]

 1. '''Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes.'''<<BR>> '''Ammar R''', Paton TA, Torti D, Shlien A, '''Bader GD.''' <<BR>>[[http://f1000research.com/articles/4-17/v1|F1000Res. 2015 Jan 21;4:17. doi: 10.12688/f1000research.6037.1. eCollection 2015.]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25901276|Pubmed]] - [[attachment:F1000Apr2015.pdf|PDF]]

 1. '''Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis.'''<<BR>> Torchia J, Picard D, Lafay-Cousin L, Hawkins CE, Kim SK, Letourneau L, Ra YS, Ho KC, Chan TS, Sin-Chan P, Dunham CP, Yip S, Ng HK, Lu JQ, Albrecht S, Pimentel J, Chan JA, Somers GR, Zielenska M, Faria CC, Roque L, Baskin B, Birks D, Foreman N, Strother D, Klekner A, Garami M, Hauser P, Hortobágyi T, Bognár L, Wilson B, Hukin J, Carret AS, Van Meter TE, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheineman K, Johnston D, Michaud J, Zelcer S,Hammond R, Ramsay DA, Fleming AJ, Lulla RR, Fangusaro JR, Sirachainan N, Larbcharoensub N, Hongeng S, Barakzai MA, Montpetit A, Stephens D, Grundy RG, Schüller U, Nicolaides T, Tihan T, Phillips J, Taylor MD, Rutka JT, Dirks P, '''Bader GD''', Warmuth-Metz M, Rutkowski S, Pietsch T, Judkins AR, Jabado N, Bouffet E, Huang A.<<BR>>[[http://www.thelancet.com/journals/lanonc/article/PIIS1470-2045(15)70114-2/abstract|Lancet Oncol. 2015 Apr 13. pii: S1470-2045(15)70114-2. doi: 10.1016/S1470-2045(15)70114-2]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25882982|Pubmed]] - [[attachment:LancetApr2015.pdf|PDF]]

 1. '''Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.'''<<BR>> Hucka M, Nickerson DP, '''Bader GD''', Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.<<BR>> [[http://journal.frontiersin.org/article/10.3389/fbioe.2015.00019/abstract|Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25759811|PubMed]] - [[attachment:CombineMar2015.pdf|PDF]]

 1. ''' IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection.'''<<BR>> Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG, Montpellier B,Kowalski PE, '''Voisin V''', Bashir S, '''Bader GD''', Krangel MS, Guidos CJ. <<BR>> [[http://www.nature.com/ni/journal/vaop/ncurrent/full/ni.3122.html|Nat Immunol. 2015 Mar 2. doi: 10.1038/ni.3122.]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25729925|PubMed]] - [[attachment:NatureImmunolotyMar2015.pdf|PDF]]

 1.  '''Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland CXCR4 Function in Mammary Progenitors.'''<<BR>> Shiah YJ, Tharmapalan P, Casey AE, Joshi PA, McKee TD, Jackson HW, Beristain AG, Chan-Seng-Yue MA, '''Bader GD''', Lydon JP, Waterhouse PD, Boutros PC, Khokha R. A<<BR>> [[http://www.cell.com/stem-cell-reports/fulltext/S2213-6711(15)00032-6|Stem Cell Reports. 2015 Feb 18. pii:S2213-6711(15)00032-6.]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25702641|PubMed]] - [[attachment:stemcellreportsFeb2015.pdf|PDF]]

 1. '''Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes.''' <<BR>>'''Reimand J''', '''Wagih O''', '''Bader GD'''.<<BR>> [[http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004919| PLoS Genet. 2015 Jan 22;11(1)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25611800| PubMed]] - [[attachment:plosgeneticsJan2015_Reimand.pdf|PDF]]

 1. '''Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity.'''<<BR>>Meyer M, '''Reimand J''', Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, '''Bader GD''', Dirks PB.<<BR>>[[http://www.pnas.org/content/early/2015/01/02/1320611111.abstract|Proc Natl Acad Sci U S A. 2015 Jan 5. pii: 201320611 ]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25561528|Pubmed Abstract]] - [[attachment:PNASJan2015.pdf|PDF]]<<BR>>

== 2014 ==
 1.  '''Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.'''<<BR>> '''Isserlin R''', Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, '''Bader GD''', Emili A.<<BR>>  [[http://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C4MB00265B|Mol Biosyst. 2014 Oct]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25361207|Pubmed Abstract]] - [[attachment:mbs2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K.'''<<BR>>Liu JC, '''Voisin V''', Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-Awar R, Egan SE, '''Bader GD''', Tsao M, Mak TW, Zacksenhaus E.<<BR>>[[http://onlinelibrary.wiley.com/doi/10.15252/emmm.201404402/abstract|EMBO Mol Med. 2014 Oct 20. pii: e201404402. doi: 10.15252/emmm.201404402]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25330770|Pubmed Abstract]] - [[attachment:embo2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli'''<<BR>>James Vlasblom, '''Khalid Zuberi''', '''Harold Rodriguez''', Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, '''Luke Chang''', Sadhna Phanse, Ashkan Golshani, Jack F. Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, '''Gary Bader''', Mohan Babu<<BR>>[[http://bioinformatics.oxfordjournals.org/content/early/2014/10/13/bioinformatics.btu671.abstract|Bioinformatics (2014) doi: 10.1093/bioinformatics/btu671]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25316676|Pubmed Abstract]] - [[attachment:genemania_ecoli.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''The Cytoscape app article collection'''<<BR>>Pico AR, '''Bader GD''', Demchak B, Guitart Pla O, Hull T, Longabaugh W, '''Lopes C''',Lotia S, Molenaar P, '''Montojo J''', Morris JH, Ono K, Schwikowski B, Welker D, Ideker T.<<BR>>[[http://f1000research.com/articles/3-138/v1|F1000Res. 2014 Jul 1;3:138.]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25580224|Pubmed Abstract]] - [[attachment:pico_f10002014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''GeneMANIA: Fast gene network construction and function prediction for Cytoscape'''<<BR>>'''Jason Montojo''','''Khalid Zuberi''', '''Harold Rodriguez''', '''Gary D. Bader''', Quaid Morris<<BR>>[[http://f1000research.com/articles/3-153/v1|F1000Res. 2014 Jul 1;3:153]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25254104|Pubmed Abstract]] - [[attachment:Montojo_f10002014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.'''<<BR>>'''Isserlin R''', Merico D, '''Voisin V''', '''Bader GD'''<<BR>>[[http://f1000research.com/articles/3-141/v1|F1000Res. 2014 Jul 1;3:141]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25075306|Pubmed Abstract]] - [[attachment:Isserlin_f10002014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''

 1. '''Intercellular network structure and regulatory motifs in the human hematopoietic system'''<<BR>>Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, '''Bader GD''', Dick JE, Zandstra PW<<BR>> [[http://msb.embopress.org/content/10/7/741.long|Mol Syst Biol. 2014 Jul 15;10(7):741]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25028490|Pubmed Abstract]] - [[attachment:Qiao_MSB2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>>

 1. '''Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma'''<<BR>> Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, '''Shih DJ''', Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, '''Cavalli FM, Zuyderduyn S, Bader GD''', VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A,  Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13379.html|Nature. 2014 Jul 24;511(7510):428-34]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25043047|PubMed Abstract]] - [[attachment:Northcott_Nature2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>>

 1. '''Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma'''<<BR>> Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, '''Voisin V''', Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, '''Bader G''', Hochedlinger K, Korshunov A, Taylor MD, Dirks PB<<BR>>[[http://www.cell.com/cancer-cell/abstract/S1535-6108(14)00220-7|Cancer Cell. 2014 Jun 17. pii: S1535-6108(14)00220-7]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24954133|PubMed Abstract]] - [[attachment:vanner_dirks_2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>>

 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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24904632|PubMed Abstract]] - [[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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24870542|PubMed Abstract]] - [[attachment:pandeymay2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24723613|PubMed Abstract]] - [[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]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24722214|PubMed Abstract]] - [[attachment:gfeller_plosone2014.pdf|PDF]] <<BR>> '''FUNCTIONAL MUTATION ANALYSIS'''<<BR>>

 1. '''!HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery'''<<BR>> '''Leung A, Bader GD, Reimand J''' <<BR>>[[http://bioinformatics.oxfordjournals.org/content/early/2014/03/28/bioinformatics.btu172.long|Bioinformatics. 2014 Apr 8]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24713437|PubMed Abstract]] - [[attachment:leung_Bioinformatics2014.pdf|PDF]] <<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>> 

 1. '''Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition'''<<BR>>Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, '''Shih D''', '''Reimand J''', Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, '''Bader GD''', McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project <<BR>>[[http://www.sciencedirect.com/science/article/pii/S1535610814000737|Cancer Cell. 2014 Mar 17;25(3):393-405]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24651015|PubMed Abstract]] - [[attachment:Kool_CancerCell2014.pdf|PDF]] <<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<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|Proteomics. 2014 May;14(9):975-88]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24596128|PubMed Abstract]] - [[attachment:abersold_prot.pdf|PDF]]<<BR>>'''PROTEOMICS'''<<BR>>

 1. '''Epigenomic alterations define lethal CIMP-positive ependymomas of infancy'''<<BR>> Mack SC, Witt H, Piro RM, Gu L, '''Zuyderduyn S''', Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, '''Shih DJ''', Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, '''Cavalli FM''', Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, '''Bader GD''', Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD <<BR>>[[http://www.nature.com/nature/journal/v506/n7489/full/nature13108.html|Nature. 2014 Feb 27;506(7489):445-50]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/24553142|PubMed Abstract]] - [[attachment:Mack_Nature2014.pdf|PDF]] <<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<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. '''Coordinate microRNA-mediated regulation of protein complexes in prostate cancer'''<<BR>>'''Alshalalfa M''', '''Bader GD''', Bismar TA, Alhajj R<<BR>>[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0084261|PLoS One. 2013 Dec 31;8(12):e84261]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24391925|PubMed Abstract]] - [[attachment:Alshalalfa_PLOSONE.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS''' <<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|Sci Rep. 2013 Oct 2;3:2650]] <<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|Sci Rep. 2013 Oct 2;3:2651]] <<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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24068901|PubMed Abstract]] - [[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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23918249|PubMed Abstract]] - [[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]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/23794635|PubMed Abstract]] - [[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://bioinformatics.oxfordjournals.org/content/29/10/1350.long|Bioinformatics. 2013 May 15;29(10):1350-1]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23595664|PubMed Abstract]] - [[attachment:Pico_Bioinformatics.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23549480|Pubmed Abstract]] - [[attachment:Xin_SH3inter_MSB.pdf|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]]<<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|Mol Syst Biol. 2013;9:637]] <<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 Jan 21;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]]<<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 Feb 15;29(4):513-4]] <<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]] <<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;1:e00078]] <<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]] <<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]]<<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]]<<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 Sep 3;1:e26]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/23552839|PubMed Abstract]] - [[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]] - [[attachment:Northcott_Nature2012.pdf|PDF]]<<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]]<<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 Nov 15;26(22):2927-8]]<<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 GD''', 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 Jul 15;466(7304):368-72]]<<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]]<<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]]<<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'''

== 2007 ==
 1. '''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 Nov;122(3-4):345-53]]<<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]]<<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'''

== 2006 ==
 1. '''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'''

== 2005 ==
 1. '''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'''

== 2004 ==
 1. '''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.ncbi.nlm.nih.gov/pubmed/14755292|PubMed Abstract]] - [[attachment:2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf|PDF]]<<BR>>'''DATA STANDARD'''

== 2003 ==
 1. '''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'''

== 2002 ==
 1. '''!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'''

== 2001 ==
 1. '''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'''

== 2000 ==
 1. '''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'''

= Textbook Chapters =
== 2014 ==
 1. '''Biological network exploration with Cytoscape 3'''<<BR>>Su G, Morris JH, Demchak B, '''Bader GD'''<<BR>>[[http://dx.doi.org/10.1002/0471250953.bi0813s47|Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-8.13.24]] - [[http://www.ncbi.nlm.nih.gov/pubmed/25199793|PubMed Abstract]] - [[attachment:CurrProtocols2014.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''

== 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'''

== 2006 ==
 1. '''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'''

== 2005 ==
 1. '''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'''

== 2004 ==
 1. '''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'''

== 2003 ==
 1. '''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'''

== 2002 ==
 1. '''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 '''Omar Wagih''' - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - [[attachment:omarwagih_thesis_msc.pdf|PDF]], University of Toronto, Department of Computer Science
 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. 2013 '''Ron Ammar''' - Understanding Genome Structure and Response to Perturbation - [[attachment:Ammar_Ron_201311_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics
 1. 2013 '''Anastasia Baryshnikova''' - Mapping Genetic Interaction Networks in Yeast - [[attachment:Baryshnikova_Anastasia_201303_PhD_thesis.pdf|PDF]], University of Toronto, Department of Molecular Genetics
 1. 2012 '''Chris Tan''' - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - [[attachment:Tan_SoonHeng_20126_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