Publications by authors named "Vincent Ferretti"

37Publications

The landscape of viral associations in human cancers.

Nat Genet 2020 03 5;52(3):320-330. Epub 2020 Feb 5.

Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41588-019-0558-9DOI Listing
March 2020

The International Cancer Genome Consortium Data Portal.

Nat Biotechnol 2019 04;37(4):367-369

Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41587-019-0055-9DOI Listing
April 2019

Fostering population-based cohort data discovery: The Maelstrom Research cataloguing toolkit.

PLoS One 2018 24;13(7):e0200926. Epub 2018 Jul 24.

Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200926PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057635PMC
January 2019

Analysis of Epstein-Barr Virus Genomes and Expression Profiles in Gastric Adenocarcinoma.

J Virol 2018 01 2;92(2). Epub 2018 Jan 2.

Ontario Institute for Cancer Research, Toronto, Canada.

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http://dx.doi.org/10.1128/JVI.01239-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5752941PMC
January 2018

The NCI Genomic Data Commons as an engine for precision medicine.

Blood 2017 07 9;130(4):453-459. Epub 2017 Jun 9.

Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD.

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http://www.bloodjournal.org/lookup/doi/10.1182/blood-2017-03
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http://dx.doi.org/10.1182/blood-2017-03-735654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533202PMC
July 2017

Toward a Shared Vision for Cancer Genomic Data.

N Engl J Med 2016 Sep;375(12):1109-12

From the Center for Data Intensive Science, University of Chicago, Chicago (R.L.G., A.P.H.); the Ontario Institute for Cancer Research, Toronto (V.F.); Weill Cornell Medicine, Cornell University, New York (H.E.V.); and the National Cancer Institute, Bethesda, MD (D.R.L., W.A.K., L.M.S.).

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http://dx.doi.org/10.1056/NEJMp1607591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309165PMC
September 2016

CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads.

Bioinformatics 2016 Feb 9;32(3):453-5. Epub 2015 Oct 9.

Informatics and Bio-computing, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734043PMC
February 2016

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

Bioinformatics 2015 May 7;31(9):1396-404. Epub 2015 Jan 7.

Department of Informatics and Bio-computing, Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410667PMC
May 2015

DataSHIELD: an ethically robust solution to multiple-site individual-level data analysis.

Public Health Genomics 2015 13;18(2):87-96. Epub 2014 Dec 13.

Division of Epidemiology, Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway.

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http://dx.doi.org/10.1159/000368959DOI Listing
July 2015

DataSHIELD: taking the analysis to the data, not the data to the analysis.

Int J Epidemiol 2014 Dec 26;43(6):1929-44. Epub 2014 Sep 26.

School of Social and Community Medicine, University of Bristol, Bristol, UK, Maelstrom Research Group, Research Institute of the McGill University Health Centre, McGill University, Montreal, Canada, Norwegian Institute of Public Health, Oslo, Norway, Department Statistical Science, University College London, London, UK, Department of Infection, Immunity and Inflammation, Health Sciences, University of Leicester, Leicester, UK, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland, Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland, Department of Health Sciences, University of Leicester, Leicester, UK, Department of Sociology, University of Leicester, Leicester, UK, Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands, Institut für Community Medicine, University Medicine of Greifswald, Greifswald, Germany, International Prevention Research Institute, Lyon, France, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia, School of Geosciences, University of Edinburgh, Edinburgh, UK, Norwegian University of Science and Technology, Levanger, Norway, HRB Centre for Diet and Health Research, Department of Epidemiology and Public Health, University College Cork, Cork, Ireland, Research Unit of Molecular Epidemiology, Research Center for Environmental Health, Neuherberg, Germany, MRC/CSO Social and Public Health Sciences Unit, University of Glasgow, Glasgow, UK, University of Tartu, Estonian Genome Center, Tartu, Estonia, University Medical Center Groningen, Medical Statistics, Groningen, The Netherlands, Centre of Genomics and Policy, McGill University, Montreal, Canada, University Medical Center Groningen, LifeLines Cohort Study, Groningen, The Netherlands, Department of Endocrinology, University Medical Center Groningen, Groningen, The Netherlands, School of Social and Community Medicine, University of Bristol, Bristol, UK and Onta

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http://dx.doi.org/10.1093/ije/dyu188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276062PMC
December 2014

Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq.

PLoS One 2013 30;8(10):e76935. Epub 2013 Oct 30.

Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076935PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813700PMC
August 2014

Genome-wide detection and characterization of positive selection in human populations.

Authors:
Pardis C Sabeti Patrick Varilly Ben Fry Jason Lohmueller Elizabeth Hostetter Chris Cotsapas Xiaohui Xie Elizabeth H Byrne Steven A McCarroll Rachelle Gaudet Stephen F Schaffner Eric S Lander Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda Todd A Johnson James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):913-8

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA.

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https://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Le
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http://www.nature.com/doifinder/10.1038/nature06250
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http://dx.doi.org/10.1038/nature06250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687721PMC
October 2007

A second generation human haplotype map of over 3.1 million SNPs.

Authors:
Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):851-61

The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA.

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https://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/In
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http://www.nature.com/doifinder/10.1038/nature06258
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http://dx.doi.org/10.1038/nature06258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689609PMC
October 2007

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

Nucleic Acids Res 2007 Jan 5;35(Database issue):D122-6. Epub 2006 Dec 5.

McGill University and Genome Quebec Innovation Center, 740 Dr Penfield, Montreal, Qc, Canada H3A 1A4.

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http://dx.doi.org/10.1093/nar/gkl879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761432PMC
January 2007

A predominant role for the HLA class II region in the association of the MHC region with multiple sclerosis.

Nat Genet 2005 Oct 25;37(10):1108-12. Epub 2005 Sep 25.

Department of Clinical Neurology, Radcliffe Infirmary, University of Oxford, Oxford OX2 6HE, UK.

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http://dx.doi.org/10.1038/ng1647DOI Listing
October 2005

Antimicrobial drug discovery through bacteriophage genomics.

Nat Biotechnol 2004 Feb 11;22(2):185-91. Epub 2004 Jan 11.

PhageTech Inc., 7170 Frederick Banting, 2nd Floor, Ville Saint Laurent, Quebec, Canada, H4S 2A1.

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http://dx.doi.org/10.1038/nbt932DOI Listing
February 2004