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| *Publications page - numbered in journal, book chapter sections | #acl All:read <<TableOfContents(1)>> See who's cited our work at [[http://scholar.google.com/citations?hl=en&user=22M9eisAAAAJ&view_op=list_works&pagesize=100|Google Scholar]] = Peer-reviewed Articles = == 2018 == 1. '''The Human Cell Atlas White Paper'''<<BR>>Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, '''Gary Bader''', Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian !McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee<<BR>>[[https://arxiv.org/abs/1810.05192|{{attachment:bioarxiv.png||width=50}}]]-[[attachment:website_pdf.pdf|PDF]]<<BR>>'''DATA STANDARDS'''<<BR>><<BR>> 1. '''Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics'''<<BR>>Dasgupta S, '''Bader GD''', Goyal S<<BR>>[[https://www.sciencedirect.com/science/article/pii/S0006349518307653|Biophys J. 2018 Jul 11]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/30033145|PubMed Abstract]] -[[attachment:Biophyd_July2018.pdf|PDF]]<<BR>>'''SINGLE CELL'''<<BR>><<BR>> 1. '''The Cytoscape Automation app article collection.'''<<BR>>Demchak B, Otasek D, Pico AR, '''Bader GD''', Ono K, Settle B, Sage E, Morris JH, Longabaugh W, '''Lopes C''', '''Kucera M''', Treister A, Schwikowski B, Molenaar P, Ideker T.<<BR>> [[https://f1000research.com/articles/7-800/v1|F1000Res. 2018 Jun 20;7:800]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29983926|PubMed Abstract]] -[[attachment:f1000_July2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities'''<<BR>>Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P,Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, '''Isserlin R''', Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, '''Bader G''', Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R<<BR>>[[http://jcb.rupress.org/content/early/2018/06/18/jcb.201804042|J Cell Biol. 2018 Jun 19]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29921600|PubMed Abstract]] -[[attachment:JCB_June2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. GeneMANIA update 2018<<BR>>'''Franz M''', '''Rodriguez H''', '''Lopes C''', Zuberi K, Montojo J, '''Bader GD''', Morris Q<<BR>>[[https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky311/5038280|Nucleic Acids Res. 2018 Jun 15]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29912392|PubMed Abstract]] -[[attachment:NAR_June2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. Transfer learning for biomedical named entity recognition with neural networks<<BR>>'''Giorgi JM, Bader GD'''<<BR>>[[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty449/5026661|Bioinformatics. 2018 Jun 1]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29868832|PubMed Abstract]] -[[attachment:Bioinformatics_June2018.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/early/2018/02/12/262790|{{attachment:bioarxiv.png||width=50}}]]<<BR>><<BR>> 1. Patient Similarity Networks for Precision Medicine<<BR>>'''Pai S, Bader GD'''<<BR>> [[https://www.sciencedirect.com/science/article/pii/S0022283618305321|J Mol Biol. 2018 May 31]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29860027|PubMed Abstract]] -[[attachment:JMB_June2018.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/early/2018/05/25/084418|{{attachment:bioarxiv.png||width=50}}]] <<BR>>'''PRECISION MEDICINE'''<<BR>><<BR>> 1. '''Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer'''<<BR>> '''Liu JC''', Granieri L, Shrestha M, Wang DY, Vorobieva I, Rubie EA, Jones R, Ju Y, Pellecchia G, Jiang Z, Palmerini CA, Ben-David Y, Egan SE, Woodgett JR, '''Bader GD''', Datti A, Zacksenhaus E<<BR>>[[http://www.cell.com/cell-reports/fulltext/S2211-1247(18)30381-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124718303814%3Fshowall%3Dtrue|Cell Rep. 2018 Apr 3;23(1):112-126]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29617654|PubMed Abstract]] -[[attachment:Cellrep_April2018.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017'''<<BR>>Schreiber F, '''Bader GD''', Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D<<BR>>[[https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0013/jib-2018-0013.xml| J Integr Bioinform. 2018 Mar 29]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29596055|PubMed Abstract]] -[[attachment:IntegrativeBio_April2018.pdf|PDF]] <<BR>>'''DATA STANDARDS''' <<BR>><<BR>> 1. '''Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A !H5N1 virus infection'''<<BR>>Zhang N, Bao YJ, Tong AH, '''Zuyderduyn S''', '''Bader GD''', Malik Peiris JS, Lok S, Lee SM<<BR>>[[https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-018-0335-0|BMC Med Genomics. 2018 Feb 23;11(1):20]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29475453|PubMed Abstract]] -[[attachment:BMC_medicalgenom_Feb2018.pdf|PDF]] <<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> == 2017 == 1. '''Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling'''<<BR>>Yuzwa SA, Borrett MJ, '''Innes BT''', Voronova A, Ketela T, Kaplan DR, '''Bader GD''', Miller FD<<BR>>[[http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31813-2|Cell Rep. 2017 Dec 26;21(13):3970-3986]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29281841|PubMed Abstract]] -[[attachment:CellRe_December2017.pdf|PDF]]<<BR>>'''SINGLE CELL'''<<BR>><<BR>> 1. '''A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling'''<<BR>>Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, '''Goebels F''', Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, '''Bader GD''', Nakamura K, Parkinson J, Babu M<<BR>>[[http://www.cell.com/cell-systems/fulltext/S2405-4712(17)30447-7|Cell Syst. 2017 Nov 7. pii:S2405-4712(17)30447-7]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29128334|PubMed Abstract]] -[[attachment:Cell_November2017.pdf|PDF]]<<BR>><<BR>> 1. '''Association analysis identifies 65 new breast cancer risk loci'''<<BR>>Michailidou K, Lindström S, Dennis J, Beesley J, '''Hui S''', Kar S, Lemaçon A,Soucy P, Glubb D, '''Rostamianfar A''', Bolla MK, Wang Q, Tyrer J, Dicks E, Lee A, Wang Z, Allen J, Keeman R, Eilber U, French JD, Qing Chen X, Fachal L, !McCue K, !McCart Reed AE, Ghoussaini M, Carroll JS, Jiang X, Finucane H, Adams M, Adank MA, Ahsan H, Aittomäki K, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Arun B, Auer PL, Bacot F, Barrdahl M, Baynes C, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Børresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Brinton L, Broberg P, Brock IW, Broeks A, Brooks-Wilson A, Brucker SY, Brüning T, Burwinkel B, Butterbach K, Cai Q, Cai H, Caldés T, Canzian F, Carracedo A, Carter BD, Castelao JE, Chan TL, David Cheng TY, Seng Chia K, Choi JY, Christiansen H, Clarke CL; NBCS Collaborators, Collée M, Conroy DM, Cordina-Duverger E, Cornelissen S, Cox DG, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Devilee P, Doheny KF, Dörk T, Dos-Santos-Silva I, Dumont M, Durcan L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Ellberg C, Elvira M, Engel C, Eriksson M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fritschi L, Gaborieau V, Gabrielson M, Gago-Dominguez M, Gao YT, Gapstur SM, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Goldberg MS, Goldgar DE, González-Neira A, Grenaker Alnæs GI, Grip M, Gronwald J, Grundy A, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hamel N, Hankinson S, Harrington P, Hart SN, Hartikainen JM, Hartman M, Hein A, Heyworth J, Hicks B, Hillemanns P, Ho DN, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Hou MF, Hsiung CN, Huang G, Humphreys K, Ishiguro J, Ito H, Iwasaki M, Iwata H, Jakubowska A, Janni W, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kasuga Y, Kerin MJ, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Kosma VM, Kristensen VN, Krüger U, Kwong A, Lambrechts D, Le Marchand L, Lee E, Lee MH, Lee JW, Neng Lee C, Lejbkowicz F, Li J, Lilyquist J, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Lophatananon A, Lubinski J, Luccarini C, Lux MP, Ma ESK, !MacInnis RJ, Maishman T, Makalic E, Malone KE, Kostovska IM, Mannermaa A, Manoukian S, Manson JE, Margolin S, Mariapun S, Martinez ME, Matsuo K, Mavroudis D, !McKay J, !McLean C, Meijers-Heijboer H, Meindl A, Menéndez P, Menon U, Meyer J, Miao H, Miller N,Taib NAM, Muir K, Mulligan AM, Mulot C, Neuhausen SL, Nevanlinna H, Neven P, Nielsen SF, Noh DY, Nordestgaard BG, Norman A, Olopade OI, Olson JE, Olsson H, Olswold C, Orr N, Pankratz VS, Park SK, Park-Simon TW, Lloyd R, Perez JIA, Peterlongo P, Peto J, Phillips KA, Pinchev M, Plaseska-Karanfilska D, Prentice R, Presneau N, Prokofyeva D, Pugh E, Pylkäs K, Rack B, Radice P, Rahman N, Rennert G, Rennert HS, Rhenius V, Romero A, Romm J, Ruddy KJ, Rüdiger T, Rudolph A, Ruebner M, Rutgers EJT, Saloustros E, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schürmann P, Scott RJ, Scott C, Seal S, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng G, Sherman ME, Shrubsole MJ, Shu XO, Smeets A, Sohn C, Southey MC, Spinelli JJ, Stegmaier C, Stewart-Brown S, Stone J, Stram DO, Surowy H, Swerdlow A, Tamimi R, Taylor JA, Tengström M, Teo SH, Beth Terry M, Tessier DC, Thanasitthichai S, Thöne K, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Truong T, Tseng CC, Tsugane S, Ulmer HU, Ursin G, Untch M, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van der Kolk L, van der Luijt RB, Vincent D, Vollenweider J, Waisfisz Q, Wang-Gohrke S, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yamaji T, Yang XR, Har Yip C, Yoo KY, Yu JC, Zheng W, Zheng Y, Zhu B, Ziogas A, Ziv E; ABCTB Investigators; ConFab/AOCS Investigators, Lakhani SR, Antoniou AC, Droit A, Andrulis IL, Amos CI, Couch FJ, Pharoah PDP, Chang-Claude J, Hall P, Hunter DJ, Milne RL, García-Closas M, Schmidt MK, Chanock SJ, Dunning AM, Edwards SL, '''Bader GD''', Chenevix-Trench G, Simard J, Kraft P, Easton DF<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature24284.html|Nature. 2017 Oct 23]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29059683|PubMed Abstract]] - [[attachment:Nature_October2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer'''<<BR>>Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindström S, '''Hui S''', Lemaçon A, Soucy P, Dennis J, Jiang X, '''Rostamianfar A''', Finucane H, Bolla MK, !McGuffog L, Wang Q, Aalfs CM; ABCTB Investigators, Adams M, Adlard J, Agata S, Ahmed S, Ahsan H, Aittomäki K, Al-Ejeh F, Allen J, Ambrosone CB, Amos CI, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Arnold N, Aronson KJ, Auber B, Auer PL, Ausems MGEM, Azzollini J, Bacot F, Balmaña J, Barile M, Barjhoux L, Barkardottir RB, Barrdahl M, Barnes D, Barrowdale D, Baynes C, Beckmann MW, Benitez J, Bermisheva M, Bernstein L, Bignon YJ, Blazer KR, Blok MJ, Blomqvist C, Blot W, Bobolis K, Boeckx B, Bogdanova NV, Bojesen A, Bojesen SE, Bonanni B, Børresen-Dale AL, Bozsik A, Bradbury AR, Brand JS, Brauch H, Brenner H, Bressac-de Paillerets B, Brewer C, Brinton L, Broberg P, Brooks-Wilson A, Brunet J, Brüning T, Burwinkel B, Buys SS, Byun J, Cai Q, Caldés T, Caligo MA, Campbell I, Canzian F, Caron O, Carracedo A, Carter BD, Castelao JE, Castera L, Caux-Moncoutier V, Chan SB, Chang-Claude J, Chanock SJ, Chen X, Cheng TD, Chiquette J, Christiansen H, Claes KBM, Clarke CL, Conner T, Conroy DM, Cook J, Cordina-Duverger E, Cornelissen S, Coupier I, Cox A, Cox DG, Cross SS, Cuk K, Cunningham JM, Czene K, Daly MB, Damiola F, Darabi H, Davidson R, De Leeneer K, Devilee P, Dicks E, Diez O, Ding YC, Ditsch N, Doheny KF, Domchek SM, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dubois S, Dugué PA, Dumont M, Dunning AM, Durcan L, Dwek M, Dworniczak B, Eccles D, Eeles R, Ehrencrona H, Eilber U, Ejlertsen B, Ekici AB, Eliassen AH; EMBRACE, Engel C, Eriksson M, Fachal L, Faivre L, Fasching PA, Faust U, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gaddam P, Gammon MD, Ganz PA, Gapstur SM, Garber J, Garcia-Barberan V, García-Sáenz JA, Gaudet MM, Gauthier-Villars M, Gehrig A; GEMO Study Collaborators, Georgoulias V, Gerdes AM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goodfellow P, Greene MH, Alnæs GIG, Grip M, Gronwald J, Grundy A, Gschwantler-Kaulich D, Guénel P, Guo Q, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hallberg E, Hamann U, Hamel N, Hankinson S, Hansen TVO, Harrington P, Hart SN, Hartikainen JM, Healey CS; HEBON, Hein A, Helbig S, Henderson A, Heyworth J, Hicks B, Hillemanns P, Hodgson S, Hogervorst FB, Hollestelle A, Hooning MJ, Hoover B, Hopper JL, Hu C, Huang G, Hulick PJ, Humphreys K, Hunter DJ, Imyanitov EN, Isaacs C, Iwasaki M, Izatt L, Jakubowska A, James P, Janavicius R, Janni W, Jensen UB, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kast K; kConFab/AOCS Investigators, Keeman R, Kerin MJ, Kets CM, Keupers M, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Konstantopoulou I, Kosma VM, Kristensen VN, Kruse TA, Kwong A, Lænkholm AV, Laitman Y, Lalloo F, Lambrechts D, Landsman K, Lasset C, Lazaro C, Le Marchand L, Lecarpentier J, Lee A, Lee E, Lee JW, Lee MH, Lejbkowicz F, Lesueur F, Li J, Lilyquist J, Lincoln A, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Loud JT, Lubinski J, Luccarini C, Lush M, !MacInnis RJ, Maishman T, Makalic E, Kostovska IM, Malone KE, Manoukian S, Manson JE, Margolin S, Martens JWM, Martinez ME, Matsuo K, Mavroudis D, Mazoyer S, !McLean C, Meijers-Heijboer H, Menéndez P, Meyer J, Miao H, Miller A, Miller N, Mitchell G, Montagna M, Muir K, Mulligan AM, Mulot C, Nadesan S, Nathanson KL; NBSC Collaborators, Neuhausen SL, Nevanlinna H, Nevelsteen I, Niederacher D, Nielsen SF, Nordestgaard BG, Norman A, Nussbaum RL, Olah E, Olopade OI, Olson JE, Olswold C, Ong KR, Oosterwijk JC, Orr N, Osorio A, Pankratz VS, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Lloyd R,Pedersen IS, Peissel B, Peixoto A, Perez JIA, Peterlongo P, Peto J, Pfeiler G,Phelan CM, Pinchev M, Plaseska-Karanfilska D, Poppe B, Porteous ME, Prentice R, Presneau N, Prokofieva D, Pugh E, Pujana MA, Pylkäs K, Rack B, Radice P, Rahman N, Rantala J, Rappaport-Fuerhauser C, Rennert G, Rennert HS, Rhenius V, Rhiem K, Richardson A, Rodriguez GC, Romero A, Romm J, Rookus MA, Rudolph A, Ruediger T,Saloustros E, Sanders J, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schoemaker MJ, Schumacher F, Schürmann P, Schwentner L, Scott C, Scott RJ, Seal S, Senter L, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng X, Shimelis H,Shrubsole MJ, Shu XO, Side LE, Singer CF, Sohn C, Southey MC, Spinelli JJ, Spurdle AB, Stegmaier C, Stoppa-Lyonnet D, Sukiennicki G, Surowy H, Sutter C, Swerdlow A, Szabo CI, Tamimi RM, Tan YY, Taylor JA, Tejada MI, Tengström M, Teo SH, Terry MB, Tessier DC, Teulé A, Thöne K, Thull DL, Tibiletti MG, Tihomirova L, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Tranchant M, Truong T, Tucker K, Tung N, Tyrer J, Ulmer HU, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van Rensburg EJ, Varesco L, Varon-Mateeva R, Vega A, Viel A, Vijai J, Vincent D, Vollenweider J, Walker L, Wang Z, Wang-Gohrke S, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wesseling J, Whittemore AS, Wijnen JT, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yang XR, Yannoukakos D, Zaffaroni D, Zheng W, Zhu B, Ziogas A, Ziv E, Zorn KK, Gago-Dominguez M, Mannermaa A, Olsson H, Teixeira MR, Stone J, Offit K, Ottini L, Park SK, Thomassen M, Hall P, Meindl A, Schmutzler RK, Droit A, '''Bader GD''', Pharoah PDP, Couch FJ, Easton DF, Kraft P, Chenevix-Trench G, García-Closas M, Schmidt MK, Antoniou AC, Simard J<<BR>>[[https://www.nature.com/articles/ng.3785|Nat Genet. 2017 Oct 23]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/29058716|PubMed Abstract]] - [[attachment:NatureGenetics_Octoboer2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities'''<<BR>>Teyra J, Huang H, '''Jain S''', Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, '''Bader GD''', Sidhu SS<<BR>>[[http://www.cell.com/structure/abstract/S0969-2126(17)30251-4|Structure. 2017 Aug 28. S0969-2126(17)30251-4]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28890361|PubMed Abstract]] - [[attachment:Structure_September2017.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION'''<<BR>><<BR>> 1. '''microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer'''<<BR>>Wang S, '''Liu JC''', Ju Y, Pellecchia G, '''Voisin V''', Wang DY, Leha L R, Ben-David Y, '''Bader GD''', Zacksenhaus E<<BR>>[[https://insight.jci.org/articles/view/93313|JCI Insight. 2017 Aug 3;2(15)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28768903|PubMed Abstract]] - [[attachment:JCI_August2017.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS ''' <<BR>><<BR>> 1. '''ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells'''<<BR>> Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X,Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, '''Voisin V''', Cusimano MD, Bernstein M, Das S, '''Bader G''', Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB<<BR>>[[http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30230-8|Cell Stem Cell. 2017 Aug 3;21(2):209-224]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28712938|PubMed Abstract]] - [[attachment:Cell_July2017.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS ''' <<BR>><<BR>> 1. '''Tracing the origins of relapse in acute myeloid leukaemia to stem cells'''<<BR>> Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, McLeod JL, Doedens M, '''Bader G''', '''Voisin V''', Xu C, McPherson JD, Hudson TJ, Wang JCY, Minden MD, Dick JE<<BR>>[[https://www.nature.com/nature/journal/v547/n7661/full/nature22993.html|Nature. 2017 Jul 6;547(7661):104-108]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28658204|PubMed Abstract]] - [[attachment:Nature_July2017.pdf|PDF]]<<BR>> ''' ''' <<BR>><<BR>> 1. '''Intertumoral Heterogeneity within Medulloblastoma Subgroups'''<<BR>> Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L,Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, '''Bader GD''', Reimand J, Goldenberg A, Ramaswamy V, Taylor MD<<BR>>[[http://www.cell.com/cancer-cell/abstract/S1535-6108(17)30201-5|Cancer Cell. 2017 Jun 12;31(6):737-754]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28609654|PubMed Abstract]] - [[attachment:CancerCell_June2017.pdf|PDF]]<<BR>>'''CANCER MUTATIONS''' <<BR>><<BR>> 1. '''Spatial heterogeneity in medulloblastoma'''<<BR>>Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, '''Bader GD''', Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD<<BR>> [[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3838.html|Nat Genet. 2017 Apr 10]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/28394352|PubMed Abstract]] - [[attachment:NatureGenetics_April2017.pdf|PDF]]<<BR>>'''CANCER MUTATIONS''' <<BR>><<BR>> 1. '''Integrative cancer pharmacogenomics to infer large-scale drug taxonomy'''<<BR>>El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, '''Isserlin R''', '''Bader G''', Goldenberg A, Haibe-Kains B<<BR>>[[http://cancerres.aacrjournals.org/content/early/2017/03/17/0008-5472.CAN-17-0096.long| Cancer Res. 2017 Mar 17 ]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28314784|PubMed Abstract]] - [[attachment:CancerResearch_March2017.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/early/2017/01/05/046219|{{attachment:bioarxiv.png||width=50}}]]<<BR>>'''NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML'''<<BR>>Liyanage SU, Hurren R, '''Voisin V''', Bridon G, Wang X, Xu C, !MacLean N, Siriwardena TP, Gronda M, Yehudai D, Sriskanthadevan S, Avizonis D, Shamas-Din A, Minden MD, '''Bader GD''', Laposa R, Schimmer AD<<BR>>[[http://www.bloodjournal.org/content/early/2017/03/10/blood-2016-10-741207.long?sso-checked=true|Blood. 2017 Mar 10]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28283480|PubMed Abstract]] - [[attachment:Blood_March2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome and tyrosine-phosphatome in acute myeloid leukemia'''<<BR>>Tong J, '''Helmy M''', '''Cavalli FM''', Jin L, St-Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, '''Bader GD''', Moran MF<<BR>>[[http://onlinelibrary.wiley.com/doi/10.1002/pmic.201600361/full|Proteomics. 2017 Feb 7.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28176486|PubMed Abstract]] - [[attachment:proteomics_Feb2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> == 2016 == 1. '''Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016'''<<BR>>Schreiber F, '''Bader GD''', Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D<<BR>>[[http://journal.imbio.de/article.php?aid=289|J Integr Bioinform. 2016 Dec 18;13(3):289]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28187405|PubMed Abstract]] - [[attachment:integerbioinfo_Feb2017.pdf|PDF]]<<BR>>'''DATA STANDARDS''' <<BR>><<BR>> 1. '''Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors'''<<BR>>Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, '''Gendoo DM''', Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, '''Bader GD''', Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N,Huang A<<BR>>[[http://www.cell.com/cancer-cell/fulltext/S1535-6108(16)30509-8|Cancer Cell. 2016 Dec 12;30(6):891-908]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27960086|PubMed Abstract]] - [[attachment:cancercell_Dec2016.pdf|PDF]]<<BR>><<BR>> 1. '''Global neuroscience and mental health research: a bibliometrics case study'''<<BR>> Buchan AMJ, Jurczyk E, '''Isserlin R''', '''Bader GD'''<<BR>>[[https://link.springer.com/article/10.1007/s11192-016-2094-z|Scientometrics 109 (1), 515-531]]<<BR>>[[attachment:Scientometrics_Oct2016.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>> 1. '''!AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations'''<<BR>>'''Kucera M''', '''Isserlin R''', '''Arkhangorodsky A''', '''Bader GD''' <<BR>>[[https://f1000research.com/articles/5-1717/v1|F1000Res. 2016 Jul 15;5:1717]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27830058|PubMed Abstract]] - [[attachment:F1000Nov2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Ten Simple Rules for Developing Public Biological Databases'''<<BR>>'''Helmy M''', Crits-Christoph A, '''Bader GD'''<<BR>> [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005128|PLoS Comput Biol. 2016 Nov 10;12(11)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27832061|PubMed Abstract]] -[[attachment:CompBioNov2016.pdf|PDF]]<<BR>><<BR>> 1. '''RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation'''<<BR>> Jones RA, Robinson TJ, '''Liu JC''', Shrestha M, '''Voisin V''', Ju Y, Chung PE, Pellecchia G, Fell VL, Bae S, Muthuswamy L, Datti A, Egan SE, Jiang Z, Leone G, '''Bader GD''', Schimmer A, Zacksenhaus E <<BR>> [[https://www.jci.org/articles/view/81568|J Clin Invest. 2016 Aug 29]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27571409|PubMed Abstract]] - [[attachment:ClinInvestAug20162016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors'''<<BR>>Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, '''Isserlin R''', van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, '''Bader GD''', Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G<<BR>>[[http://www.cell.com/cell-stem-cell/abstract/S1934-5909(16)30158-8|Cell Stem Cell. 2016 Jul 12. pii: S1934-5909(16)30158-8]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27424784|PubMed Abstract]] - [[attachment:StemCellJuly2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness'''<<BR>> Walsh CJ, Batt J, Herridge MS, Mathur S, '''Bader GD''', Hu P, Dos Santos CC<<BR>>[[http://www.nature.com/articles/srep29334|Sci Rep. 2016 Jul 14;6:29334]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27411715|PubMed Abstract]] - [[attachment:ScirepJuly2016.pdf|PDF]]<<BR>><<BR>> 1. '''Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells'''<<BR>> Dolma S, Selvadurai HJ, Lan X, Lee L, Kushida M, '''Voisin V''', Whetstone H, So M, Aviv T, Park N, Zhu X, Xu C, Head R, Rowland KJ, Bernstein M, Clarke ID, '''Bader G''', Harrington L, Brumell JH, Tyers M, Dirks PB<<BR>>[[http://www.sciencedirect.com/science/article/pii/S1535610816302070|Cancer Cell. 2016 Jun 13;29(6):859-73]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27300435|PubMed Abstract]] - [[attachment:CancerCellJune2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer'''<<BR>> Narayan S, '''Bader GD''', '''Reimand J'''<<BR>>[[http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0311-2|Genome Med. 2016 May 12;8(1):55]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27175787|PubMed Abstract]] - [[attachment:GenomeMedMay2016.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells'''<<BR>> Rentas S, Holzapfel NT, Belew MS, Pratt GA, '''Voisin V''', Wilhelm BT, '''Bader GD''', Yeo GW, Hope KJ<<BR>>[[http://www.nature.com/nature/journal/v532/n7600/full/nature17665.html|Nature. 2016 Apr 28;532(7600):508-11]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27121842|PubMed Abstract]] - [[attachment:NatureApril2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''HOX gene complement and expression in the planarian Schmidtea mediterranea'''<<BR>> Currie KW, Brown DD, Zhu S, '''Xu C''', '''Voisin V''', '''Bader GD''', Pearson BJ<<BR>>[[http://evodevojournal.biomedcentral.com/articles/10.1186/s13227-016-0044-8| Evodevo. 2016 Mar 30;7:7]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/27034770|PubMed Abstract]] - [[attachment:EvodevoMarch2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Social Network: a Cytoscape app for visualizing co-authorship networks'''<<BR>> '''Kofia V''', '''Isserlin R''', Buchan AM, '''Bader GD'''<<BR>> [[http://f1000research.com/articles/10.12688/f1000research.6804.3/doi|F1000Res. 2015 Aug 5;4:481]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26949516|PubMed Abstract]] - [[attachment:f1000March2016.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>> 1. '''Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast'''<<BR>> '''Jain S''', '''Bader GD'''<<BR>>[[http://bioinformatics.oxfordjournals.org/content/early/2016/02/09/bioinformatics.btw045.abstract|Bioinformatics. 2016 Feb 9]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26861823|PubMed Abstract]] - [[attachment:BioinfoFeb2016.pdf|PDF]]<<BR>>'''PROTEIN INTERACTION PREDICTION'''<<BR>><<BR>> 1. '''miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells'''<<BR>> Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, '''Isserlin R''', '''Voisin V''', '''Bader GD''', Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE<<BR>>[[http://www.cell.com/cancer-cell/abstract/S1535-6108(15)00475-4|Cancer Cell. 2016 Apr 11;29(4):602-606]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26832662|PubMed Abstract]] - [[attachment:CancerCellFeb2016.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance'''<<BR>>Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, '''Reimand J''', Haider M, Virtanen C, Bradner JE, '''Bader GD''', Mills GB, Pe'er D, Moffat J, Neel BG<<BR>> [[http://www.cell.com/cell/abstract/S0092-8674(15)01624-4|Cell. 2016 Jan 14;164(1-2):293-309]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26771497|PubMed Abstract]] - [[attachment:CellJan2016.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Divergent clonal selection dominates medulloblastoma at recurrence'''<<BR>>Morrissy AS, Garzia L, Shih DJ, '''Zuyderduyn S''', Huang X, Skowron P, Remke M, '''Cavalli FM''', Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, '''Matan-Lithwick S''', Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, '''Reimand J''', Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, '''Bader GD''', Jones SJ, Malkin D, Marra MA, Taylor MD<<BR>>[[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16478.html|Nature. 2016 Jan 13. doi: 10.1038/nature16478]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26760213|PubMed Abstract]] - [[attachment:NatureJan2016.pdf|PDF]]<<BR>>'''CANCER MUTATIONS''' == 2015 == 1. '''!NetMatchStar: an enhanced Cytoscape network querying app'''<<BR>>Rinnone F, Micale G, Bonnici V, '''Bader GD''', Shasha D, Ferro A, Pulvirenti A,Giugno R [[http://f1000research.com/articles/4-479/v2|F1000Res.2015 Aug 5;4:479]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26594341|PubMed Abstract]] - [[attachment:f10000Nov2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Specifications of Standards in Systems and Synthetic Biology'''<<BR>>Schreiber F, '''Bader GD''', Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S<<BR>>[[http://journal.imbio.de/article.php?aid=258|J Integr Bioinform. 2015 Sep 4;12(2):258]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26528556|PubMed Abstract]] - [[attachment:IntbioNov2015.pdf|PDF]]<<BR>>'''DATA STANDARDS''' <<BR>><<BR>> 1. '''Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma'''<<BR>> Wei Q, Tang YJ, '''Voisin V''', Sato S, Hirata M, Whetstone H, Han I, Ailles L, '''Bader GD''', Wunder J, Alman BA<<BR>>[[http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path[]=5375&pubmed-linkout=1|Oncotarget. 2015 Oct 26.]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26517673|PubMed Abstract]] - [[attachment:OncotargetOct2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer'''<<BR>>Cuenca-López MD, Serrano-Heras G, Montero JC, Corrales-Sánchez V, Gomez-Juarez M, Gascón-Escribano MJ, Morales JC, '''Voisin V''', Núñez LE, Morís F, '''Bader GD''', Pandiella A, Ocaña A<<BR>>[[http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path[]=4736&pubmed-linkout=1|Oncotarget. 2015 Sep 29;6(29):27923-37]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26314846|PubMed Abstract]] - [[attachment:OncotargetSept2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Systematic analysis of somatic mutations impacting gene expression in 12 tumour types'''<<BR>> Ding J, !McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, '''Reimand J''', Bashashati A, '''Bader GD''', Huntsman D, Aparicio S, Condon A, Shah SP<<BR>>[[http://www.nature.com/ncomms/2015/151005/ncomms9554/full/ncomms9554.html|Nat Commun. 2015 Oct 5;6:8554]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26436532|PubMed Abstract]] - [[attachment:NatCommun2015.pdf|PDF]]<<BR>>'''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Cytoscape.js: a graph theory library for visualisation and analysis'''<<BR>>'''Franz M''', '''Lopes CT''', '''Huck G''', '''Dong Y''', Sumer O, '''Bader GD'''<<BR>> [[http://bioinformatics.oxfordjournals.org/content/early/2015/09/28/bioinformatics.btv557.abstract|Bioinformatics 2015 Sep 28]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26415722|PubMed Abstract]] - [[attachment:bioinfoSept2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''EAG2 potassium channel with evolutionarily conserved function as a brain tumor target'''<<BR>>Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, '''Reimand J''', Yang H, Wang TA,Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, '''Bader GD''', Mueller S, Taylor MD, Jan YN, Jan LY<<BR>> [[http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4088.html|Nat Neurosci 2015 Aug 10]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26258683|PubMed Abstract]] - [[attachment:NatNeuro2015.pdf|PDF]]<<BR>> '''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''!GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks'''<<BR>> '''Law B''', '''Bader GD''' <<BR>> [[http://www.nature.com/articles/srep12074|Sci Rep 2015 Jul 13;5:12074]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26165520|PubMed Abstract]] - [[attachment:SciRepJuly2015.pdf|PDF]]<<BR>>'''PROTEIN INTERACTIONS'''<<BR>><<BR>> 1. '''Inferring interaction type in gene regulatory networks using co-expression data'''<<BR>> '''Khosravi P''', Gazestani VH, Pirhaji L, '''Law B''', Sadeghi M, '''Bader GD''',Goliaei B<<BR>>[[http://www.almob.org/content/10/1/23|Algorithms Mol Biol 2015 Jul 8;10:23]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26157474|PubMed Abstract]] - [[attachment:Algorithm2015.pdf|PDF]]<<BR>>'''GENE REGULATORY INTERACTIONS'''<<BR>><<BR>> 1. '''Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations'''<<BR>>Lerner-Ellis J, Wang M, White S, Lebo MS; Canadian Open Genetics Repository Group<<BR>>[[http://jmg.bmj.com/cgi/pmidlookup?view=long&pmid=25904639|J Med Genet 2015 Jul;52(7):438-45]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25904639|PubMed Abstract]] - [[attachment:JMedGen2015.pdf|PDF]]<<BR>> '''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Pathway and network analysis of cancer genomes'''<<BR>>Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium<<BR>>[[http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3440.html|Nat Methods 2015 Jun 30;12(7):615-21]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26125594|PubMed Abstract]] - [[attachment:NatMethods2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Cardioprotective Signature of Short-Term Caloric Restriction'''<<BR>> Noyan H, El-Mounayri O, '''Isserlin R''', Arab S, Momen A, Cheng HS, Wu J, Afroze T,Li RK, Fish JE, '''Bader GD''', Husain M<<BR>>[[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130658|PLoS One 2015 Jun 22;10(6)]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26098549|PubMed Abstract]] - [[attachment:PlosOneJune2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia'''<<BR>>Cole A, Wang Z, Coyaud E, '''Voisin V''', Gronda M, Jitkova Y, Mattson R, Hurren R, Babovic S, Maclean N, Restall I, Wang X, Jeyaraju DV, Sukhai MA, Prabha S, Bashir S, Ramakrishnan A, Leung E, Qia YH, Zhang N, Combes KR, Ketela T, Lin F, Houry WA, Aman A, Al-Awar R, Zheng W, Wienholds E, Xu CJ, Dick J, Wang JC, Moffat J, Minden MD, Eaves CJ, '''Bader GD''', Hao Z, Kornblau SM, Raught B, Schimmer AD<<BR>>[[http://www.cell.com/cancer-cell/abstract/S1535-6108(15)00180-4|Cancer Cell 2015 Jun 8;27(6):864-76]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/26058080|PubMed Abstract]] - [[attachment:CancerCellJune2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''MIMP: predicting the impact of mutations on kinase-substrate phosphorylation'''<<BR>>'''Wagih O''', '''Reimand J''', '''Bader GD'''<<BR>>[[http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3396.html|Nat Methods 2015 Jun;12(6):531-3]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25938373|PubMed Abstract]] - [[attachment:NatureMethosMay2015.pdf|PDF]]<<BR>> '''CANCER MUTATIONS'''<<BR>><<BR>> 1. '''Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups'''<<BR>>Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, '''Reimand J''', Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, '''Bader G''', Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM<<BR>>[[http://www.sciencedirect.com/science/article/pii/S153561081500135X|Cancer Cell 2015 May 11;27(5):728-43]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25965575|PubMed Abstract]] - [[attachment:CancerCell2015.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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/content/469/1/71.long|Biochem J 2015 Jul 1;469(1):71-82]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25915851|PubMed Abstract]] - [[attachment:BiochemApr2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25901276|PubMed Abstract]] - [[attachment:F1000Apr2015.pdf|PDF]]<<BR>>'''DNA SEQUENCING'''<<BR>><<BR>> 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 May;16(5):569-82]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25882982|PubMed Abstract]] - [[attachment:LancetApr2015.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25759811|PubMed Abstract]] - [[attachment:CombineMar2015.pdf|PDF]]<<BR>>'''DATA STANDARDS'''<<BR>><<BR>> 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 Apr;16(4):397-405]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25729925|PubMed Abstract]] - [[attachment:NatureImmunolotyMar2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 1. '''A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.'''<<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<<BR>>[[http://www.sciencedirect.com/science/article/pii/S2213671115000326|Stem Cell Reports. 2015 Mar 10;4(3):313-322]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/28447939|PubMed Abstract]] - [[attachment:Nstemcellreports_April2017.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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 Abstract]] - [[attachment:plosgeneticsJan2015_Reimand.pdf|PDF]]<<BR>> '''CANCER MUTATIONS'''<<BR>><<BR>> 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 20;112(3):851-6]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25561528|Pubmed Abstract]] - [[attachment:PNASJan2015.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS''' == 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 2015 Jan;11(1):239-51]] <<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25361207|Pubmed Abstract]] - [[attachment:mbs2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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;6(12):1542-60]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/25330770|Pubmed Abstract]] - [[attachment:embo2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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 2015 Feb 1;31(3):306-10]]<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/25316676|Pubmed Abstract]] - [[attachment:genemania_ecoli.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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>><<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>><<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 Jul 14;26(1):33-47]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/24954133|PubMed Abstract]] - [[attachment:vanner_dirks_2014.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<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>><<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>><<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>><<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>><<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>><<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>><<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>><<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''' == 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>><<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>><<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>><<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>><<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>><<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>><<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 Aug;10(8):723-9]] <<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/23900255|PubMed Abstract]] - [[attachment:GonzalezPerez_cancer_mutations_NatMeth.pdf|PDF]]<<BR>> '''CANCER MUTATIONS''' <<BR>><<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>><<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>><<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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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>><<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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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 Jan 12;2011: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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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 = == 2018 == 1. '''Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data'''<<BR>>'''Goebels F., Hu L., Bader G.,''' Emili A.<<BR>>[[https://link.springer.com/protocol/10.1007/978-1-4939-7759-8_25|Methods Mol Bio 2018;1764:391-399]] - [[https://www.ncbi.nlm.nih.gov/pubmed/29605929|PubMed Abstract]] - [[attachment:automatedcopm.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE''' == 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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'''<<BR>><<BR>> 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. 2018 '''Shobhit Jain''' - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - [[attachment:Jain_Shobhit_201806_PhD_thesis.pdf|PDF]], University of Toronto, Department of Computer Science<<BR>><<BR>> 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<<BR>><<BR>> 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<<BR>><<BR>> 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<<BR>><<BR>> 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<<BR>><<BR>> 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<<BR>><<BR>> 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<<BR>><<BR>> |
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Peer-reviewed Articles
2018
The Human Cell Atlas White Paper
Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee
-PDF
DATA STANDARDS
Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics
Dasgupta S, Bader GD, Goyal S
Biophys J. 2018 Jul 11
PubMed Abstract -PDF
SINGLE CELL
The Cytoscape Automation app article collection.
Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T.
F1000Res. 2018 Jun 20;7:800
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities
Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P,Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R
J Cell Biol. 2018 Jun 19
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
GeneMANIA update 2018
Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q
Nucleic Acids Res. 2018 Jun 15
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Transfer learning for biomedical named entity recognition with neural networks
Giorgi JM, Bader GD
Bioinformatics. 2018 Jun 1
PubMed Abstract -PDF
Patient Similarity Networks for Precision Medicine
Pai S, Bader GD
J Mol Biol. 2018 May 31
PubMed Abstract -PDF
PRECISION MEDICINE
Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer
Liu JC, Granieri L, Shrestha M, Wang DY, Vorobieva I, Rubie EA, Jones R, Ju Y, Pellecchia G, Jiang Z, Palmerini CA, Ben-David Y, Egan SE, Woodgett JR, Bader GD, Datti A, Zacksenhaus E
Cell Rep. 2018 Apr 3;23(1):112-126
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D
J Integr Bioinform. 2018 Mar 29
PubMed Abstract -PDF
DATA STANDARDS
Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection
Zhang N, Bao YJ, Tong AH, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SM
BMC Med Genomics. 2018 Feb 23;11(1):20
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
2017
Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling
Yuzwa SA, Borrett MJ, Innes BT, Voronova A, Ketela T, Kaplan DR, Bader GD, Miller FD
Cell Rep. 2017 Dec 26;21(13):3970-3986
PubMed Abstract -PDF
SINGLE CELL
A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling
Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M
Cell Syst. 2017 Nov 7. pii:S2405-4712(17)30447-7
PubMed Abstract -PDF
Association analysis identifies 65 new breast cancer risk loci
Michailidou K, Lindström S, Dennis J, Beesley J, Hui S, Kar S, Lemaçon A,Soucy P, Glubb D, Rostamianfar A, Bolla MK, Wang Q, Tyrer J, Dicks E, Lee A, Wang Z, Allen J, Keeman R, Eilber U, French JD, Qing Chen X, Fachal L, McCue K, McCart Reed AE, Ghoussaini M, Carroll JS, Jiang X, Finucane H, Adams M, Adank MA, Ahsan H, Aittomäki K, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Arun B, Auer PL, Bacot F, Barrdahl M, Baynes C, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Børresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Brinton L, Broberg P, Brock IW, Broeks A, Brooks-Wilson A, Brucker SY, Brüning T, Burwinkel B, Butterbach K, Cai Q, Cai H, Caldés T, Canzian F, Carracedo A, Carter BD, Castelao JE, Chan TL, David Cheng TY, Seng Chia K, Choi JY, Christiansen H, Clarke CL; NBCS Collaborators, Collée M, Conroy DM, Cordina-Duverger E, Cornelissen S, Cox DG, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Devilee P, Doheny KF, Dörk T, Dos-Santos-Silva I, Dumont M, Durcan L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Ellberg C, Elvira M, Engel C, Eriksson M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fritschi L, Gaborieau V, Gabrielson M, Gago-Dominguez M, Gao YT, Gapstur SM, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Goldberg MS, Goldgar DE, González-Neira A, Grenaker Alnæs GI, Grip M, Gronwald J, Grundy A, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hamel N, Hankinson S, Harrington P, Hart SN, Hartikainen JM, Hartman M, Hein A, Heyworth J, Hicks B, Hillemanns P, Ho DN, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Hou MF, Hsiung CN, Huang G, Humphreys K, Ishiguro J, Ito H, Iwasaki M, Iwata H, Jakubowska A, Janni W, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kasuga Y, Kerin MJ, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Kosma VM, Kristensen VN, Krüger U, Kwong A, Lambrechts D, Le Marchand L, Lee E, Lee MH, Lee JW, Neng Lee C, Lejbkowicz F, Li J, Lilyquist J, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Lophatananon A, Lubinski J, Luccarini C, Lux MP, Ma ESK, MacInnis RJ, Maishman T, Makalic E, Malone KE, Kostovska IM, Mannermaa A, Manoukian S, Manson JE, Margolin S, Mariapun S, Martinez ME, Matsuo K, Mavroudis D, McKay J, McLean C, Meijers-Heijboer H, Meindl A, Menéndez P, Menon U, Meyer J, Miao H, Miller N,Taib NAM, Muir K, Mulligan AM, Mulot C, Neuhausen SL, Nevanlinna H, Neven P, Nielsen SF, Noh DY, Nordestgaard BG, Norman A, Olopade OI, Olson JE, Olsson H, Olswold C, Orr N, Pankratz VS, Park SK, Park-Simon TW, Lloyd R, Perez JIA, Peterlongo P, Peto J, Phillips KA, Pinchev M, Plaseska-Karanfilska D, Prentice R, Presneau N, Prokofyeva D, Pugh E, Pylkäs K, Rack B, Radice P, Rahman N, Rennert G, Rennert HS, Rhenius V, Romero A, Romm J, Ruddy KJ, Rüdiger T, Rudolph A, Ruebner M, Rutgers EJT, Saloustros E, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schürmann P, Scott RJ, Scott C, Seal S, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng G, Sherman ME, Shrubsole MJ, Shu XO, Smeets A, Sohn C, Southey MC, Spinelli JJ, Stegmaier C, Stewart-Brown S, Stone J, Stram DO, Surowy H, Swerdlow A, Tamimi R, Taylor JA, Tengström M, Teo SH, Beth Terry M, Tessier DC, Thanasitthichai S, Thöne K, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Truong T, Tseng CC, Tsugane S, Ulmer HU, Ursin G, Untch M, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van der Kolk L, van der Luijt RB, Vincent D, Vollenweider J, Waisfisz Q, Wang-Gohrke S, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yamaji T, Yang XR, Har Yip C, Yoo KY, Yu JC, Zheng W, Zheng Y, Zhu B, Ziogas A, Ziv E; ABCTB Investigators; ConFab/AOCS Investigators, Lakhani SR, Antoniou AC, Droit A, Andrulis IL, Amos CI, Couch FJ, Pharoah PDP, Chang-Claude J, Hall P, Hunter DJ, Milne RL, García-Closas M, Schmidt MK, Chanock SJ, Dunning AM, Edwards SL, Bader GD, Chenevix-Trench G, Simard J, Kraft P, Easton DF
Nature. 2017 Oct 23
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer
Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindström S, Hui S, Lemaçon A, Soucy P, Dennis J, Jiang X, Rostamianfar A, Finucane H, Bolla MK, McGuffog L, Wang Q, Aalfs CM; ABCTB Investigators, Adams M, Adlard J, Agata S, Ahmed S, Ahsan H, Aittomäki K, Al-Ejeh F, Allen J, Ambrosone CB, Amos CI, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Arnold N, Aronson KJ, Auber B, Auer PL, Ausems MGEM, Azzollini J, Bacot F, Balmaña J, Barile M, Barjhoux L, Barkardottir RB, Barrdahl M, Barnes D, Barrowdale D, Baynes C, Beckmann MW, Benitez J, Bermisheva M, Bernstein L, Bignon YJ, Blazer KR, Blok MJ, Blomqvist C, Blot W, Bobolis K, Boeckx B, Bogdanova NV, Bojesen A, Bojesen SE, Bonanni B, Børresen-Dale AL, Bozsik A, Bradbury AR, Brand JS, Brauch H, Brenner H, Bressac-de Paillerets B, Brewer C, Brinton L, Broberg P, Brooks-Wilson A, Brunet J, Brüning T, Burwinkel B, Buys SS, Byun J, Cai Q, Caldés T, Caligo MA, Campbell I, Canzian F, Caron O, Carracedo A, Carter BD, Castelao JE, Castera L, Caux-Moncoutier V, Chan SB, Chang-Claude J, Chanock SJ, Chen X, Cheng TD, Chiquette J, Christiansen H, Claes KBM, Clarke CL, Conner T, Conroy DM, Cook J, Cordina-Duverger E, Cornelissen S, Coupier I, Cox A, Cox DG, Cross SS, Cuk K, Cunningham JM, Czene K, Daly MB, Damiola F, Darabi H, Davidson R, De Leeneer K, Devilee P, Dicks E, Diez O, Ding YC, Ditsch N, Doheny KF, Domchek SM, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dubois S, Dugué PA, Dumont M, Dunning AM, Durcan L, Dwek M, Dworniczak B, Eccles D, Eeles R, Ehrencrona H, Eilber U, Ejlertsen B, Ekici AB, Eliassen AH; EMBRACE, Engel C, Eriksson M, Fachal L, Faivre L, Fasching PA, Faust U, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gaddam P, Gammon MD, Ganz PA, Gapstur SM, Garber J, Garcia-Barberan V, García-Sáenz JA, Gaudet MM, Gauthier-Villars M, Gehrig A; GEMO Study Collaborators, Georgoulias V, Gerdes AM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goodfellow P, Greene MH, Alnæs GIG, Grip M, Gronwald J, Grundy A, Gschwantler-Kaulich D, Guénel P, Guo Q, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hallberg E, Hamann U, Hamel N, Hankinson S, Hansen TVO, Harrington P, Hart SN, Hartikainen JM, Healey CS; HEBON, Hein A, Helbig S, Henderson A, Heyworth J, Hicks B, Hillemanns P, Hodgson S, Hogervorst FB, Hollestelle A, Hooning MJ, Hoover B, Hopper JL, Hu C, Huang G, Hulick PJ, Humphreys K, Hunter DJ, Imyanitov EN, Isaacs C, Iwasaki M, Izatt L, Jakubowska A, James P, Janavicius R, Janni W, Jensen UB, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kast K; kConFab/AOCS Investigators, Keeman R, Kerin MJ, Kets CM, Keupers M, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Konstantopoulou I, Kosma VM, Kristensen VN, Kruse TA, Kwong A, Lænkholm AV, Laitman Y, Lalloo F, Lambrechts D, Landsman K, Lasset C, Lazaro C, Le Marchand L, Lecarpentier J, Lee A, Lee E, Lee JW, Lee MH, Lejbkowicz F, Lesueur F, Li J, Lilyquist J, Lincoln A, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Loud JT, Lubinski J, Luccarini C, Lush M, MacInnis RJ, Maishman T, Makalic E, Kostovska IM, Malone KE, Manoukian S, Manson JE, Margolin S, Martens JWM, Martinez ME, Matsuo K, Mavroudis D, Mazoyer S, McLean C, Meijers-Heijboer H, Menéndez P, Meyer J, Miao H, Miller A, Miller N, Mitchell G, Montagna M, Muir K, Mulligan AM, Mulot C, Nadesan S, Nathanson KL; NBSC Collaborators, Neuhausen SL, Nevanlinna H, Nevelsteen I, Niederacher D, Nielsen SF, Nordestgaard BG, Norman A, Nussbaum RL, Olah E, Olopade OI, Olson JE, Olswold C, Ong KR, Oosterwijk JC, Orr N, Osorio A, Pankratz VS, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Lloyd R,Pedersen IS, Peissel B, Peixoto A, Perez JIA, Peterlongo P, Peto J, Pfeiler G,Phelan CM, Pinchev M, Plaseska-Karanfilska D, Poppe B, Porteous ME, Prentice R, Presneau N, Prokofieva D, Pugh E, Pujana MA, Pylkäs K, Rack B, Radice P, Rahman N, Rantala J, Rappaport-Fuerhauser C, Rennert G, Rennert HS, Rhenius V, Rhiem K, Richardson A, Rodriguez GC, Romero A, Romm J, Rookus MA, Rudolph A, Ruediger T,Saloustros E, Sanders J, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schoemaker MJ, Schumacher F, Schürmann P, Schwentner L, Scott C, Scott RJ, Seal S, Senter L, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng X, Shimelis H,Shrubsole MJ, Shu XO, Side LE, Singer CF, Sohn C, Southey MC, Spinelli JJ, Spurdle AB, Stegmaier C, Stoppa-Lyonnet D, Sukiennicki G, Surowy H, Sutter C, Swerdlow A, Szabo CI, Tamimi RM, Tan YY, Taylor JA, Tejada MI, Tengström M, Teo SH, Terry MB, Tessier DC, Teulé A, Thöne K, Thull DL, Tibiletti MG, Tihomirova L, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Tranchant M, Truong T, Tucker K, Tung N, Tyrer J, Ulmer HU, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van Rensburg EJ, Varesco L, Varon-Mateeva R, Vega A, Viel A, Vijai J, Vincent D, Vollenweider J, Walker L, Wang Z, Wang-Gohrke S, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wesseling J, Whittemore AS, Wijnen JT, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yang XR, Yannoukakos D, Zaffaroni D, Zheng W, Zhu B, Ziogas A, Ziv E, Zorn KK, Gago-Dominguez M, Mannermaa A, Olsson H, Teixeira MR, Stone J, Offit K, Ottini L, Park SK, Thomassen M, Hall P, Meindl A, Schmutzler RK, Droit A, Bader GD, Pharoah PDP, Couch FJ, Easton DF, Kraft P, Chenevix-Trench G, García-Closas M, Schmidt MK, Antoniou AC, Simard J
Nat Genet. 2017 Oct 23
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities
Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS
Structure. 2017 Aug 28. S0969-2126(17)30251-4
PubMed Abstract - PDF
PROTEIN INTERACTION
microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer
Wang S, Liu JC, Ju Y, Pellecchia G, Voisin V, Wang DY, Leha L R, Ben-David Y, Bader GD, Zacksenhaus E
JCI Insight. 2017 Aug 3;2(15)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells
Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X,Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB
Cell Stem Cell. 2017 Aug 3;21(2):209-224
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Tracing the origins of relapse in acute myeloid leukaemia to stem cells
Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, McLeod JL, Doedens M, Bader G, Voisin V, Xu C, McPherson JD, Hudson TJ, Wang JCY, Minden MD, Dick JE
Nature. 2017 Jul 6;547(7661):104-108
PubMed Abstract - PDF
Intertumoral Heterogeneity within Medulloblastoma Subgroups
Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L,Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A, Ramaswamy V, Taylor MD
Cancer Cell. 2017 Jun 12;31(6):737-754
PubMed Abstract - PDF
CANCER MUTATIONS
Spatial heterogeneity in medulloblastoma
Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD
Nat Genet. 2017 Apr 10
PubMed Abstract - PDF
CANCER MUTATIONS
Integrative cancer pharmacogenomics to infer large-scale drug taxonomy
El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains B
Cancer Res. 2017 Mar 17
PubMed Abstract - PDF
NETWORK ANALYSIS
Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML
Liyanage SU, Hurren R, Voisin V, Bridon G, Wang X, Xu C, MacLean N, Siriwardena TP, Gronda M, Yehudai D, Sriskanthadevan S, Avizonis D, Shamas-Din A, Minden MD, Bader GD, Laposa R, Schimmer AD
Blood. 2017 Mar 10
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome and tyrosine-phosphatome in acute myeloid leukemia
Tong J, Helmy M, Cavalli FM, Jin L, St-Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, Bader GD, Moran MF
Proteomics. 2017 Feb 7.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2016
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D
J Integr Bioinform. 2016 Dec 18;13(3):289
PubMed Abstract - PDF
DATA STANDARDS
Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors
Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DM, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N,Huang A
Cancer Cell. 2016 Dec 12;30(6):891-908
PubMed Abstract - PDF
Global neuroscience and mental health research: a bibliometrics case study
Buchan AMJ, Jurczyk E, Isserlin R, Bader GD
Scientometrics 109 (1), 515-531
PDF
NETWORK ANALYSIS SOFTWARE
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
Kucera M, Isserlin R, Arkhangorodsky A, Bader GD
F1000Res. 2016 Jul 15;5:1717
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Ten Simple Rules for Developing Public Biological Databases
Helmy M, Crits-Christoph A, Bader GD
PLoS Comput Biol. 2016 Nov 10;12(11)
PubMed Abstract -PDF
RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation
Jones RA, Robinson TJ, Liu JC, Shrestha M, Voisin V, Ju Y, Chung PE, Pellecchia G, Fell VL, Bae S, Muthuswamy L, Datti A, Egan SE, Jiang Z, Leone G, Bader GD, Schimmer A, Zacksenhaus E
J Clin Invest. 2016 Aug 29
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors
Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G
Cell Stem Cell. 2016 Jul 12. pii: S1934-5909(16)30158-8
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness
Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Dos Santos CC
Sci Rep. 2016 Jul 14;6:29334
PubMed Abstract - PDF
Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells
Dolma S, Selvadurai HJ, Lan X, Lee L, Kushida M, Voisin V, Whetstone H, So M, Aviv T, Park N, Zhu X, Xu C, Head R, Rowland KJ, Bernstein M, Clarke ID, Bader G, Harrington L, Brumell JH, Tyers M, Dirks PB
Cancer Cell. 2016 Jun 13;29(6):859-73
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer
Narayan S, Bader GD, Reimand J
Genome Med. 2016 May 12;8(1):55
PubMed Abstract - PDF
CANCER MUTATIONS
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells
Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ
Nature. 2016 Apr 28;532(7600):508-11
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
HOX gene complement and expression in the planarian Schmidtea mediterranea
Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ
Evodevo. 2016 Mar 30;7:7
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Social Network: a Cytoscape app for visualizing co-authorship networks
Kofia V, Isserlin R, Buchan AM, Bader GD
F1000Res. 2015 Aug 5;4:481
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast
Jain S, Bader GD
Bioinformatics. 2016 Feb 9
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells
Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE
Cancer Cell. 2016 Apr 11;29(4):602-606
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance
Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe'er D, Moffat J, Neel BG
Cell. 2016 Jan 14;164(1-2):293-309
PubMed Abstract - PDF
CANCER MUTATIONS
Divergent clonal selection dominates medulloblastoma at recurrence
Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD
Nature. 2016 Jan 13. doi: 10.1038/nature16478
PubMed Abstract - PDF
CANCER MUTATIONS
2015
NetMatchStar: an enhanced Cytoscape network querying app
Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A,Giugno R F1000Res.2015 Aug 5;4:479
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Specifications of Standards in Systems and Synthetic Biology
Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S
J Integr Bioinform. 2015 Sep 4;12(2):258
PubMed Abstract - PDF
DATA STANDARDS
Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma
Wei Q, Tang YJ, Voisin V, Sato S, Hirata M, Whetstone H, Han I, Ailles L, Bader GD, Wunder J, Alman BA
Oncotarget. 2015 Oct 26.
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer
Cuenca-López MD, Serrano-Heras G, Montero JC, Corrales-Sánchez V, Gomez-Juarez M, Gascón-Escribano MJ, Morales JC, Voisin V, Núñez LE, Morís F, Bader GD, Pandiella A, Ocaña A
Oncotarget. 2015 Sep 29;6(29):27923-37
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types
Ding J, McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, Reimand J, Bashashati A, Bader GD, Huntsman D, Aparicio S, Condon A, Shah SP
Nat Commun. 2015 Oct 5;6:8554
PubMed Abstract - PDF
CANCER MUTATIONS
Cytoscape.js: a graph theory library for visualisation and analysis
Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD
Bioinformatics 2015 Sep 28
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
EAG2 potassium channel with evolutionarily conserved function as a brain tumor target
Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA,Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY
Nat Neurosci 2015 Aug 10
PubMed Abstract - PDF
CANCER MUTATIONS
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks
Law B, Bader GD
Sci Rep 2015 Jul 13;5:12074
PubMed Abstract - PDF
PROTEIN INTERACTIONS
Inferring interaction type in gene regulatory networks using co-expression data
Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Bader GD,Goliaei B
Algorithms Mol Biol 2015 Jul 8;10:23
PubMed Abstract - PDF
GENE REGULATORY INTERACTIONS
Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations
Lerner-Ellis J, Wang M, White S, Lebo MS; Canadian Open Genetics Repository Group
J Med Genet 2015 Jul;52(7):438-45
PubMed Abstract - PDF
CANCER MUTATIONS
Pathway and network analysis of cancer genomes
Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium
Nat Methods 2015 Jun 30;12(7):615-21
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Cardioprotective Signature of Short-Term Caloric Restriction
Noyan H, El-Mounayri O, Isserlin R, Arab S, Momen A, Cheng HS, Wu J, Afroze T,Li RK, Fish JE, Bader GD, Husain M
PLoS One 2015 Jun 22;10(6)
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia
Cole A, Wang Z, Coyaud E, Voisin V, Gronda M, Jitkova Y, Mattson R, Hurren R, Babovic S, Maclean N, Restall I, Wang X, Jeyaraju DV, Sukhai MA, Prabha S, Bashir S, Ramakrishnan A, Leung E, Qia YH, Zhang N, Combes KR, Ketela T, Lin F, Houry WA, Aman A, Al-Awar R, Zheng W, Wienholds E, Xu CJ, Dick J, Wang JC, Moffat J, Minden MD, Eaves CJ, Bader GD, Hao Z, Kornblau SM, Raught B, Schimmer AD
Cancer Cell 2015 Jun 8;27(6):864-76
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation
Wagih O, Reimand J, Bader GD
Nat Methods 2015 Jun;12(6):531-3
PubMed Abstract - PDF
CANCER MUTATIONS
Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups
Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM
Cancer Cell 2015 May 11;27(5):728-43
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action
Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G
Biochem J 2015 Jul 1;469(1):71-82
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
Ammar R, Paton TA, Torti D, Shlien A, Bader GD
F1000Res 2015 Jan 21;4:17
PubMed Abstract - PDF
DNA SEQUENCING
Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis
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
Lancet Oncol 2015 May;16(5):569-82
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative
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
Front Bioeng Biotechnol 2015 Feb 24;3:19
PubMed Abstract - PDF
DATA STANDARDS
IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection
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
Nat Immunol 2015 Apr;16(4):397-405
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.
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
Stem Cell Reports. 2015 Mar 10;4(3):313-322
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes
Reimand J, Wagih O, Bader GD
PLoS Genet 2015 Jan 22;11(1)
PubMed Abstract - PDF
CANCER MUTATIONS
Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity
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
Proc Natl Acad Sci U S A 2015 Jan 20;112(3):851-6
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2014
Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy
Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A
Mol Biosyst 2015 Jan;11(1):239-51
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K
Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-Awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E
EMBO Mol Med 2014 Oct 20;6(12):1542-60
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack F. Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary Bader, Mohan Babu
Bioinformatics 2015 Feb 1;31(3):306-10
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The Cytoscape app article collection
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.
F1000Res 2014 Jul 1;3:138.
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
Jason Montojo,Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris
F1000Res 2014 Jul 1;3:153
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results
Isserlin R, Merico D, Voisin V, Bader GD
F1000Res 2014 Jul 1;3:141
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Intercellular network structure and regulatory motifs in the human hematopoietic system
Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW
Mol Syst Biol 2014 Jul 15;10(7):741
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma
Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, VandenBerg S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM
Nature 2014 Jul 24;511(7510):428-34
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma
Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB
Cancer Cell 2014 Jul 14;26(1):33-47
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction
Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q
Front Genet 2014 May 16;5:123
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A draft map of the human proteome
Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A
Nature 2014 May 29;509(7502):575-81
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Mapping the cellular response to small molecules using chemogenomic fitness signatures
Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G
Science 2014 Apr 11;344(6180):208-11
PubMed Abstract - PDF
CHEMICAL GENOMICS
Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs
Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD
PLoS One 2014 Apr 10;9(4):e94507
PubMed Abstract - PDF
FUNCTIONAL MUTATION ANALYSIS
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
Leung A, Bader GD, Reimand J
Bioinformatics 2014 Apr 8
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition
Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC PedBrain Tumor Project
Cancer Cell 2014 Mar 17;25(3):393-405
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Highlights of B/D-HPP and HPP Resource Pillar Workshops at Yokohama 12th Annual HUPO World Congress of Proteomics
Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS
Proteomics 2014 May;14(9):975-88
PubMed Abstract - PDF
PROTEOMICS
Epigenomic alterations define lethal CIMP-positive ependymomas of infancy
Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD
Nature 2014 Feb 27;506(7489):445-50
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2013
TCGA pan-cancer project, thread 2: Network models
Reimand J, Bader GD, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton
Nature Genetics (2013) doi:10.1038/ng.2787
CANCER MUTATIONS, NETWORKS
Coordinate microRNA-mediated regulation of protein complexes in prostate cancer
Alshalalfa M, Bader GD, Bismar TA, Alhajj R
PLoS One 2013 Dec 31;8(12):e84261
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Comprehensive identification of mutational cancer driver genes across 12 tumor types
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N
Sci Rep 2013 Oct 2;3:2650
PubMed Abstract - PDF
CANCER MUTATIONS
The mutational landscape of phosphorylation signaling in cancer
Reimand J, Wagih O, Bader GD
Sci Rep 2013 Oct 2;3:2651
PubMed Abstract - PDF
CANCER MUTATIONS, NETWORKS
Using biological pathway data with paxtools
Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.
PLoS Comput Biol 2013;9(9):e1003194
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The BioPAX Validator
Rodchenkov I, Demir E, Sander C, Bader GD
Bioinformatics 2013 Oct 15;29(20):2659-60
PubMed Abstract - PDF
DATA STANDARD
Computational approaches to identify functional genetic variants in cancer genomes
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group
Nature Methods 2013 Aug;10(8):723-9
PubMed Abstract - PDF
CANCER MUTATIONS
GeneMANIA prediction server 2013 update
Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q
Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Cytoscape App Store
Lotia S, Montojo J, Dong Y, Bader GD, Pico AR
Bioinformatics 2013 May 15;29(10):1350-1
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
SH3 interactome conserves general function over specific form
Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD
Mol Syst Biol 2013 Apr 2;9:652
Pubmed Abstract - PDF
Interactions in Intact Database
PROTEIN INTERACTION PREDICTION
Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells
Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD.
PLoS One 2013;8(3):e58367
Pubmed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
Reimand J, Bader GD
Mol Syst Biol 2013;9:637
PubMed Abstract - PDF
Research Highlight in Genome Medicine (2013)
CANCER MUTATIONS, SIGNALING NETWORKS
Predicting PDZ domain mediated protein interactions from structure
Hui S, Xing X, Bader GD
BMC Bioinformatics 2013 Jan 21;14:27
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation
Karagiannis GS, Weile J, Bader GD, Minta J.
BMC Cardiovasc Disord 2013 Jan 16;13:4
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
GESTODIFFERENT: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process
Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi and Giancarlo Mauri
Bioinformatics 2013 Feb 15;29(4):513-4
PubMed Abstract - PDF
NETWORK SIMULATION
2012
The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community
Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS
J Proteome Res 2013 Jan 4;12(1):23-7
PubMed Abstract - PDF
PROTEOMICS
Chromatin is an ancient innovation conserved between Archaea and Eukarya
Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C
Elife 2012 Dec 13;1:e00078
PubMed Abstract - PDF
ANALYSIS OF ARCHAEAL CHROMATIN
Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion
Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L
Cell Stem Cell 2012 Nov 7
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A travel guide to Cytoscape plugins
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T
Nat Methods 2012 Nov;9(11):1069-76
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R
BMC Syst Biol 2012 Aug 28;6:112
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice
Xiong X, Chorzalska A, Dubielecka PM, White JR, Vedvyas Y, Hedvat CV, Haimovitz-Friedman A, Koutcher JA, Reimand J, Bader GD, Sawicki JA, Kotula L
Oncogenesis 2012 Sep 3;1:e26
PubMed Abstract - PDF
CANCER GENOMICS
Subgroup-specific structural variation across 1,000 medulloblastoma genomes
Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD
Nature 2012 Aug 2;488(7409):49-56
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals
Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ
Stem Cells 2012 Jun 13
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction
Michaut M, Bader GD
PLoS Comput Biol 8(6): e1002559
PubMed Abstract - PDF
GENETIC INTERACTIONS
Domain-mediated protein interaction prediction: From genome to network
Reimand J, Hui S, Jain S, Law B, Bader GD
FEBS Lett 2012 May 3
PubMed Abstract - PDF
PROTEIN INTERACTIONS
Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer
Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E
Proc Natl Acad Sci U S A 2012 Mar 28
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Phosphorylation sites of higher stoichiometry are more conserved
Tan CS, Bader GD
Nat Methods 2012 Mar 27;9(4):317
PubMed Abstract -PDF
PHOSPHOPROTEOMICS
Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry
Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE
PLoS Genet 2012 Mar;8(3):e1002562
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
2011
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets
Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM
Nucleic Acids Res 2011 Dec 30
PubMed Abstract - PDF
DOMAIN SPECIFICITY SOFTWARE
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A
Stand Genomic Sci 2011 Nov 30;5(2):230-42
PubMed Abstract - PDF
DATA STANDARD
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE
BMC Bioinformatics 2011 Nov 9;12(1):436
PubMed Abstract -PDF
NETWORK ANALYSIS SOFTWARE
Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms
Iain M. Wallace, Malene L. Urbanus, Genna M. Luciani,Andrew R. Burns,Mitchell K.L. Han, Hao Wang, Kriti Arora, Lawrence E. Heisler, Michael Proctor, Robert P. St. Onge, Terry Roemer, Peter J. Roy,Carolyn L. Cummins, Gary D. Bader, Corey Nislow, Guri Giaever
Cell Chemistry & Biology 2011 18, 1273–1283
PubMed Abstract - PDF
Chemistry & Biology 2011 18:10, 1204-1205 Commentary on paper
CHEMICAL GENOMICS
NetSlim: high-confidence curated signaling maps
Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Sameer Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A
Database (Oxford) 2011 Sep 29;2011(0):bar032
PubMed Abstract - PDF
PATHWAY DATABASE
Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM
Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011
PubMed Abstract - PDF
PATHWAY ANALYSIS
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway
Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, Pandey A
Database (Oxford) 2011 Jul 8;2011
PubMed Abstract -PDF
PATHWAY DATABASE
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H
Nature Methods 2011 Jun 29;8(7):528-9
Pubmed Abstract - PDF
PROTEIN INTERACTIONS
Response to Comment on Positive Selection of Tyrosine Loss in Metazoan Evolution,
Tan CS, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD and Linding R
Science 332(6032):917, 20 May 2011
PDF
NETWORK EVOLUTION
The multiple-specificity landscape of modular peptide recognition domains
Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, Ernst A, Dar N, Stagljar I, Serrano L, Sidhu SS, Bader GD, Kim PM
Molecular Systems Biology 7:484, 26 April 2011
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks
Oesper L, Merico D, Isserlin R, Bader GD
Source Code for Biology and Medicine 2011, 6:7, 7 April 2011
PubMed Abstract -PDF
NETWORK ANALYSIS SOFTWARE
Protein Complexes are Central in the Yeast Genetic Landscape
Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD
PLoS Computational Biology 7(2): e1001092 Feb 24 2011
February 2011 Issue Cover
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
Bringing order to protein disorder through comparative genomics and genetic interactions
Bellay J*, Han S*, Michaut M*, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM
Genome Biology 12(2):R14 Feb 15 2011
PubMed Abstract - PDF
PROTEIN DISORDER AND COMPARATIVE GENOMICS
Too Many Roads Not Taken
Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH
Nature. (470) 163-165 Feb 9 2011
PubMed Abstract - PDF
Full Paper on arxiv.org
BIBLIOMETRIC ANALYSIS
The Biomolecular Interaction Network Database in PSI-MI 2.5
Isserlin R, El-Badrawi RA, Bader GD
Database 2011 Jan 12;2011:baq037
PubMed Abstract - PDF
PROTEIN INTERACTION DATABASE
2010
A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence
Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD
Bioinformatics 2010 Dec 2
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
Merico D, Isserlin R, Stueker O, Emili A, Bader GD
PLoS One 2010 Nov 15;5(11):e13984
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology
Jain S, Bader GD
BMC Bioinformatics 2010 Nov 15;11(1):562
PubMed Abstract -PDF
PROTEIN INTERACTION PREDICTION
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL
Nat Methods 2010 Nov 14
PubMed Abstract -PDF
GENETIC INTERACTION NETWORK ANALYSIS
Pathway Commons, a web resource for biological pathway data
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C
Nucleic Acids Res 2010 Nov 10
PubMed Abstract - PDF
PATHWAY DATABASE
Proteome scanning to predict PDZ domain interactions using support vector machines
Hui S, Bader GD
BMC Bioinformatics 2010 Oct 12;11(1):50
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD
Bioinformatics 2010 Nov 15;26(22):2927-8
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Dynamic interaction networks in a hierarchically organized tissue
Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW
Mol Syst Biol 2010 Oct 5;6:417
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling
Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, Gfeller D, Bader GD, Sidhu S, Vandekerckhove J, Gettemans J, Sudol M
Biochem J 2010 Sep 24
PubMed Abstract - PDF
PROTEIN INTERACTION PREDICTION
The BioPAX community standard for pathway data sharing
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Novère NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD
Nat Biotechnol 2010 Sep;28(9):935-42
PubMed Abstract - PDF
DATA STANDARD
Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS
Mol. BioSyst., 2010, Advance Article
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Cytoscape Web: an interactive web-based network browser
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD
Bioinformatics 2010 Jul 23
PubMed Abstract - PDF
NETWORK VISUALIZATION
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q
Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
Functional impact of global rare copy number variation in autism spectrum disorders
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C
Nature 2010 Jul 15;466(7304):368-72
PubMed Abstract - PDF
Nature Blogs - In the news (The Globe and Mail)
PATHWAY AND NETWORK ANALYSIS
A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans
Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ
Nat Chem Biol 2010 May 30
PubMed Abstract - PDF
NCB_News&Views.pdf
CHEMICAL GENOMICS
International network of cancer genome projects
International Cancer Genome Consortium
Nature 2010 Apr 15;464(7291):993-8
PubMed Abstract - PDF
CANCER GENOMICS
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A
Proteomics 2010, March 10(6):1316-27
Pubmed Abstract - PDF
PATHWAY ANALYSIS
The Genetic Landscape of a Cell
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C
Science 2010 Jan 22;327(5964):425-31
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
NetPath: a public resource of curated signal transduction pathways
Kandasamy K, Mohan S, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro DJ, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman A, Keshava Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu S, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A
Genome Biology 2010 Jan 12;11(1):R3
PubMed Abstract - PDF
PATHWAY DATABASE
DRYGIN: a database of quantitative genetic interaction networks in yeast
Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C
Nucleic Acids Res 2010 Jan;38(Database issue):D502-7
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK DATABASE
2009
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins
Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C
PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218
PubMed Abstract - PDF
PROTEIN-PROTEIN INTERACTION ANALYSIS
How to visually interpret biological data using networks
Merico D, Gfeller D, Bader GD
Nature Biotechnology 2009 Oct 27, 921-924
PubMed Abstract - PDF
Data: http://www.baderlab.org/NetworkPrimerNBT
NETWORK PRIMER
Rapid evolution of functional complexity in a domain family
Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS
Science Signaling 2009 Sep 8;2(87):ra50
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Positive Selection of Tyrosine Loss in Metazoan Evolution
Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R
Science. Sep 25;325(5948):1686-8
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases
Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R
Science Signaling 2(81):r39 (2009)
PubMed Abstract - PDF
PROTEIN INTERACTION NETWORK EVOLUTION
2008
A Specificity Map for the PDZ Domain Family
Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS
PLoS Biology Vol. 6, No. 9, e239
PubMed Abstract - PDF
PROTEIN-PROTEIN INTERACTION ANALYSIS
Cytoscape ESP: simple search of complex biological networks
Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ
Bioinformatics 2008 Jun 15;24(12):1465-6
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Computational prediction of protein-protein interactions
Skrabanek L, Saini HK, Bader GD, Enright AJ
Molecular Biotechnology 2008 Jan;38(1):1-17
PubMed Abstract - PDF
REVIEW
2007
Integration of biological networks and gene expression data using Cytoscape
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
Nature Protocols 2007;2(10):2366-82
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H
BMC Biology 2007 Oct 9;5(1):44
PubMed Abstract - PDF
DATA STANDARD
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas Jde L, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H
Nat Biotechnol 2007 Aug;25(8):894-8
PubMed Abstract - PDF
DATA STANDARD
Germ-line DNA copy number variation frequencies in a large North American population
Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S
Hum Genet 2007 Nov;122(3-4):345-53
PubMed Abstract - PDF
GENOMICS
From bytes to bedside: data integration and computational biology for translational cancer research
Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B
PLoS Comput Biol 2007 Feb 23;3(2):e12
PubMed Abstract - PDF
CANCER REVIEW
NetMatch: a Cytoscape Plugin for Searching Biological Networks
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D
Bioinformatics 2007 Apr 1;23(7):910-2
PubMed Abstract - PDF
Download software
NETWORK ANALYSIS SOFTWARE
Computational prediction of cancer-gene function
Hu P, Bader G, Wigle DA, Emili A
Nature Reviews Cancer 2007 Jan;7(1):23-34
PubMed Abstract - PDF
CANCER REVIEW
2006
cPath: open source software for collecting, storing, and querying biological pathways
Cerami EG, Bader GD, Gross BE, Sander C
BMC Bioinformatics 2006, 7:497
PubMed Abstract - PDF
PATHWAY SOFTWARE
Pathguide: a Pathway Resource List
Bader GD, Cary MP, Sander C
Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6
PubMed Abstract - PDF
PATHWAY WEBSITE
2005
Pathway information for systems biology
Cary MP, Bader GD, Sander C
FEBS Lett 2005 Mar 21;579(8):1815-20
PubMed Abstract - PDF
PATHWAY REVIEW
2004
Global Mapping of the Yeast Genetic Interaction Network
Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C
Science 2004 Feb 6;303(5659):808-813
PubMed Abstract - PDF
Science Perspective PDF
GENETIC INTERACTION NETWORK ANALYSIS
The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R
Nature Biotechnology 2004 Feb;22(2):177-83
PubMed Abstract - PDF
DATA STANDARD
2003
Playing tag with the yeast proteome
Andrews BJ, Bader GD, Boone C
Nature Biotechnology Nov;21(11):1297-1299
PubMed Abstract - PDF
REVIEW
Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell
Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C
Trends in Cell Biology Jul, 2003 13(7):344-56
PubMed Abstract - PDF
REVIEW
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine
Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW
BMC Bioinformatics Mar 27, 2003 4(1):11
PubMed Abstract - PDF
TEXT MINING SOFTWARE
Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
Sidhu SS, Bader GD, Boone C
Current Opinion in Chemical Biology 2003 Feb;7(1):97-102
PubMed Abstract - PDF
REVIEW
An automated method for finding molecular complexes in large protein interaction networks
Bader GD, Hogue CWV
BMC Bioinformatics 2003 Jan 13;4(1):2
PubMed Abstract - PDF
ALGORITHM
BIND-The Biomolecular Interaction Network Database
Bader GD, Betel D, Hogue CWV
Nucleic Acids Research Jan 1, 2003 31(1):248-250
PubMed Abstract - PDF
INTERACTION DATABASE
2002
SeqHound: biological sequence and structure database as a platform for bioinformatics research
Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW
BMC Bioinformatics 2002, 3:32 (25 October 2002)
PubMed Abstract - PDF
PROTEIN DATABASE
Analyzing yeast protein–protein interaction data obtained from different sources
Bader GD, Hogue CW
Nature Biotechnology 2002 Oct;20(10):991-997
PubMed Abstract - PDF
META-ANALYSIS
A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules
Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G
Science 2002 Jan 11;295(5553):321-324
PubMed Abstract - PDF
Science Perspective PDF
PROTEIN INTERACTION PREDICTION
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M
Nature 2002 Jan 10;415(6868): 180-183
PubMed Abstract - PDF
Nature News and Views PDF
PROTEIN INTERACTION NETWORK ANALYSIS
2001
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C
Science 2001 Dec 14;294(5550):2364-8
PubMed Abstract - PDF
GENETIC INTERACTION NETWORK ANALYSIS
BIND - The Biomolecular Interaction Network Database
Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW
Nucleic Acids Research Jan 1, 2001 29(1):242-245
PubMed Abstract - PDF
INTERACTION DATABASE
2000
BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways
Bader GD, Hogue CW
Bioinformatics 2000 May;16(5):465-77
PubMed Abstract - PDF
INTERACTION DATABASE
Textbook Chapters
2018
Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data
Goebels F., Hu L., Bader G., Emili A.
Methods Mol Bio 2018;1764:391-399 - PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
2014
Biological network exploration with Cytoscape 3
Su G, Morris JH, Demchak B, Bader GD
Curr Protoc Bioinformatics 2014 Sep 8;47:8.13.1-8.13.24 - PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
2011
Displaying chemical information on a biological network using cytoscape
Wallace IM, Bader GD, Giaever G, Nislow C
Methods Mol Biol 2011;781:363-76 - PubMed Abstract - PDF Supplemental Website
NETWORK ANALYSIS SOFTWARE
Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
Merico D, Isserlin R, Bader GD
Methods Mol Biol 2011;781:257-77 - PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
2008
Exploring Biological Networks with Cytoscape Software
Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and Gary D. Bader
Current Protocols in Bioinformatics - PubMed Abstract - PDF
John Wiley & Sons, Inc.
NETWORK ANALYSIS SOFTWARE
2006
BioPAX - Biological Pathway Data Exchange Format
Gary D. Bader, Michael Cary, Chris Sander
Encyclopedia of Genomics, Proteomics and Bioinformatics
Humana Press, New Jersey
DATA STANDARD
2005
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Rowan Christmas, Iliana Avila-Campillo, Hamid Bolouri, Benno Schwikowski, Mark Anderson, Ryan Kelley, Nerius Landys, Chris Workman, Trey Ideker, Ethan Cerami, Rob Sheridan, Gary D. Bader, and Chris Sander
Am Assoc Cancer Res Educ Book 2005: 12-16
NETWORK ANALYSIS SOFTWARE
Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes
Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone
in Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition
Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA
GENETIC INTERACTION NETWORK ANALYSIS
2004
Interaction Databases, in Genomics and Bioinformatics, 2nd Edition
Gary D. Bader, Christopher W.V. Hogue
in Volume 5B of the Series: Biotechnology, 2nd Edition
Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany
INTERACTION DATABASE
Intermolecular Interactions and Biological Pathways
Gary D. Bader, Anton J. Enright
in Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey
INTERACTION DATABASE
Computational Prediction of Protein-Protein Interactions
Anton J. Enright, Lucy Skrabanek, Gary D. Bader
in The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)
PROTEIN INTERACTION PREDICTION
2003
Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions
Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone
in Handbook of Cell Signaling
Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press)
PDF
PROTEIN INTERACTION PREDICTION
2002
Interaction Databases
Gary D. Bader, Christopher W.V. Hogue
Chapter 18, in Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)
Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P.
Wiley-VCH, Germany
INTERACTION DATABASE
Theses
2018 Shobhit Jain - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Computer Science
2013 Omar Wagih - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - PDF, University of Toronto, Department of Computer Science
2013 Shirley Hui - Computational Prediction of PDZ Mediated Protein-Protein Interactions - PDF, University of Toronto, Department of Molecular Genetics
2013 Ron Ammar - Understanding Genome Structure and Response to Perturbation - PDF, University of Toronto, Department of Molecular Genetics
2013 Anastasia Baryshnikova - Mapping Genetic Interaction Networks in Yeast - PDF, University of Toronto, Department of Molecular Genetics
2012 Chris Tan - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - PDF, University of Toronto, Department of Molecular Genetics
2011 Xiaojian Shao - Prediction of Protein-Nucleic Acids and Protein-Protein Interactions Using Kernel Methods - PDF (in Mandarin), China Agricultural University and the University of Toronto