Gary D Bader

Gary D Bader

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Gary D Bader

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EPIC: software toolkit for elution profile-based inference of protein complexes.

Nat Methods 2019 Jul 15. Epub 2019 Jul 15.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41592-019-0461-4DOI Listing
July 2019

Towards reliable named entity recognition in the biomedical domain.

Bioinformatics 2019 Jun 20. Epub 2019 Jun 20.

Department of Computer Science, University of Toronto, 10 Kings College Road, Toronto, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btz504DOI Listing
June 2019

netDx: interpretable patient classification using integrated patient similarity networks.

Mol Syst Biol 2019 Mar 14;15(3):e8497. Epub 2019 Mar 14.

The Donnelly Centre, University of Toronto, Toronto, ON, Canada

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http://dx.doi.org/10.15252/msb.20188497DOI Listing
March 2019

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic.

PLoS Genet 2019 03 15;15(3):e1007530. Epub 2019 Mar 15.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436759PMC
March 2019

Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression.

Clin Epigenetics 2019 03 27;11(1):54. Epub 2019 Mar 27.

Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 60 Murray Street, L6-304B, Toronto, ON, M5T 3L9, Canada.

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http://dx.doi.org/10.1186/s13148-019-0651-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438015PMC
March 2019

The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety.

Biol Psychiatry 2019 Feb 5;85(3):257-267. Epub 2018 Oct 5.

Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Departments of Pharmacology and Toxicology, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00063223183189
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http://dx.doi.org/10.1016/j.biopsych.2018.09.019DOI Listing
February 2019

Transfer learning for biomedical named entity recognition with neural networks.

Bioinformatics 2018 12;34(23):4087-4094

Department of Computer Science, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1093/bioinformatics/bty449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247938PMC
December 2018

Patient Similarity Networks for Precision Medicine.

J Mol Biol 2018 Sep 1;430(18 Pt A):2924-2938. Epub 2018 Jun 1.

The Donnelly Centre, University of Toronto, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada; Department of Computer Science, University of Toronto, Toronto, Canada; The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.05.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097926PMC
September 2018

scClustViz - Single-cell RNAseq cluster assessment and visualization.

F1000Res 2018 21;7. Epub 2018 Sep 21.

Molecular Genetics, University of Toronto, Toronto, Ontario, M5S3E1, Canada.

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http://dx.doi.org/10.12688/f1000research.16198.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456841PMC
September 2018

Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics.

Biophys J 2018 08 11;115(3):429-435. Epub 2018 Jul 11.

Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084636PMC
August 2018

GeneMANIA update 2018.

Nucleic Acids Res 2018 Jul;46(W1):W60-W64

The Donnelly Centre, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/nar/gky311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030815PMC
July 2018

Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer.

Cell Rep 2018 04;23(1):112-126

Toronto General Research Institute - University Health Network, 67 College Street, Toronto, ON, Canada M5G 2M1; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.039DOI Listing
April 2018

Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection.

BMC Med Genomics 2018 02 23;11(1):20. Epub 2018 Feb 23.

HKU-Pasteur Research Pole and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.1186/s12920-018-0335-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389164PMC
February 2018

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer.

Authors:
Roger L Milne Karoline B Kuchenbaecker Kyriaki Michailidou Jonathan Beesley Siddhartha Kar Sara Lindström Shirley Hui Audrey Lemaçon Penny Soucy Joe Dennis Xia Jiang Asha Rostamianfar Hilary Finucane Manjeet K Bolla Lesley McGuffog Qin Wang Cora M Aalfs Marcia Adams Julian Adlard Simona Agata Shahana Ahmed Habibul Ahsan Kristiina Aittomäki Fares Al-Ejeh Jamie Allen Christine B Ambrosone Christopher I Amos Irene L Andrulis Hoda Anton-Culver Natalia N Antonenkova Volker Arndt Norbert Arnold Kristan J Aronson Bernd Auber Paul L Auer Margreet G E M Ausems Jacopo Azzollini François Bacot Judith Balmaña Monica Barile Laure Barjhoux Rosa B Barkardottir Myrto Barrdahl Daniel Barnes Daniel Barrowdale Caroline Baynes Matthias W Beckmann Javier Benitez Marina Bermisheva Leslie Bernstein Yves-Jean Bignon Kathleen R Blazer Marinus J Blok Carl Blomqvist William Blot Kristie Bobolis Bram Boeckx Natalia V Bogdanova Anders Bojesen Stig E Bojesen Bernardo Bonanni Anne-Lise Børresen-Dale Aniko Bozsik Angela R Bradbury Judith S Brand Hiltrud Brauch Hermann Brenner Brigitte Bressac-de Paillerets Carole Brewer Louise Brinton Per Broberg Angela Brooks-Wilson Joan Brunet Thomas Brüning Barbara Burwinkel Saundra S Buys Jinyoung Byun Qiuyin Cai Trinidad Caldés Maria A Caligo Ian Campbell Federico Canzian Olivier Caron Angel Carracedo Brian D Carter J Esteban Castelao Laurent Castera Virginie Caux-Moncoutier Salina B Chan Jenny Chang-Claude Stephen J Chanock Xiaoqing Chen Ting-Yuan David Cheng Jocelyne Chiquette Hans Christiansen Kathleen B M Claes Christine L Clarke Thomas Conner Don M Conroy Jackie Cook Emilie Cordina-Duverger Sten Cornelissen Isabelle Coupier Angela Cox David G Cox Simon S Cross Katarina Cuk Julie M Cunningham Kamila Czene Mary B Daly Francesca Damiola Hatef Darabi Rosemarie Davidson Kim De Leeneer Peter Devilee Ed Dicks Orland Diez Yuan Chun Ding Nina Ditsch Kimberly F Doheny Susan M Domchek Cecilia M Dorfling Thilo Dörk Isabel Dos-Santos-Silva Stéphane Dubois Pierre-Antoine Dugué Martine Dumont Alison M Dunning Lorraine Durcan Miriam Dwek Bernd Dworniczak Diana Eccles Ros Eeles Hans Ehrencrona Ursula Eilber Bent Ejlertsen Arif B Ekici A Heather Eliassen Christoph Engel Mikael Eriksson Laura Fachal Laurence Faivre Peter A Fasching Ulrike Faust Jonine Figueroa Dieter Flesch-Janys Olivia Fletcher Henrik Flyger William D Foulkes Eitan Friedman Lin Fritschi Debra Frost Marike Gabrielson Pragna Gaddam Marilie D Gammon Patricia A Ganz Susan M Gapstur Judy Garber Vanesa Garcia-Barberan José A García-Sáenz Mia M Gaudet Marion Gauthier-Villars Andrea Gehrig Vassilios Georgoulias Anne-Marie Gerdes Graham G Giles Gord Glendon Andrew K Godwin Mark S Goldberg David E Goldgar Anna González-Neira Paul Goodfellow Mark H Greene Grethe I Grenaker Alnæs Mervi Grip Jacek Gronwald Anne Grundy Daphne Gschwantler-Kaulich Pascal Guénel Qi Guo Lothar Haeberle Eric Hahnen Christopher A Haiman Niclas Håkansson Emily Hallberg Ute Hamann Nathalie Hamel Susan Hankinson Thomas V O Hansen Patricia Harrington Steven N Hart Jaana M Hartikainen Catherine S Healey Alexander Hein Sonja Helbig Alex Henderson Jane Heyworth Belynda Hicks Peter Hillemanns Shirley Hodgson Frans B Hogervorst Antoinette Hollestelle Maartje J Hooning Bob Hoover John L Hopper Chunling Hu Guanmengqian Huang Peter J Hulick Keith Humphreys David J Hunter Evgeny N Imyanitov Claudine Isaacs Motoki Iwasaki Louise Izatt Anna Jakubowska Paul James Ramunas Janavicius Wolfgang Janni Uffe Birk Jensen Esther M John Nichola Johnson Kristine Jones Michael Jones Arja Jukkola-Vuorinen Rudolf Kaaks Maria Kabisch Katarzyna Kaczmarek Daehee Kang Karin Kast Renske Keeman Michael J Kerin Carolien M Kets Machteld Keupers Sofia Khan Elza Khusnutdinova Johanna I Kiiski Sung-Won Kim Julia A Knight Irene Konstantopoulou Veli-Matti Kosma Vessela N Kristensen Torben A Kruse Ava Kwong Anne-Vibeke Lænkholm Yael Laitman Fiona Lalloo Diether Lambrechts Keren Landsman Christine Lasset Conxi Lazaro Loic Le Marchand Julie Lecarpentier Andrew Lee Eunjung Lee Jong Won Lee Min Hyuk Lee Flavio Lejbkowicz Fabienne Lesueur Jingmei Li Jenna Lilyquist Anne Lincoln Annika Lindblom Jolanta Lissowska Wing-Yee Lo Sibylle Loibl Jirong Long Jennifer T Loud Jan Lubinski Craig Luccarini Michael Lush Robert J MacInnis Tom Maishman Enes Makalic Ivana Maleva Kostovska Kathleen E Malone Siranoush Manoukian JoAnn E Manson Sara Margolin John W M Martens Maria Elena Martinez Keitaro Matsuo Dimitrios Mavroudis Sylvie Mazoyer Catriona McLean Hanne Meijers-Heijboer Primitiva Menéndez Jeffery Meyer Hui Miao Austin Miller Nicola Miller Gillian Mitchell Marco Montagna Kenneth Muir Anna Marie Mulligan Claire Mulot Sue Nadesan Katherine L Nathanson Susan L Neuhausen Heli Nevanlinna Ines Nevelsteen Dieter Niederacher Sune F Nielsen Børge G Nordestgaard Aaron Norman Robert L Nussbaum Edith Olah Olufunmilayo I Olopade Janet E Olson Curtis Olswold Kai-Ren Ong Jan C Oosterwijk Nick Orr Ana Osorio V Shane Pankratz Laura Papi Tjoung-Won Park-Simon Ylva Paulsson-Karlsson Rachel Lloyd Inge Søkilde Pedersen Bernard Peissel Ana Peixoto Jose I A Perez Paolo Peterlongo Julian Peto Georg Pfeiler Catherine M Phelan Mila Pinchev Dijana Plaseska-Karanfilska Bruce Poppe Mary E Porteous Ross Prentice Nadege Presneau Darya Prokofieva Elizabeth Pugh Miquel Angel Pujana Katri Pylkäs Brigitte Rack Paolo Radice Nazneen Rahman Johanna Rantala Christine Rappaport-Fuerhauser Gad Rennert Hedy S Rennert Valerie Rhenius Kerstin Rhiem Andrea Richardson Gustavo C Rodriguez Atocha Romero Jane Romm Matti A Rookus Anja Rudolph Thomas Ruediger Emmanouil Saloustros Joyce Sanders Dale P Sandler Suleeporn Sangrajrang Elinor J Sawyer Daniel F Schmidt Minouk J Schoemaker Fredrick Schumacher Peter Schürmann Lukas Schwentner Christopher Scott Rodney J Scott Sheila Seal Leigha Senter Caroline Seynaeve Mitul Shah Priyanka Sharma Chen-Yang Shen Xin Sheng Hermela Shimelis Martha J Shrubsole Xiao-Ou Shu Lucy E Side Christian F Singer Christof Sohn Melissa C Southey John J Spinelli Amanda B Spurdle Christa Stegmaier Dominique Stoppa-Lyonnet Grzegorz Sukiennicki Harald Surowy Christian Sutter Anthony Swerdlow Csilla I Szabo Rulla M Tamimi Yen Y Tan Jack A Taylor Maria-Isabel Tejada Maria Tengström Soo H Teo Mary B Terry Daniel C Tessier Alex Teulé Kathrin Thöne Darcy L Thull Maria Grazia Tibiletti Laima Tihomirova Marc Tischkowitz Amanda E Toland Rob A E M Tollenaar Ian Tomlinson Ling Tong Diana Torres Martine Tranchant Thérèse Truong Kathy Tucker Nadine Tung Jonathan Tyrer Hans-Ulrich Ulmer Celine Vachon Christi J van Asperen David Van Den Berg Ans M W van den Ouweland Elizabeth J van Rensburg Liliana Varesco Raymonda Varon-Mateeva Ana Vega Alessandra Viel Joseph Vijai Daniel Vincent Jason Vollenweider Lisa Walker Zhaoming Wang Shan Wang-Gohrke Barbara Wappenschmidt Clarice R Weinberg Jeffrey N Weitzel Camilla Wendt Jelle Wesseling Alice S Whittemore Juul T Wijnen Walter Willett Robert Winqvist Alicja Wolk Anna H Wu Lucy Xia Xiaohong R Yang Drakoulis Yannoukakos Daniela Zaffaroni Wei Zheng Bin Zhu Argyrios Ziogas Elad Ziv Kristin K Zorn Manuela Gago-Dominguez Arto Mannermaa Håkan Olsson Manuel R Teixeira Jennifer Stone Kenneth Offit Laura Ottini Sue K Park Mads Thomassen Per Hall Alfons Meindl Rita K Schmutzler Arnaud Droit Gary D Bader Paul D P Pharoah Fergus J Couch Douglas F Easton Peter Kraft Georgia Chenevix-Trench Montserrat García-Closas Marjanka K Schmidt Antonis C Antoniou Jacques Simard

Nat Genet 2017 Dec 23;49(12):1767-1778. Epub 2017 Oct 23.

Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Québec, Canada.

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http://dx.doi.org/10.1038/ng.3785DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808456PMC
December 2017

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling.

Cell Rep 2017 12;21(13):3970-3986

Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Institute of Medical Science , University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Molecular Genetics , University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Physiology, University of Toronto, Toronto, ON M5G 1A8, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247173181
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http://dx.doi.org/10.1016/j.celrep.2017.12.017DOI Listing
December 2017

Association analysis identifies 65 new breast cancer risk loci.

Authors:
Kyriaki Michailidou Sara Lindström Joe Dennis Jonathan Beesley Shirley Hui Siddhartha Kar Audrey Lemaçon Penny Soucy Dylan Glubb Asha Rostamianfar Manjeet K Bolla Qin Wang Jonathan Tyrer Ed Dicks Andrew Lee Zhaoming Wang Jamie Allen Renske Keeman Ursula Eilber Juliet D French Xiao Qing Chen Laura Fachal Karen McCue Amy E McCart Reed Maya Ghoussaini Jason S Carroll Xia Jiang Hilary Finucane Marcia Adams Muriel A Adank Habibul Ahsan Kristiina Aittomäki Hoda Anton-Culver Natalia N Antonenkova Volker Arndt Kristan J Aronson Banu Arun Paul L Auer François Bacot Myrto Barrdahl Caroline Baynes Matthias W Beckmann Sabine Behrens Javier Benitez Marina Bermisheva Leslie Bernstein Carl Blomqvist Natalia V Bogdanova Stig E Bojesen Bernardo Bonanni Anne-Lise Børresen-Dale Judith S Brand Hiltrud Brauch Paul Brennan Hermann Brenner Louise Brinton Per Broberg Ian W Brock Annegien Broeks Angela Brooks-Wilson Sara Y Brucker Thomas Brüning Barbara Burwinkel Katja Butterbach Qiuyin Cai Hui Cai Trinidad Caldés Federico Canzian Angel Carracedo Brian D Carter Jose E Castelao Tsun L Chan Ting-Yuan David Cheng Kee Seng Chia Ji-Yeob Choi Hans Christiansen Christine L Clarke Margriet Collée Don M Conroy Emilie Cordina-Duverger Sten Cornelissen David G Cox Angela Cox Simon S Cross Julie M Cunningham Kamila Czene Mary B Daly Peter Devilee Kimberly F Doheny Thilo Dörk Isabel Dos-Santos-Silva Martine Dumont Lorraine Durcan Miriam Dwek Diana M Eccles Arif B Ekici A Heather Eliassen Carolina Ellberg Mingajeva Elvira Christoph Engel Mikael Eriksson Peter A Fasching Jonine Figueroa Dieter Flesch-Janys Olivia Fletcher Henrik Flyger Lin Fritschi Valerie Gaborieau Marike Gabrielson Manuela Gago-Dominguez Yu-Tang Gao Susan M Gapstur José A García-Sáenz Mia M Gaudet Vassilios Georgoulias Graham G Giles Gord Glendon Mark S Goldberg David E Goldgar Anna González-Neira Grethe I Grenaker Alnæs Mervi Grip Jacek Gronwald Anne Grundy Pascal Guénel Lothar Haeberle Eric Hahnen Christopher A Haiman Niclas Håkansson Ute Hamann Nathalie Hamel Susan Hankinson Patricia Harrington Steven N Hart Jaana M Hartikainen Mikael Hartman Alexander Hein Jane Heyworth Belynda Hicks Peter Hillemanns Dona N Ho Antoinette Hollestelle Maartje J Hooning Robert N Hoover John L Hopper Ming-Feng Hou Chia-Ni Hsiung Guanmengqian Huang Keith Humphreys Junko Ishiguro Hidemi Ito Motoki Iwasaki Hiroji Iwata Anna Jakubowska Wolfgang Janni Esther M John Nichola Johnson Kristine Jones Michael Jones Arja Jukkola-Vuorinen Rudolf Kaaks Maria Kabisch Katarzyna Kaczmarek Daehee Kang Yoshio Kasuga Michael J Kerin Sofia Khan Elza Khusnutdinova Johanna I Kiiski Sung-Won Kim Julia A Knight Veli-Matti Kosma Vessela N Kristensen Ute Krüger Ava Kwong Diether Lambrechts Loic Le Marchand Eunjung Lee Min Hyuk Lee Jong Won Lee Chuen Neng Lee Flavio Lejbkowicz Jingmei Li Jenna Lilyquist Annika Lindblom Jolanta Lissowska Wing-Yee Lo Sibylle Loibl Jirong Long Artitaya Lophatananon Jan Lubinski Craig Luccarini Michael P Lux Edmond S K Ma Robert J MacInnis Tom Maishman Enes Makalic Kathleen E Malone Ivana Maleva Kostovska Arto Mannermaa Siranoush Manoukian JoAnn E Manson Sara Margolin Shivaani Mariapun Maria Elena Martinez Keitaro Matsuo Dimitrios Mavroudis James McKay Catriona McLean Hanne Meijers-Heijboer Alfons Meindl Primitiva Menéndez Usha Menon Jeffery Meyer Hui Miao Nicola Miller Nur Aishah Mohd Taib Kenneth Muir Anna Marie Mulligan Claire Mulot Susan L Neuhausen Heli Nevanlinna Patrick Neven Sune F Nielsen Dong-Young Noh Børge G Nordestgaard Aaron Norman Olufunmilayo I Olopade Janet E Olson Håkan Olsson Curtis Olswold Nick Orr V Shane Pankratz Sue K Park Tjoung-Won Park-Simon Rachel Lloyd Jose I A Perez Paolo Peterlongo Julian Peto Kelly-Anne Phillips Mila Pinchev Dijana Plaseska-Karanfilska Ross Prentice Nadege Presneau Darya Prokofyeva Elizabeth Pugh Katri Pylkäs Brigitte Rack Paolo Radice Nazneen Rahman Gadi Rennert Hedy S Rennert Valerie Rhenius Atocha Romero Jane Romm Kathryn J Ruddy Thomas Rüdiger Anja Rudolph Matthias Ruebner Emiel J T Rutgers Emmanouil Saloustros Dale P Sandler Suleeporn Sangrajrang Elinor J Sawyer Daniel F Schmidt Rita K Schmutzler Andreas Schneeweiss Minouk J Schoemaker Fredrick Schumacher Peter Schürmann Rodney J Scott Christopher Scott Sheila Seal Caroline Seynaeve Mitul Shah Priyanka Sharma Chen-Yang Shen Grace Sheng Mark E Sherman Martha J Shrubsole Xiao-Ou Shu Ann Smeets Christof Sohn Melissa C Southey John J Spinelli Christa Stegmaier Sarah Stewart-Brown Jennifer Stone Daniel O Stram Harald Surowy Anthony Swerdlow Rulla Tamimi Jack A Taylor Maria Tengström Soo H Teo Mary Beth Terry Daniel C Tessier Somchai Thanasitthichai Kathrin Thöne Rob A E M Tollenaar Ian Tomlinson Ling Tong Diana Torres Thérèse Truong Chiu-Chen Tseng Shoichiro Tsugane Hans-Ulrich Ulmer Giske Ursin Michael Untch Celine Vachon Christi J van Asperen David Van Den Berg Ans M W van den Ouweland Lizet van der Kolk Rob B van der Luijt Daniel Vincent Jason Vollenweider Quinten Waisfisz Shan Wang-Gohrke Clarice R Weinberg Camilla Wendt Alice S Whittemore Hans Wildiers Walter Willett Robert Winqvist Alicja Wolk Anna H Wu Lucy Xia Taiki Yamaji Xiaohong R Yang Cheng Har Yip Keun-Young Yoo Jyh-Cherng Yu Wei Zheng Ying Zheng Bin Zhu Argyrios Ziogas Elad Ziv Sunil R Lakhani Antonis C Antoniou Arnaud Droit Irene L Andrulis Christopher I Amos Fergus J Couch Paul D P Pharoah Jenny Chang-Claude Per Hall David J Hunter Roger L Milne Montserrat García-Closas Marjanka K Schmidt Stephen J Chanock Alison M Dunning Stacey L Edwards Gary D Bader Georgia Chenevix-Trench Jacques Simard Peter Kraft Douglas F Easton

Nature 2017 11 23;551(7678):92-94. Epub 2017 Oct 23.

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/nature24284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798588PMC
November 2017

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.

Structure 2017 10 7;25(10):1598-1610.e3. Epub 2017 Sep 7.

The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.07.017DOI Listing
October 2017

microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer.

JCI Insight 2017 Aug 3;2(15). Epub 2017 Aug 3.

Division of Advanced Diagnostics, Toronto General Research Institute - University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1172/jci.insight.93313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543917PMC
August 2017

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

Cancer Res 2017 06 17;77(11):3057-3069. Epub 2017 Mar 17.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0096DOI Listing
June 2017

Intertumoral Heterogeneity within Medulloblastoma Subgroups.

Authors:
Florence M G Cavalli Marc Remke Ladislav Rampasek John Peacock David J H Shih Betty Luu Livia Garzia Jonathon Torchia Carolina Nor A Sorana Morrissy Sameer Agnihotri Yuan Yao Thompson Claudia M Kuzan-Fischer Hamza Farooq Keren Isaev Craig Daniels Byung-Kyu Cho Seung-Ki Kim Kyu-Chang Wang Ji Yeoun Lee Wieslawa A Grajkowska Marta Perek-Polnik Alexandre Vasiljevic Cecile Faure-Conter Anne Jouvet Caterina Giannini Amulya A Nageswara Rao Kay Ka Wai Li Ho-Keung Ng Charles G Eberhart Ian F Pollack Ronald L Hamilton G Yancey Gillespie James M Olson Sarah Leary William A Weiss Boleslaw Lach Lola B Chambless Reid C Thompson Michael K Cooper Rajeev Vibhakar Peter Hauser Marie-Lise C van Veelen Johan M Kros Pim J French Young Shin Ra Toshihiro Kumabe Enrique López-Aguilar Karel Zitterbart Jaroslav Sterba Gaetano Finocchiaro Maura Massimino Erwin G Van Meir Satoru Osuka Tomoko Shofuda Almos Klekner Massimo Zollo Jeffrey R Leonard Joshua B Rubin Nada Jabado Steffen Albrecht Jaume Mora Timothy E Van Meter Shin Jung Andrew S Moore Andrew R Hallahan Jennifer A Chan Daniela P C Tirapelli Carlos G Carlotti Maryam Fouladi José Pimentel Claudia C Faria Ali G Saad Luca Massimi Linda M Liau Helen Wheeler Hideo Nakamura Samer K Elbabaa Mario Perezpeña-Diazconti Fernando Chico Ponce de León Shenandoah Robinson Michal Zapotocky Alvaro Lassaletta Annie Huang Cynthia E Hawkins Uri Tabori Eric Bouffet Ute Bartels Peter B Dirks James T Rutka Gary D Bader Jüri Reimand Anna Goldenberg Vijay Ramaswamy Michael D Taylor

Cancer Cell 2017 06;31(6):737-754.e6

The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6163053PMC
June 2017

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors.

Authors:
Jonathon Torchia Brian Golbourn Shengrui Feng King Ching Ho Patrick Sin-Chan Alexandre Vasiljevic Joseph D Norman Paul Guilhamon Livia Garzia Natalia R Agamez Mei Lu Tiffany S Chan Daniel Picard Pasqualino de Antonellis Dong-Anh Khuong-Quang Aline C Planello Constanze Zeller Dalia Barsyte-Lovejoy Lucie Lafay-Cousin Louis Letourneau Mathieu Bourgey Man Yu Deena M A Gendoo Misko Dzamba Mark Barszczyk Tiago Medina Alexandra N Riemenschneider A Sorana Morrissy Young-Shin Ra Vijay Ramaswamy Marc Remke Christopher P Dunham Stephen Yip Ho-Keung Ng Jian-Qiang Lu Vivek Mehta Steffen Albrecht Jose Pimentel Jennifer A Chan Gino R Somers Claudia C Faria Lucia Roque Maryam Fouladi Lindsey M Hoffman Andrew S Moore Yin Wang Seung Ah Choi Jordan R Hansford Daniel Catchpoole Diane K Birks Nicholas K Foreman Doug Strother Almos Klekner Laszló Bognár Miklós Garami Péter Hauser Tibor Hortobágyi Beverly Wilson Juliette Hukin Anne-Sophie Carret Timothy E Van Meter Eugene I Hwang Amar Gajjar Shih-Hwa Chiou Hideo Nakamura Helen Toledano Iris Fried Daniel Fults Takafumi Wataya Chris Fryer David D Eisenstat Katrin Scheinemann Adam J Fleming Donna L Johnston Jean Michaud Shayna Zelcer Robert Hammond Samina Afzal David A Ramsay Nongnuch Sirachainan Suradej Hongeng Noppadol Larbcharoensub Richard G Grundy Rishi R Lulla Jason R Fangusaro Harriet Druker Ute Bartels Ronald Grant David Malkin C Jane McGlade Theodore Nicolaides Tarik Tihan Joanna Phillips Jacek Majewski Alexandre Montpetit Guillaume Bourque Gary D Bader Alyssa T Reddy G Yancey Gillespie Monika Warmuth-Metz Stefan Rutkowski Uri Tabori Mathieu Lupien Michael Brudno Ulrich Schüller Torsten Pietsch Alexander R Judkins Cynthia E Hawkins Eric Bouffet Seung-Ki Kim Peter B Dirks Michael D Taylor Anat Erdreich-Epstein Cheryl H Arrowsmith Daniel D De Carvalho James T Rutka Nada Jabado Annie Huang

Cancer Cell 2016 Dec;30(6):891-908

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500911PMC
December 2016

Ten Simple Rules for Developing Public Biological Databases.

PLoS Comput Biol 2016 Nov 10;12(11):e1005128. Epub 2016 Nov 10.

The Donnelly Centre, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1005128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5104318PMC
November 2016

AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations.

F1000Res 2016 15;5:1717. Epub 2016 Jul 15.

The Donnelly Centre, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.12688/f1000research.9090.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082607PMC
July 2016

Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast.

Bioinformatics 2016 06 9;32(12):1865-72. Epub 2016 Feb 9.

Department of Computer Science and The Donnelly Centre, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908317PMC
June 2016

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.

Genome Med 2016 05 12;8(1):55. Epub 2016 May 12.

The Donnelly Centre, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1186/s13073-016-0311-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864925PMC
May 2016

HOX gene complement and expression in the planarian Schmidtea mediterranea.

Evodevo 2016 30;7. Epub 2016 Mar 30.

Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada ; Ontario Institute for Cancer Research, Toronto, ON M5G10A4 Canada.

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http://dx.doi.org/10.1186/s13227-016-0044-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815179PMC
April 2016

Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells.

Nature 2016 Apr;532(7600):508-511

Department of Biochemistry and Biomedical Sciences, Stem Cell and Cancer Research Institute, McMaster University, Hamilton, ON, Canada.

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http://dx.doi.org/10.1038/nature17665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880456PMC
April 2016

Social Network: a Cytoscape app for visualizing co-authorship networks.

F1000Res 2015 5;4:481. Epub 2015 Aug 5.

The Donnelly Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada.

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http://dx.doi.org/10.12688/f1000research.6804.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760270PMC
March 2016

Cardioprotective Signature of Short-Term Caloric Restriction.

PLoS One 2015 22;10(6):e0130658. Epub 2015 Jun 22.

Division of Experimental Therapeutics, Toronto General Research Institute, Toronto, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada; Heart and Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, University of Toronto, Toronto, Ontario, Canada; Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Ted Rogers Centre for Heart Research, University Health Network, Toronto, Ontario, Canada.

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https://www.researchgate.net/profile/Omar_El-Mounayri/public
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476723PMC
March 2016

Cytoscape.js: a graph theory library for visualisation and analysis.

Bioinformatics 2016 Jan 28;32(2):309-11. Epub 2015 Sep 28.

The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4708103PMC
January 2016

Divergent clonal selection dominates medulloblastoma at recurrence.

Authors:
A Sorana Morrissy Livia Garzia David J H Shih Scott Zuyderduyn Xi Huang Patryk Skowron Marc Remke Florence M G Cavalli Vijay Ramaswamy Patricia E Lindsay Salomeh Jelveh Laura K Donovan Xin Wang Betty Luu Kory Zayne Yisu Li Chelsea Mayoh Nina Thiessen Eloi Mercier Karen L Mungall Yusanne Ma Kane Tse Thomas Zeng Karey Shumansky Andrew J L Roth Sohrab Shah Hamza Farooq Noriyuki Kijima Borja L Holgado John J Y Lee Stuart Matan-Lithwick Jessica Liu Stephen C Mack Alex Manno K A Michealraj Carolina Nor John Peacock Lei Qin Juri Reimand Adi Rolider Yuan Y Thompson Xiaochong Wu Trevor Pugh Adrian Ally Mikhail Bilenky Yaron S N Butterfield Rebecca Carlsen Young Cheng Eric Chuah Richard D Corbett Noreen Dhalla An He Darlene Lee Haiyan I Li William Long Michael Mayo Patrick Plettner Jenny Q Qian Jacqueline E Schein Angela Tam Tina Wong Inanc Birol Yongjun Zhao Claudia C Faria José Pimentel Sofia Nunes Tarek Shalaby Michael Grotzer Ian F Pollack Ronald L Hamilton Xiao-Nan Li Anne E Bendel Daniel W Fults Andrew W Walter Toshihiro Kumabe Teiji Tominaga V Peter Collins Yoon-Jae Cho Caitlin Hoffman David Lyden Jeffrey H Wisoff James H Garvin Duncan S Stearns Luca Massimi Ulrich Schüller Jaroslav Sterba Karel Zitterbart Stephanie Puget Olivier Ayrault Sandra E Dunn Daniela P C Tirapelli Carlos G Carlotti Helen Wheeler Andrew R Hallahan Wendy Ingram Tobey J MacDonald Jeffrey J Olson Erwin G Van Meir Ji-Yeoun Lee Kyu-Chang Wang Seung-Ki Kim Byung-Kyu Cho Torsten Pietsch Gudrun Fleischhack Stephan Tippelt Young Shin Ra Simon Bailey Janet C Lindsey Steven C Clifford Charles G Eberhart Michael K Cooper Roger J Packer Maura Massimino Maria Luisa Garre Ute Bartels Uri Tabori Cynthia E Hawkins Peter Dirks Eric Bouffet James T Rutka Robert J Wechsler-Reya William A Weiss Lara S Collier Adam J Dupuy Andrey Korshunov David T W Jones Marcel Kool Paul A Northcott Stefan M Pfister David A Largaespada Andrew J Mungall Richard A Moore Nada Jabado Gary D Bader Steven J M Jones David Malkin Marco A Marra Michael D Taylor

Nature 2016 Jan 13;529(7586):351-7. Epub 2016 Jan 13.

Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

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http://dx.doi.org/10.1038/nature16478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936195PMC
January 2016

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance.

Cell 2016 Jan;164(1-2):293-309

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Laura and Isaac Perlmutter Cancer Centre, NYU-Langone Medical Center, NY 10016, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.11.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724865PMC
January 2016

NetMatchStar: an enhanced Cytoscape network querying app.

F1000Res 2015 5;4:479. Epub 2015 Aug 5.

Department of Clinical and Experimental Medicine, University of Catania, Catania, 95125, Italy.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642848PMC
http://dx.doi.org/10.12688/f1000research.6656.2DOI Listing
December 2015

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

Nat Commun 2015 Oct 5;6:8554. Epub 2015 Oct 5.

Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3.

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http://dx.doi.org/10.1038/ncomms9554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600750PMC
October 2015

Erratum to: Inferring interaction type in gene regulatory networks using co-expression data.

Algorithms Mol Biol 2015 11;10:25. Epub 2015 Aug 11.

Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

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http://dx.doi.org/10.1186/s13015-015-0055-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532253PMC
August 2015

GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks.

Sci Rep 2015 Jul 13;5:12074. Epub 2015 Jul 13.

1] Department of Computer Science, University of Toronto, Toronto, ON, Canada [2] The Donnelly Centre, University of Toronto, Toronto, ON, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1038/srep12074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499810PMC
July 2015

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nat Methods 2015 Jun 4;12(6):531-3. Epub 2015 May 4.

The Donnelly Centre, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1038/nmeth.3396DOI Listing
June 2015

Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis.

Lancet Oncol 2015 May 14;16(5):569-82. Epub 2015 Apr 14.

Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1016/S1470-2045(15)70114-2DOI Listing
May 2015

IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection.

Nat Immunol 2015 Apr 2;16(4):397-405. Epub 2015 Mar 2.

1] Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, Canada. [2] Department of Immunology, University of Toronto, Toronto, Canada.

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http://www.nature.com/articles/ni.3122
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http://dx.doi.org/10.1038/ni.3122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368453PMC
April 2015

A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland.

Stem Cell Reports 2015 Mar 19;4(3):313-322. Epub 2015 Feb 19.

Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2015.01.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376056PMC
March 2015

Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.

Mol Biosyst 2015 Jan 31;11(1):239-51. Epub 2014 Oct 31.

The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1.

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http://dx.doi.org/10.1039/c4mb00265bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856157PMC
January 2015

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity.

Proc Natl Acad Sci U S A 2015 Jan 5;112(3):851-6. Epub 2015 Jan 5.

Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5S 1A8

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http://dx.doi.org/10.1073/pnas.1320611111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311802PMC
January 2015

Long read nanopore sequencing for detection of and variants and haplotypes.

F1000Res 2015 21;4:17. Epub 2015 Jan 21.

The Donnelly Centre, University of Toronto, Toronto, ON, M5S3E1, Canada.

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http://dx.doi.org/10.12688/f1000research.6037.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392832PMC
January 2015

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.

PLoS Genet 2015 Jan 22;11(1):e1004919. Epub 2015 Jan 22.

The Donnelly Centre, University of Toronto, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1004919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303425PMC
January 2015

Prediction and experimental characterization of nsSNPs altering human PDZ-binding motifs.

PLoS One 2014 10;9(4):e94507. Epub 2014 Apr 10.

The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094507PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983204PMC
December 2014

Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K.

EMBO Mol Med 2014 Dec;6(12):1542-60

Division of Advanced Diagnostics, Toronto General Research Institute - University Health Network, Toronto, ON, Canada Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada Department of Medical Biophysics, University Health Network, Toronto, ON, Canada

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http://dx.doi.org/10.15252/emmm.201404402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287974PMC
December 2014

Coordinate microRNA-mediated regulation of protein complexes in prostate cancer.

PLoS One 2013 31;8(12):e84261. Epub 2013 Dec 31.

Department of Computer Science, University of Calgary, Calgary, Alberta, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084261PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877262PMC
September 2014

Biological network exploration with Cytoscape 3.

Curr Protoc Bioinformatics 2014 Sep 8;47:8.13.1-24. Epub 2014 Sep 8.

Molecular Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan.

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http://dx.doi.org/10.1002/0471250953.bi0813s47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174321PMC
September 2014

GeneMANIA: Fast gene network construction and function prediction for Cytoscape.

F1000Res 2014 1;3:153. Epub 2014 Jul 1.

Departments of Molecular Genetics and Computer Science, The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.

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http://dx.doi.org/10.12688/f1000research.4572.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168749PMC
September 2014

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.

Bioinformatics 2014 Aug 8;30(15):2230-2. Epub 2014 Apr 8.

The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1 Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btu172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103591PMC
August 2014

Intercellular network structure and regulatory motifs in the human hematopoietic system.

Mol Syst Biol 2014 Jul 15;10:741. Epub 2014 Jul 15.

Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada The Donnelly Centre, University of Toronto, Toronto, ON, Canada Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada McEwen Centre for Regenerative Medicine, University of Health Network, Toronto, ON, Canada Heart & Stroke/Richard Lewar Centre of Excellence, Toronto, ON, Canada

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299490PMC
http://dx.doi.org/10.15252/msb.20145141DOI Listing
July 2014

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

Nature 2014 Jul 22;511(7510):428-34. Epub 2014 Jun 22.

1] Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany.

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http://www.abta.org/resources/enhancers-hijacking-activates.
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http://www.nature.com/doifinder/10.1038/nature13379
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http://dx.doi.org/10.1038/nature13379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201514PMC
July 2014

Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.

F1000Res 2014 1;3:141. Epub 2014 Jul 1.

The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.12688/f1000research.4536.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103489PMC
July 2014

Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction.

Front Genet 2014 16;5:123. Epub 2014 May 16.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto Toronto, ON, Canada.

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http://dx.doi.org/10.3389/fgene.2014.00123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032932PMC
June 2014

A draft map of the human proteome.

Nature 2014 May;509(7502):575-81

1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [3] Institute of Bioinformatics, International Tech Park, Bangalore 560066, India [4] Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana 70130, USA [5] The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [6] Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA [7] Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana 70130, USA.

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http://dx.doi.org/10.1038/nature13302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403737PMC
May 2014

Using biological pathway data with paxtools.

PLoS Comput Biol 2013 19;9(9):e1003194. Epub 2013 Sep 19.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1003194
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http://dx.doi.org/10.1371/journal.pcbi.1003194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777916PMC
April 2014

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.

Cancer Cell 2014 Mar;25(3):393-405

Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.ccr.2014.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493053PMC
March 2014

The BioPAX Validator.

Bioinformatics 2013 Oct 5;29(20):2659-60. Epub 2013 Aug 5.

The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789551PMC
October 2013

Comprehensive identification of mutational cancer driver genes across 12 tumor types.

Sci Rep 2013 Oct 2;3:2650. Epub 2013 Oct 2.

1] Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain [2].

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http://dx.doi.org/10.1038/srep02650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788361PMC
October 2013

The mutational landscape of phosphorylation signaling in cancer.

Sci Rep 2013 Oct 2;3:2651. Epub 2013 Oct 2.

The Donnelly Centre, University of Toronto, Canada.

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http://www.nature.com/articles/srep02651
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http://dx.doi.org/10.1038/srep02651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788619PMC
October 2013

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers.

Mol Syst Biol 2013 ;9:637

The Donnelly Centre, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1038/msb.2012.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564258PMC
September 2013

GeneMANIA prediction server 2013 update.

Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22

The Donnelly Centre, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/nar/gkt533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692113PMC
July 2013

Cytoscape app store.

Bioinformatics 2013 May 16;29(10):1350-1. Epub 2013 Apr 16.

Gladstone Institutes, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654709PMC
May 2013

Predicting PDZ domain mediated protein interactions from structure.

BMC Bioinformatics 2013 Jan 21;14:27. Epub 2013 Jan 21.

The Donnelly Centre, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1186/1471-2105-14-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602153PMC
January 2013