Peer-reviewed Articles and Preprints

2019

Single-cell transcriptomic profiling of the aging mouse brain
Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, Bader GD, Levin JZ, Rubin LL
Nat Neurosci. 2019 Oct;22(10):1696-1708
PubMed Abstract - PDF

SINGLE CELL GENOMICS
Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis
Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M
iScience. 2019 Sep 4;19:1114-1132
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture
Baker AEG, Bahlmann LC, Tam RY, Liu JC, Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, Bader GD, Shoichet MS
Adv Mater. 2019 Jul 19
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
EPIC: software toolkit for elution profile-based inference of protein complexes
Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A
Nat Methods. 2019 July 15
PubMed Abstract - PDF
NETWORK ANALYSIS SOFTWARE
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. . J
Integr Bioinform. 2019 Jul 13
PubMed Abstract - PDF
DATA STANDARDS
Towards reliable named entity recognition in the biomedical domain
Giorgi JM, Bader GD
Bioinformatics. 2019 Jun 20
PubMed Abstract - PDF
TEXT MINING
Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells
Vora P, Seyfrid M, Venugopal C, Qazi MA, Salim S, Isserlin R, Subapanditha M, O'Farrell E, Mahendram S, Singh M, Bakhshinyan D, Chokshi C, McFarlane N, Dvorkin-Gheva A, Brown KR, Murty N, Moffat J, Bader GD, Singh SK
J Neurooncol. 2019 May 21
PubMed Abstract - PDF
PATHWAY AND NETWORK ANALYSIS
The Mitochondrial Transacylase, Tafazzin, Regulates for AML Stemness by Modulating Intracellular Levels of Phospholipids
Seneviratne AK, Xu M, Henao JJA, Fajardo VA, Hao Z, Voisin V, Xu GW, Hurren R, Kim S, MacLean N, Wang X, Gronda M, Jeyaraju D, Jitkova Y, Ketela T, Mullokandov M, Sharon D, Thomas G, Chouinard-Watkins R, Hawley JR, Schafer C, Yau HL, Khuchua Z, Aman A, Al-Awar R, Gross A, Claypool SM, Bazinet R, Lupien M, Chan S, De Carvalho DD, Minden MD, Bader GD, Stark KD, LeBlanc P, Schimmer AD
Cell Stem Cell. 2019 Mar 19
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression
Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B
Clin Epigenetics. 2019 Mar 27;11(1):54
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
netDx: interpretable patient classification using integrated patient similarity networks
Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD
Mol Syst Biol. 2019 Mar 14;15(3):e8497
PubMed Abstract -PDF

PRECISION MEDICINE
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.
Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH
F1000Res. 2019 Mar 15;8. pii: ISCB Comm J-296
PubMed Abstract -PDF
SINGLE CELL GENOMICS
Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic
Sun R, Hui S, Bader GD, Lin X, Kraft P
PLoS Genet. 2019 Mar 15;15(3)
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD
Nat Protoc. 2019 Feb;14(2):482-517
PubMed Abstract -PDF

PATHWAY AND NETWORK ANALYSIS
ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development
Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL
Nucleic Acids Res. 2019 Jan 30
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS

2018

Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells
Khalili S, Ballios BG, Belair-Hickey J, Donaldson L, Liu J, Coles BLK, Grisé KN, Baakdhah T, Bader GD, Wallace VA, Bernier G, Shoichet MS, van der Kooy D
Stem Cell Res. 2018 Nov 13;33:215-227
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety
Shukla R, Prevot TD, French L, Isserlin R, Rocco BR, Banasr M, Bader GD, Sibille E
Biol Psychiatry. 2018 Oct 5
PubMed Abstract -PDF
PATHWAY AND NETWORK ANALYSIS
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
MacParland SA, Liu, JC, Ma X, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID
Nat Commun. 2018 Oct 22;9(1):4383
PubMed Abstract -PDF
SINGLE CELL GENOMICS
scClustViz - Single-cell RNAseq cluster assessment and visualization
Innes BT, Bader GD
F1000Res. 2018 Sep 21;7
PubMed Abstract -PDF
SINGLE CELL GENOMICS
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
SINGLE CELL GENOMICS, PREPRINT
Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics
Dasgupta S, Bader GD, Goyal S
Biophys J. 2018 Aug 7;115(3):429-435
PubMed Abstract -PDF
SINGLE CELL GENOMICS
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 GENOMICS
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

-  ⇤ ← Revision 413 as of 2019-04-25 15:22:28 → 
  Size: 131222
  Editor: RuthIsserlin
  Comment:
+   ← Revision 446 as of 2019-09-27 04:22:55 → ⇥
  Size: 136517
  Editor: GaryBader
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-See who's cited our work at [[http://scholar.google.com/citations?hl=en&user=22M9eisAAAAJ&view_op=list_works&pagesize=100|Google Scholar]]
+See who's cited our work at [[http://scholar.google.com/citations?hl=en&user=22M9eisAAAAJ&view_op=list_works&pagesize=100|Google Scholar]] and our [[https://orcid.org/0000-0003-0185-8861|ORCID]] profile.
 Line 8:
-. '''scClustViz - Single-cell RNAseq cluster assessment and visualization'''<<BR>>'''Innes BT''', '''Bader GD'''<<BR>> [[https://f1000research.com/articles/7-1522/v2|F1000Res. 2018 Sep 21;7]]<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31016009|PubMed Abstract]] -[[attachment:f1000_April2019.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>>
+. '''Single-cell transcriptomic profiling of the aging mouse brain'''<<BR>>Ximerakis M, Lipnick SL, '''Innes BT''', Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, '''Isserlin R''', Buchanan SM, Levine SS, Regev A, '''Bader GD''', Levin JZ, Rubin LL<<BR>>  [[https://www.nature.com/articles/s41593-019-0491-3|Nat Neurosci. 2019 Oct;22(10):1696-1708]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31551601|PubMed Abstract]] - [[attachment:iNatneuro_Oct2019.pdf|PDF]]<<BR>>[[https://www.biorxiv.org/content/10.1101/440032v1|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/10.1101/440032v1|width="50"}}]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis'''<<BR>>Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, '''Goebels F''', Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, '''Bader GD''', Cayabyab FS, Babu M<<BR>>[[https://www.sciencedirect.com/science/article/pii/S2589004219303360|iScience. 2019 Sep 4;19:1114-1132]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31536960|PubMed Abstract]] - [[attachment:iScience_Sept2019.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>

 1. '''Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture'''<<BR>>Baker AEG, Bahlmann LC, Tam RY, '''Liu JC''', Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, '''Bader GD''', Shoichet MS<<BR>>[[https://onlinelibrary.wiley.com/doi/full/10.1002/adma.201901166|Adv Mater. 2019 Jul 19]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31322299|PubMed Abstract]] - [[attachment:AdvMater_July2019.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>

 1. '''EPIC: software toolkit for elution profile-based inference of protein complexes'''<<BR>>'''Hu LZ''', '''Goebels F''', Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, '''Xu C''', Schertzberg M, Fraser AG, '''Bader GD''', Emili A <<BR>>[[https://www.nature.com/articles/s41592-019-0461-4|Nat Methods. 2019 July 15]] <<BR>> [[https://www.ncbi.nlm.nih.gov/pubmed/31308550|PubMed Abstract]] - [[attachment:NatureMethod_July2019.pdf|PDF]]<<BR>>'''NETWORK ANALYSIS SOFTWARE'''<<BR>><<BR>>

 1. '''Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019'''<<BR>>Schreiber F, Sommer B, '''Bader GD''', Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. . J<<BR>> [[https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2019-0035/jib-2019-0035.xml?format=INT|Integr Bioinform. 2019 Jul 13 ]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31301675|PubMed Abstract]] - [[attachment:InteBioinfo_July2019.pdf|PDF]]<<BR>>'''DATA STANDARDS''' <<BR>><<BR>>

 1. '''Towards reliable named entity recognition in the biomedical domain'''<<BR>>'''Giorgi JM''', '''Bader GD'''<<BR>>[[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz504/5520946| Bioinformatics. 2019 Jun 20]] <<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31218364|PubMed Abstract]] - [[attachment:Bioinfo_June2019.pdf|PDF]]<<BR>> '''TEXT MINING'''<<BR>><<BR>>

 1. '''Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells'''<<BR>> Vora P, Seyfrid M, Venugopal C, Qazi MA, Salim S, '''Isserlin R''', Subapanditha M, O'Farrell E, Mahendram S, Singh M, Bakhshinyan D, Chokshi C, !McFarlane N, Dvorkin-Gheva A, Brown KR, Murty N, Moffat J, '''Bader GD''', Singh SK<<BR>> [[https://link.springer.com/article/10.1007/s11060-019-03192-1|J Neurooncol. 2019 May 21]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31115870|PubMed Abstract]] - [[attachment:JNeruor_May2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 14:
+Line 26:
-. '''netDx: interpretable patient classification using integrated patient similarity networks'''<<BR>> '''Pai S''', '''Hui S''', '''Isserlin R''', '''Shah MA''', '''Kaka H''', '''Bader GD'''<<BR>>[[http://msb.embopress.org/content/15/3/e8497.long||Mol Syst Biol. 2019 Mar 14;15(3)]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30872331|PubMed Abstract]] -[[attachment:MSB_Mar2019.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/10.1101/084418v4|{{attachment:bioarxiv.png||width=50}}]]<<BR>>'''PRECISION MEDICINE'''<<BR>><<BR>>

 1. '''Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic'''<<BR>>Sun R, '''Hui S''', '''Bader GD''', Lin X, Kraft P<<BR>>[[https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007530| PLoS Genet. 2019 Mar 15;15(3)]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30875371|PubMed Abstract]] -[[attachment:PlosGenet_Mar2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
+. '''netDx: interpretable patient classification using integrated patient similarity networks'''<<BR>> '''Pai S''', '''Hui S''', '''Isserlin R''', '''Shah MA''', '''Kaka H''', '''Bader GD'''<<BR>>[[http://msb.embopress.org/content/15/3/e8497.long|Mol Syst Biol. 2019 Mar 14;15(3):e8497]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30872331|PubMed Abstract]] -[[attachment:MSB_Mar2019.pdf|PDF]]<<BR>> [[https://www.biorxiv.org/content/10.1101/084418v4|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/10.1101/084418v4|width="50"}}]]<<BR>>'''PRECISION MEDICINE'''<<BR>><<BR>>

 1. '''Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.''' <<BR>> Diaz-Mejia JJ, Meng EC, Pico AR, !MacParland SA, Ketela T, Pugh TJ, '''Bader GD''', Morris JH<<BR>>[[https://f1000research.com/articles/8-296|F1000Res. 2019 Mar 15;8. pii: ISCB Comm J-296]] <<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31508207 |PubMed Abstract]] -[[attachment:f1000_Mar2019.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<BR>><<BR>>

 1. '''Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic'''<<BR>>Sun R, '''Hui S''', '''Bader GD''', Lin X, Kraft P<<BR>>[[https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007530|PLoS Genet. 2019 Mar 15;15(3)]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30875371|PubMed Abstract]] -[[attachment:PlosGenet_Mar2019.pdf|PDF]]<<BR>> '''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>

 1. <<Anchor(EM_2019)>> '''Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and !EnrichmentMap'''<<BR>>'''Reimand J''', '''Isserlin R''', '''Voisin V''', '''Kucera M''', '''Tannus-Lopes C''', '''Rostamianfar A''', Wadi L, Meyer M, '''Wong J''', '''Xu C''', Merico D, '''Bader GD'''<<BR>>[[https://www.nature.com/articles/s41596-018-0103-9|Nat Protoc. 2019 Feb;14(2):482-517]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30664679|PubMed Abstract]] -[[attachment:NatProt_Jan2019.pdf|PDF]]<<BR>>[[https://www.biorxiv.org/content/early/2017/12/12/232835|{{attachment:bioarxiv.png|https://www.biorxiv.org/content/early/2017/12/12/232835|width="50"}}]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 19:
+Line 35:
-. '''Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and !EnrichmentMap'''<<BR>>'''Reimand J''', '''Isserlin R''', '''Voisin V''', '''Kucera M''', '''Tannus-Lopes C''', '''Rostamianfar A''', Wadi L, Meyer M, '''Wong J''', '''Xu C''', Merico D, '''Bader GD'''<<BR>>[[https://www.nature.com/articles/s41596-018-0103-9|Nat Protoc. 2019 Feb;14(2):482-517]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30664679|PubMed Abstract]] -[[attachment:NatProt_Jan2019.pdf|PDF]]<<BR>>[[https://www.biorxiv.org/content/early/2017/12/12/232835|{{attachment:bioarxiv.png||width=50}}]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 25:
+Line 39:
 . '''The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety'''<<BR>>Shukla R, Prevot TD, French L, '''Isserlin R''', Rocco BR, Banasr M, '''Bader GD''', Sibille E <<BR>>[[https://www.biologicalpsychiatryjournal.com/article/S0006-3223(18)31890-0/fulltext|Biol Psychiatry. 2018 Oct 5]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/30446205|PubMed Abstract]] -[[attachment:Psychiatry_Nov2018.pdf|PDF]]<<BR>>'''PATHWAY AND NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 29:
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-. '''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>>'''SINGLE CELL GENOMICS, PREPRINT'''<<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 GENOMICS'''<<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>>
+. '''scClustViz - Single-cell RNAseq cluster assessment and visualization'''<<BR>>'''Innes BT''', '''Bader GD'''<<BR>> [[https://f1000research.com/articles/7-1522/v2|F1000Res. 2018 Sep 21;7]]<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/31016009|PubMed Abstract]] -[[attachment:f1000_April2019.pdf|PDF]]<<BR>> '''SINGLE CELL GENOMICS'''<<BR>><<BR>>


 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|https://arxiv.org/abs/1810.05192|width="50"}}]]-[[attachment:website_pdf.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS, PREPRINT'''<<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 Aug 7;115(3):429-435]]<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/30033145|PubMed Abstract]] -[[attachment:Biophyd_July2018.pdf|PDF]]<<BR>>'''SINGLE CELL GENOMICS'''<<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. <<Anchor(GeneMANIA_2018)>> 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|https://www.biorxiv.org/content/early/2018/02/12/262790|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|https://www.biorxiv.org/content/early/2018/05/25/084418|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://linkinghub.elsevier.com/retrieve/pii/S2211124718303814?showall=true|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>>
-Line 69:
+Line 85:
-. '''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>>
+. '''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|https://www.biorxiv.org/content/early/2017/01/05/046219|width="50"}}]]<<BR>>'''NETWORK ANALYSIS'''<<BR>><<BR>>
-Line 82:
+Line 96:
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-.  '''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>>
+. '''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>>
-Line 103:
+Line 116:
-. '''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>>
+. '''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>>
-Line 158:
+Line 171:
-. '''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>>
+. '''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>>
-Line 163:
+Line 176:
-.  '''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>>
+. '''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>>
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+Line 180:
-. '''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>>
+. <<Anchor(GeneMANIA_2015)>> '''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>>
-Line 171:
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-. '''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>>
+. <<Anchor(GeneMANIA_2014)>> '''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>>
-Line 187:
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-. '''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>>
+. '''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:doi/10.1371/journal.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>>
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+Line 213:
-. '''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>>
+. '''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:doi/10.1371/journal.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>>
-Line 203:
+Line 216:
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+Line 219:
-. '''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>>
+. '''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:doi/10.1371/journal.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>>
-Line 212:
+Line 225:
-. '''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>>
+. <<Anchor(GeneMANIA_2013)>> '''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>>
-Line 216:
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-. '''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>>
+. '''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:doi/10.1371/journal.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>>
-Line 227:
+Line 239:
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+Line 242:
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+Line 312:
-. '''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>>
+. <<Anchor(GeneMANIA_2010)>> '''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>>
-Line 314:
+Line 324:
-. '''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>>
+. <<Anchor(GeneMANIA_original)>> '''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>>
-Line 333:
+Line 343:
-. '''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>>
+. <<Anchor(interpret_networks)>> '''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>>
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+. 2019 '''Brian Law''' - Protein-Protein Interaction Network Alignment and Evolution - [[attachment:Law_Brian_201911_PhD_thesis.pdf|PDF]], University of Toronto, Department of Computer Science<<BR>><<BR>>