Mathieu Lupien

Mathieu Lupien

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Mathieu Lupien

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C3D: a tool to predict 3D genomic interactions between cis-regulatory elements.

Bioinformatics 2019 Mar;35(5):877-879

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

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http://dx.doi.org/10.1093/bioinformatics/bty717DOI Listing
March 2019

The Proteogenomic Landscape of Curable Prostate Cancer.

Cancer Cell 2019 Mar;35(3):414-427.e6

Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Human Genetics, University of California, 12-109 CHS, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA; Department of Urology, University of California, Los Angeles, CA 90024, USA; Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA 90024, USA; Institute for Precision Health, University of California, Los Angeles, CA 90024, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2019.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511374PMC
March 2019

Characterization of inv(3) cell line OCI-AML-20 with stroma-dependent CD34 expression.

Exp Hematol 2019 01 22;69:27-36. Epub 2018 Oct 22.

Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0301472X183086
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http://dx.doi.org/10.1016/j.exphem.2018.10.006DOI Listing
January 2019

SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations.

BMC Bioinformatics 2018 Nov 26;19(1):454. Epub 2018 Nov 26.

Princess Margaret Cancer Centre, The MaRS Center, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2501-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258448PMC
November 2018

Organizing combinatorial transcription factor recruitment at cis-regulatory modules.

Transcription 2018 28;9(4):233-239. Epub 2017 Nov 28.

a Université de Lille - Inserm - Chru de Lille, Institut Pasteur de Lille , U1011- EGID, F-59000 Lille , France.

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http://dx.doi.org/10.1080/21541264.2017.1394424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104691PMC
October 2018

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19.

Cell 2018 07 19;174(3):564-575.e18. Epub 2018 Jul 19.

Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.014DOI Listing
July 2018

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19.

Cell 2018 07 19;174(3):564-575.e18. Epub 2018 Jul 19.

Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.06.014DOI Listing
July 2018

Publisher Correction: Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.

Authors:
Maya Ghoussaini Stacey L Edwards Kyriaki Michailidou Silje Nord Richard Cowper-Sal Lari Kinjal Desai Siddhartha Kar Kristine M Hillman Susanne Kaufmann Dylan M Glubb Jonathan Beesley Joe Dennis Manjeet K Bolla Qin Wang Ed Dicks Qi Guo Marjanka K Schmidt Mitul Shah Robert Luben Judith Brown Kamila Czene Hatef Darabi Mikael Eriksson Daniel Klevebring Stig E Bojesen Børge G Nordestgaard Sune F Nielsen Henrik Flyger Diether Lambrechts Bernard Thienpont Patrick Neven Hans Wildiers Annegien Broeks Laura J Van't Veer Emiel J Th Rutgers Fergus J Couch Janet E Olson Emily Hallberg Celine Vachon Jenny Chang-Claude Anja Rudolph Petra Seibold Dieter Flesch-Janys Julian Peto Isabel Dos-Santos-Silva Lorna Gibson Heli Nevanlinna Taru A Muranen Kristiina Aittomäki Carl Blomqvist Per Hall Jingmei Li Jianjun Liu Keith Humphreys Daehee Kang Ji-Yeob Choi Sue K Park Dong-Young Noh Keitaro Matsuo Hidemi Ito Hiroji Iwata Yasushi Yatabe Pascal Guénel Thérèse Truong Florence Menegaux Marie Sanchez Barbara Burwinkel Frederik Marme Andreas Schneeweiss Christof Sohn Anna H Wu Chiu-Chen Tseng David Van Den Berg Daniel O Stram Javier Benitez M Pilar Zamora Jose Ignacio Arias Perez Primitiva Menéndez Xiao-Ou Shu Wei Lu Yu-Tang Gao Qiuyin Cai Angela Cox Simon S Cross Malcolm W R Reed Irene L Andrulis Julia A Knight Gord Glendon Sandrine Tchatchou Elinor J Sawyer Ian Tomlinson Michael J Kerin Nicola Miller Christopher A Haiman Brian E Henderson Fredrick Schumacher Loic Le Marchand Annika Lindblom Sara Margolin Soo Hwang Teo Cheng Har Yip Daphne S C Lee Tien Y Wong Maartje J Hooning John W M Martens J Margriet Collée Carolien H M van Deurzen John L Hopper Melissa C Southey Helen Tsimiklis Miroslav K Kapuscinski Chen-Yang Shen Pei-Ei Wu Jyh-Cherng Yu Shou-Tung Chen Grethe Grenaker Alnæs Anne-Lise Borresen-Dale Graham G Giles Roger L Milne Catriona McLean Kenneth Muir Artitaya Lophatananon Sarah Stewart-Brown Pornthep Siriwanarangsan Mikael Hartman Hui Miao Shaik Ahmad Bin Syed Buhari Yik Ying Teo Peter A Fasching Lothar Haeberle Arif B Ekici Matthias W Beckmann Hermann Brenner Aida Karina Dieffenbach Volker Arndt Christa Stegmaier Anthony Swerdlow Alan Ashworth Nick Orr Minouk J Schoemaker Montserrat García-Closas Jonine Figueroa Stephen J Chanock Jolanta Lissowska Jacques Simard Mark S Goldberg France Labrèche Martine Dumont Robert Winqvist Katri Pylkäs Arja Jukkola-Vuorinen Hiltrud Brauch Thomas Brüning Yon-Dschun Koto Paolo Radice Paolo Peterlongo Bernardo Bonanni Sara Volorio Thilo Dörk Natalia V Bogdanova Sonja Helbig Arto Mannermaa Vesa Kataja Veli-Matti Kosma Jaana M Hartikainen Peter Devilee Robert A E M Tollenaar Caroline Seynaeve Christi J Van Asperen Anna Jakubowska Jan Lubinski Katarzyna Jaworska-Bieniek Katarzyna Durda Susan Slager Amanda E Toland Christine B Ambrosone Drakoulis Yannoukakos Suleeporn Sangrajrang Valerie Gaborieau Paul Brennan James McKay Ute Hamann Diana Torres Wei Zheng Jirong Long Hoda Anton-Culver Susan L Neuhausen Craig Luccarini Caroline Baynes Shahana Ahmed Mel Maranian Catherine S Healey Anna González-Neira Guillermo Pita M Rosario Alonso Nuria Álvarez Daniel Herrero Daniel C Tessier Daniel Vincent Francois Bacot Ines de Santiago Jason Carroll Carlos Caldas Melissa A Brown Mathieu Lupien Vessela N Kristensen Paul D P Pharoah Georgia Chenevix-Trench Juliet D French Douglas F Easton Alison M Dunning

Nat Commun 2018 04 10;9:16193. Epub 2018 Apr 10.

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http://dx.doi.org/10.1038/ncomms16193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898457PMC
April 2018

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.

Nature 2018 01 20;553(7686):101-105. Epub 2017 Dec 20.

Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.

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http://dx.doi.org/10.1038/nature25169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993422PMC
January 2018

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.

Nat Commun 2017 10 24;8(1):1126. Epub 2017 Oct 24.

Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON, Canada, M5G1L7.

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http://dx.doi.org/10.1038/s41467-017-01153-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655668PMC
October 2017

TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer.

Nat Genet 2017 Sep 7;49(9):1336-1345. Epub 2017 Aug 7.

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

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http://dx.doi.org/10.1038/ng.3930DOI Listing
September 2017

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

Cell Stem Cell 2017 08 14;21(2):209-224.e7. Epub 2017 Jul 14.

Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Division of Neurosurgery, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.06.004DOI Listing
August 2017

Early-life antibiotic treatment enhances the pathogenicity of CD4 T cells during intestinal inflammation.

J Leukoc Biol 2017 04 29;101(4):893-900. Epub 2016 Dec 29.

The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada;

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http://dx.doi.org/10.1189/jlb.3MA0716-334RRDOI Listing
April 2017

Variant Set Enrichment: an R package to identify disease-associated functional genomic regions.

BioData Min 2017 22;10. Epub 2017 Feb 22.

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

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http://dx.doi.org/10.1186/s13040-017-0129-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320724PMC
February 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

Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations.

Cancer Discov 2016 11 19;6(11):1215-1229. Epub 2016 Oct 19.

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

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http://dx.doi.org/10.1158/2159-8290.CD-16-0745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5117653PMC
November 2016

Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2.

Cancer Cell 2016 08 14;30(2):337-348. Epub 2016 Jul 14.

The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5022794PMC
August 2016

The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence.

Cell Rep 2016 08 4;16(7):1829-37. Epub 2016 Aug 4.

Goodman Cancer Research Center, Departments of Microbiology and Immunology and Physiology, McGill University, Montreal, QC H3G 1Y6, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.07.026DOI Listing
August 2016

Molecular Insights of Pathways Resulting from Two Common PIK3CA Mutations in Breast Cancer.

Cancer Res 2016 07 25;76(13):3989-4001. Epub 2016 Apr 25.

Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana. Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana. VA Roudebush Medical Center, Indianapolis, Indiana.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-3174DOI Listing
July 2016

Blockade of AP-1 Potentiates Endocrine Therapy and Overcomes Resistance.

Mol Cancer Res 2016 05 10;14(5):470-81. Epub 2016 Mar 10.

Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas. Department of Medicine, Baylor College of Medicine, Houston, Texas. Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.

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http://dx.doi.org/10.1158/1541-7786.MCR-15-0423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867274PMC
May 2016

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

Bioinformatics 2016 04 9;32(8):1244-6. Epub 2015 Dec 9.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv723DOI Listing
April 2016

MLL5 Orchestrates a Cancer Self-Renewal State by Repressing the Histone Variant H3.3 and Globally Reorganizing Chromatin.

Cancer Cell 2015 Dec 25;28(6):715-729. Epub 2015 Nov 25.

Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Division of Neurosurgery, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address:

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http://www.cell.com/cancer-cell/pdf/S1535-6108(15)00382-7.pd
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S153561081500382
Publisher Site
http://dx.doi.org/10.1016/j.ccell.2015.10.005DOI Listing
December 2015

The histone variant H2A.Z is an important regulator of enhancer activity.

Nucleic Acids Res 2015 Nov 28;43(20):9742-56. Epub 2015 Aug 28.

Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada

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http://dx.doi.org/10.1093/nar/gkv825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787790PMC
November 2015

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.

Bioinformatics 2015 Sep 20;31(18):3057-9. Epub 2015 May 20.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and Ontario Institute for Cancer Research, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668780PMC
September 2015

Personalized diagnosis of medulloblastoma subtypes across patients and model systems.

Genomics 2015 Aug 12;106(2):96-106. Epub 2015 May 12.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada; Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2015.05.002DOI Listing
August 2015

BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors.

J Proteomics 2015 Apr 18;118:95-111. Epub 2014 Oct 18.

Princess Margaret Cancer Centre, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto, ON Canada. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S18743919140046
Publisher Site
http://dx.doi.org/10.1016/j.jprot.2014.09.029DOI Listing
April 2015

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.

Nat Commun 2015 Feb 3;2:6186. Epub 2015 Feb 3.

1] The Princess Margaret Cancer Centre-University Health Network, Toronto, Ontario, Canada M5G 1L7 [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7 [3] Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7.

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http://dx.doi.org/10.1038/ncomms7186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431651PMC
February 2015

Enhancer alterations in cancer: a source for a cell identity crisis.

Genome Med 2014 23;6(9):77. Epub 2014 Sep 23.

The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada ; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3 Canada.

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http://dx.doi.org/10.1186/s13073-014-0077-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254433PMC
December 2014

A global assessment of cancer genomic alterations in epigenetic mechanisms.

Epigenetics Chromatin 2014 4;7(1):29. Epub 2014 Dec 4.

Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7 ON Canada ; Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON Canada.

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http://dx.doi.org/10.1186/1756-8935-7-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258301PMC
December 2014

Chromatin profiling reveals regulatory network shifts and a protective role for hepatocyte nuclear factor 4α during colitis.

Mol Cell Biol 2014 Sep 30;34(17):3291-304. Epub 2014 Jun 30.

Human Genetics Institute of New Jersey and Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA

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http://dx.doi.org/10.1128/MCB.00349-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135557PMC
September 2014

Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.

Authors:
Maya Ghoussaini Stacey L Edwards Kyriaki Michailidou Silje Nord Richard Cowper-Sal Lari Kinjal Desai Siddhartha Kar Kristine M Hillman Susanne Kaufmann Dylan M Glubb Jonathan Beesley Joe Dennis Manjeet K Bolla Qin Wang Ed Dicks Qi Guo Marjanka K Schmidt Mitul Shah Robert Luben Judith Brown Kamila Czene Hatef Darabi Mikael Eriksson Daniel Klevebring Stig E Bojesen Børge G Nordestgaard Sune F Nielsen Henrik Flyger Diether Lambrechts Bernard Thienpont Patrick Neven Hans Wildiers Annegien Broeks Laura J Van't Veer Emiel J Th Rutgers Fergus J Couch Janet E Olson Emily Hallberg Celine Vachon Jenny Chang-Claude Anja Rudolph Petra Seibold Dieter Flesch-Janys Julian Peto Isabel Dos-Santos-Silva Lorna Gibson Heli Nevanlinna Taru A Muranen Kristiina Aittomäki Carl Blomqvist Per Hall Jingmei Li Jianjun Liu Keith Humphreys Daehee Kang Ji-Yeob Choi Sue K Park Dong-Young Noh Keitaro Matsuo Hidemi Ito Hiroji Iwata Yasushi Yatabe Pascal Guénel Thérèse Truong Florence Menegaux Marie Sanchez Barbara Burwinkel Frederik Marme Andreas Schneeweiss Christof Sohn Anna H Wu Chiu-Chen Tseng David Van Den Berg Daniel O Stram Javier Benitez M Pilar Zamora Jose Ignacio Arias Perez Primitiva Menéndez Xiao-Ou Shu Wei Lu Yu-Tang Gao Qiuyin Cai Angela Cox Simon S Cross Malcolm W R Reed Irene L Andrulis Julia A Knight Gord Glendon Sandrine Tchatchou Elinor J Sawyer Ian Tomlinson Michael J Kerin Nicola Miller Christopher A Haiman Brian E Henderson Fredrick Schumacher Loic Le Marchand Annika Lindblom Sara Margolin Soo Hwang Teo Cheng Har Yip Daphne S C Lee Tien Y Wong Maartje J Hooning John W M Martens J Margriet Collée Carolien H M van Deurzen John L Hopper Melissa C Southey Helen Tsimiklis Miroslav K Kapuscinski Chen-Yang Shen Pei-Ei Wu Jyh-Cherng Yu Shou-Tung Chen Grethe Grenaker Alnæs Anne-Lise Borresen-Dale Graham G Giles Roger L Milne Catriona McLean Kenneth Muir Artitaya Lophatananon Sarah Stewart-Brown Pornthep Siriwanarangsan Mikael Hartman Hui Miao Shaik Ahmad Bin Syed Buhari Yik Ying Teo Peter A Fasching Lothar Haeberle Arif B Ekici Matthias W Beckmann Hermann Brenner Aida Karina Dieffenbach Volker Arndt Christa Stegmaier Anthony Swerdlow Alan Ashworth Nick Orr Minouk J Schoemaker Montserrat García-Closas Jonine Figueroa Stephen J Chanock Jolanta Lissowska Jacques Simard Mark S Goldberg France Labrèche Martine Dumont Robert Winqvist Katri Pylkäs Arja Jukkola-Vuorinen Hiltrud Brauch Thomas Brüning Yon-Dschun Koto Paolo Radice Paolo Peterlongo Bernardo Bonanni Sara Volorio Thilo Dörk Natalia V Bogdanova Sonja Helbig Arto Mannermaa Vesa Kataja Veli-Matti Kosma Jaana M Hartikainen Peter Devilee Robert A E M Tollenaar Caroline Seynaeve Christi J Van Asperen Anna Jakubowska Jan Lubinski Katarzyna Jaworska-Bieniek Katarzyna Durda Susan Slager Amanda E Toland Christine B Ambrosone Drakoulis Yannoukakos Suleeporn Sangrajrang Valerie Gaborieau Paul Brennan James McKay Ute Hamann Diana Torres Wei Zheng Jirong Long Hoda Anton-Culver Susan L Neuhausen Craig Luccarini Caroline Baynes Shahana Ahmed Mel Maranian Catherine S Healey Anna González-Neira Guillermo Pita M Rosario Alonso Nuria Alvarez Daniel Herrero Daniel C Tessier Daniel Vincent Francois Bacot Ines de Santiago Jason Carroll Carlos Caldas Melissa A Brown Mathieu Lupien Vessela N Kristensen Paul D P Pharoah Georgia Chenevix-Trench Juliet D French Douglas F Easton Alison M Dunning

Nat Commun 2014 Sep 23;4:4999. Epub 2014 Sep 23.

Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK.

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http://dx.doi.org/10.1038/ncomms5999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321900PMC
September 2014

Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer.

Cell Rep 2014 Aug 24;8(3):798-806. Epub 2014 Jul 24.

Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; The German Cancer Consortium, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.06.053DOI Listing
August 2014

Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation.

Cell Rep 2014 Jul 26;8(1):297-310. Epub 2014 Jun 26.

Banting and Best Department of Medical Research, University of Toronto, CCBR, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.05.050DOI Listing
July 2014

Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'.

Trends Genet 2014 Apr 22;30(4):140-9. Epub 2014 Mar 22.

The Princess Margaret Cancer Centre - University Health Network, Toronto, ON, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2014.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026049PMC
April 2014

Estrogen controls the survival of BRCA1-deficient cells via a PI3K-NRF2-regulated pathway.

Proc Natl Acad Sci U S A 2014 Mar 24;111(12):4472-7. Epub 2014 Feb 24.

The Campbell Family Institute for Breast Cancer Research, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada M5G 2C1.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1324136111
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970526PMC
March 2014

Chromatin and epigenetic determinants of estrogen receptor alpha (ESR1) signaling.

Mol Cell Endocrinol 2014 Jan 16;382(1):633-641. Epub 2013 May 16.

Ontario Cancer Institute, Princess Margaret Cancer Centre-University Health Network, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.mce.2013.04.026DOI Listing
January 2014

Exploiting tumor epigenetics to improve oncolytic virotherapy.

Front Genet 2013 Sep 20;4:184. Epub 2013 Sep 20.

Center for Innovative Cancer Research, Ottawa Hospital Research Institute Ottawa, ON, Canada ; Faculty of Medicine, University of Ottawa Ottawa, ON, Canada.

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http://dx.doi.org/10.3389/fgene.2013.00184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778850PMC
September 2013

Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer.

Proc Natl Acad Sci U S A 2013 Apr 1;110(16):E1490-9. Epub 2013 Apr 1.

Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA.

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http://dx.doi.org/10.1073/pnas.1219992110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631697PMC
April 2013

Chromatin landscape and endocrine response in breast cancer.

Epigenomics 2012 Dec;4(6):675-83

Ontario Cancer Institute, Princess Margaret Hospital-University Health Network & the Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.2217/epi.12.64DOI Listing
December 2012

Cancer heterogeneity: origins and implications for genetic association studies.

Trends Genet 2012 Nov 31;28(11):538-43. Epub 2012 Jul 31.

Institute for Quantitative Biomedical Sciences, The Geisel School of Medicine, Dartmouth College, One Medical Center Drive, Lebanon, NH 03756, USA.

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http://dx.doi.org/10.1016/j.tig.2012.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477266PMC
November 2012

Dual suppression of the cyclin-dependent kinase inhibitors CDKN2C and CDKN1A in human melanoma.

J Natl Cancer Inst 2012 Nov 20;104(21):1673-9. Epub 2012 Sep 20.

Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/jnci/djs373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3490842PMC
November 2012

Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression.

Nat Genet 2012 Nov 23;44(11):1191-8. Epub 2012 Sep 23.

Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire, USA.

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http://www.nature.com/articles/ng.2416
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483423PMC
November 2012

[Colorectal cancer is typified by enhancer specific epigenetic mutations].

Med Sci (Paris) 2012 Nov 12;28(11):929-31. Epub 2012 Nov 12.

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http://dx.doi.org/10.1051/medsci/20122811009DOI Listing
November 2012

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus.

Genome Res 2012 Aug 4;22(8):1437-46. Epub 2012 Jun 4.

Department of Genetics and Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA.

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http://dx.doi.org/10.1101/gr.135665.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409257PMC
August 2012

Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies.

Wiley Interdiscip Rev Syst Biol Med 2011 Sep-Oct;3(5):513-26. Epub 2010 Dec 31.

Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA.

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http://dx.doi.org/10.1002/wsbm.132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062944PMC
December 2011

Pioneer factors: directing transcriptional regulators within the chromatin environment.

Trends Genet 2011 Nov 30;27(11):465-74. Epub 2011 Aug 30.

Norris Cotton Cancer Center, Institute for Quantitative Biomedical Sciences, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA.

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http://dx.doi.org/10.1016/j.tig.2011.07.002DOI Listing
November 2011

A comprehensive view of nuclear receptor cancer cistromes.

Cancer Res 2011 Nov 22;71(22):6940-7. Epub 2011 Sep 22.

Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China.

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http://dx.doi.org/10.1158/0008-5472.CAN-11-2091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610570PMC
November 2011

PBX1 genomic pioneer function drives ERα signaling underlying progression in breast cancer.

PLoS Genet 2011 Nov 17;7(11):e1002368. Epub 2011 Nov 17.

Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219601PMC
November 2011

Genomic collaboration of estrogen receptor alpha and extracellular signal-regulated kinase 2 in regulating gene and proliferation programs.

Mol Cell Biol 2011 Jan 18;31(1):226-36. Epub 2010 Oct 18.

University of Illinois, Department of Molecular and Integrative Physiology, 407 South Goodwin Ave., Urbana, IL 61801-3704, USA.

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http://dx.doi.org/10.1128/MCB.00821-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019850PMC
January 2011

Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.

Genes Dev 2010 Oct;24(19):2219-27

Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gad.1944810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947773PMC
October 2010

Multimodal regulation of E2F1 gene expression by progestins.

Mol Cell Biol 2010 Apr 1;30(8):1866-77. Epub 2010 Feb 1.

Duke University Medical Center, Department of Pharmacology and Cancer Biology, Durham, NC 27710, USA.

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http://dx.doi.org/10.1128/MCB.01060-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849472PMC
April 2010

Nucleosome dynamics define transcriptional enhancers.

Nat Genet 2010 Apr 7;42(4):343-7. Epub 2010 Mar 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932437PMC
April 2010

Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies.

Methods Mol Biol 2009 ;556:155-64

Division of Molecular and Cellular Oncology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-60327-192-9_11DOI Listing
September 2009

Coactivator function defines the active estrogen receptor alpha cistrome.

Mol Cell Biol 2009 Jun 13;29(12):3413-23. Epub 2009 Apr 13.

Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney St., Boston, MA 02115, USA.

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http://dx.doi.org/10.1128/MCB.00020-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2698732PMC
June 2009

Cistromics of hormone-dependent cancer.

Endocr Relat Cancer 2009 Jun 15;16(2):381-9. Epub 2009 Apr 15.

Dartmouth Medical School, Norris Cotton Cancer Center, Lebanon, New Hampshire 03756, USA.

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http://dx.doi.org/10.1677/ERC-09-0038DOI Listing
June 2009

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.

Genome Res 2009 Mar 7;19(3):372-80. Epub 2009 Jan 7.

Université de Rennes I, CNRS, UMR 6026, Equipe SPARTE, Campus de Beaulieu, 35042 Rennes cedex, France.

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http://dx.doi.org/10.1101/gr.084582.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661808PMC
March 2009

Unique ERalpha cistromes control cell type-specific gene regulation.

Mol Endocrinol 2008 Nov 25;22(11):2393-406. Epub 2008 Sep 25.

Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, D730, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1210/me.2008-0100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582540PMC
November 2008

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.

Cell 2008 Mar;132(6):958-70

Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.cell.2008.01.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323438PMC
March 2008

CARM1 regulates estrogen-stimulated breast cancer growth through up-regulation of E2F1.

Cancer Res 2008 Jan;68(1):301-6

Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-07-1983DOI Listing
January 2008

Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer.

Cancer Res 2007 Jul;67(13):6477-83

Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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http://dx.doi.org/10.1158/0008-5472.CAN-07-0746DOI Listing
July 2007

Tamoxifen and raloxifene differ in their functional interactions with aspartate 351 of estrogen receptor alpha.

Mol Pharmacol 2006 Aug 5;70(2):579-88. Epub 2006 May 5.

Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128 Succursale Centre Ville, Montréal, Québec H3C 3J7, Canada.

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http://dx.doi.org/10.1124/mol.105.021931DOI Listing
August 2006