Alain Viari

Alain Viari

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Alain Viari

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Toll-like receptor 3 downregulation is an escape mechanism from apoptosis during hepatocarcinogenesis.

Authors:
Marc Bonnin Nadim Fares Barbara Testoni Yann Estornes Kathrin Weber Béatrice Vanbervliet Lydie Lefrançois Amandine Garcia Alain Kfoury Floriane Pez Isabelle Coste Pierre Saintigny Alain Viari Kévin Lang Baptiste Guey Valérie Hervieu Brigitte Bancel Birke Bartoch David Durantel Toufic Renno Philippe Merle Serge Lebecque

J Hepatol 2019 Oct 18;71(4):763-772. Epub 2019 Jun 18.

INSERM, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France; Hospices Civils de Lyon, Laboratoire d'Anatomie et Cytologie Pathologiques, Centre Hospitalier Lyon Sud, Pierre Bénite, France. Electronic address:

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http://dx.doi.org/10.1016/j.jhep.2019.05.031DOI Listing
October 2019

Actionable molecular alterations in advanced gynaecologic malignancies: updated results from the ProfiLER programme.

Authors:
Romain Varnier Olivia Le Saux Sylvie Chabaud Gwenaëlle Garin Emilie Sohier Qing Wang Sandrine Paindavoine David Pérol Christian Baudet Valéry Attignon Daniel Pissaloux Pierre Heudel Benoit You Cécile Leyronnas Olivier Collard Olivier Trédan Nathalie Bonnin Jérôme Long Jean-Philippe Jacquin Philippe A Cassier Olfa Derbel Gilles Freyer Alain Viari Jean-Yves Blay Isabelle Ray-Coquard

Eur J Cancer 2019 Sep 24;118:156-165. Epub 2019 Jul 24.

Medical Practices Evaluation Team - HESPER EA7425, Centre Léon Bérard, Lyon, France; Université Claude Bernard Lyon 1, Lyon, France; Department of Medical Oncology, Centre Léon Bérard, Lyon, France. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09598049193038
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http://dx.doi.org/10.1016/j.ejca.2019.06.017DOI Listing
September 2019

The circular RNome of primary breast cancer.

Authors:
Marcel Smid Saskia M Wilting Katharina Uhr F Germán Rodríguez-González Vanja de Weerd Wendy J C Prager-Van der Smissen Michelle van der Vlugt-Daane Anne van Galen Serena Nik-Zainal Adam Butler Sancha Martin Helen R Davies Johan Staaf Marc J van de Vijver Andrea L Richardson Gaëten MacGrogan Roberto Salgado Gert G G M van den Eynden Colin A Purdie Alastair M Thompson Carlos Caldas Paul N Span Fred C G J Sweep Peter T Simpson Sunil R Lakhani Steven Van Laere Christine Desmedt Angelo Paradiso Jorunn Eyfjord Annegien Broeks Anne Vincent-Salomon Andrew P Futreal Stian Knappskog Tari King Alain Viari Anne-Lise Børresen-Dale Hendrik G Stunnenberg Mike Stratton John A Foekens Anieta M Sieuwerts John W M Martens

Genome Res 2019 03 28;29(3):356-366. Epub 2019 Jan 28.

Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.238121.118
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http://dx.doi.org/10.1101/gr.238121.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396421PMC
March 2019

Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Authors:
Serena Nik-Zainal Helen Davies Johan Staaf Manasa Ramakrishna Dominik Glodzik Xueqing Zou Inigo Martincorena Ludmil B Alexandrov Sancha Martin David C Wedge Peter Van Loo Young Seok Ju Marcel Smid Arie B Brinkman Sandro Morganella Miriam R Aure Ole Christian Lingjærde Anita Langerød Markus Ringnér Sung-Min Ahn Sandrine Boyault Jane E Brock Annegien Broeks Adam Butler Christine Desmedt Luc Dirix Serge Dronov Aquila Fatima John A Foekens Moritz Gerstung Gerrit K J Hooijer Se Jin Jang David R Jones Hyung-Yong Kim Tari A King Savitri Krishnamurthy Hee Jin Lee Jeong-Yeon Lee Yilong Li Stuart McLaren Andrew Menzies Ville Mustonen Sarah O'Meara Iris Pauporté Xavier Pivot Colin A Purdie Keiran Raine Kamna Ramakrishnan F Germán Rodríguez-González Gilles Romieu Anieta M Sieuwerts Peter T Simpson Rebecca Shepherd Lucy Stebbings Olafur A Stefansson Jon Teague Stefania Tommasi Isabelle Treilleux Gert G Van den Eynden Peter Vermeulen Anne Vincent-Salomon Lucy Yates Carlos Caldas Laura Van't Veer Andrew Tutt Stian Knappskog Benita Kiat Tee Tan Jos Jonkers Åke Borg Naoto T Ueno Christos Sotiriou Alain Viari P Andrew Futreal Peter J Campbell Paul N Span Steven Van Laere Sunil R Lakhani Jorunn E Eyfjord Alastair M Thompson Ewan Birney Hendrik G Stunnenberg Marc J van de Vijver John W M Martens Anne-Lise Børresen-Dale Andrea L Richardson Gu Kong Gilles Thomas Michael R Stratton

Nature 2019 02;566(7742):E1

Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

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http://www.nature.com/articles/s41586-019-0883-2
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http://dx.doi.org/10.1038/s41586-019-0883-2DOI Listing
February 2019

Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men.

Authors:
Laurie Tonon Gaëlle Fromont Sandrine Boyault Emilie Thomas Anthony Ferrari Anne-Sophie Sertier Janice Kielbassa Vincent Le Texier Aurélie Kamoun Nabila Elarouci Jacques Irani Luc Multigner Ivo Glynne Gut Marta Gut Pascal Blanchet Aurélien De Reynies Géraldine Cancel-Tassin Alain Viari Olivier Cussenot

Eur Urol 2019 01 21;75(1):11-15. Epub 2018 Sep 21.

CeRePP, Paris, France; Sorbonne Université, GRC n(∘)5, ONCOTYPE-URO, Paris, France; Assistance Publique Hôpitaux de Paris, Department of Urology, Academic Hospital Paris Est, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.eururo.2018.08.026DOI Listing
January 2019

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.

Authors:
Laetitia Guillot Ludovic Delage Alain Viari Yves Vandenbrouck Emmanuelle Com Andrés Ritter Régis Lavigne Dominique Marie Pierre Peterlongo Philippe Potin Charles Pineau

BMC Genomics 2019 Jan 17;20(1):56. Epub 2019 Jan 17.

Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.

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http://dx.doi.org/10.1186/s12864-019-5431-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337836PMC
January 2019

Immunological and classical subtypes of oral premalignant lesions.

Authors:
Jean-Philippe Foy Chloé Bertolus Sandra Ortiz-Cuaran Marie-Alexandra Albaret William N Williams Wenhua Lang Solène Destandau Geneviève De Souza Emilie Sohier Janice Kielbassa Emilie Thomas Sophie Deneuve Patrick Goudot Alain Puisieux Alain Viari Li Mao Christophe Caux S M Lippman P Saintigny

Oncoimmunology 2018 21;7(12):e1496880. Epub 2018 Sep 21.

Univ Lyon, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France.

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https://www.tandfonline.com/doi/full/10.1080/2162402X.2018.1
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http://dx.doi.org/10.1080/2162402X.2018.1496880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279331PMC
September 2018

Integrated analysis highlights APC11 protein expression as a likely new independent predictive marker for colorectal cancer.

Authors:
Youenn Drouet Isabelle Treilleux Alain Viari Sophie Léon Mojgan Devouassoux-Shisheboran Nicolas Voirin Christelle de la Fouchardière Brigitte Manship Alain Puisieux Christine Lasset Caroline Moyret-Lalle

Sci Rep 2018 05 9;8(1):7386. Epub 2018 May 9.

Centre Léon Bérard, Lyon, F-69008, France.

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http://dx.doi.org/10.1038/s41598-018-25631-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943309PMC
May 2018

A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts.

Authors:
Sarah Huet Bruno Tesson Jean-Philippe Jais Andrew L Feldman Laura Magnano Emilie Thomas Alexandra Traverse-Glehen Benoit Albaud Marjorie Carrère Luc Xerri Stephen M Ansell Lucile Baseggio Cécile Reyes Karin Tarte Sandrine Boyault Corinne Haioun Brian K Link Pierre Feugier Armando Lopez-Guillermo Hervé Tilly Pauline Brice Sandrine Hayette Fabrice Jardin Fritz Offner Pierre Sujobert David Gentien Alain Viari Elias Campo James R Cerhan Gilles Salles

Lancet Oncol 2018 04 20;19(4):549-561. Epub 2018 Feb 20.

Cancer Research Center of Lyon, INSERM U1052 UMR CNRS 5286, Lyon, France; Service d'Hématologie Clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France. Electronic address:

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http://dx.doi.org/10.1016/S1470-2045(18)30102-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882539PMC
April 2018

Corrigendum: A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Authors:
Dominik Glodzik Sandro Morganella Helen Davies Peter T Simpson Yilong Li Xueqing Zou Javier Diez-Perez Johan Staaf Ludmil B Alexandrov Marcel Smid Arie B Brinkman Inga Hansine Rye Hege Russnes Keiran Raine Colin A Purdie Sunil R Lakhani Alastair M Thompson Ewan Birney Hendrik G Stunnenberg Marc J van de Vijver John W M Martens Anne-Lise Børresen-Dale Andrea L Richardson Gu Kong Alain Viari Douglas Easton Gerard Evan Peter J Campbell Michael R Stratton Serena Nik-Zainal

Nat Genet 2017 10;49(11):1661

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http://dx.doi.org/10.1038/ng1117-1661aDOI Listing
October 2017

A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes.

Authors:
Jean-Philippe Foy Louis Bazire Sandra Ortiz-Cuaran Sophie Deneuve Janice Kielbassa Emilie Thomas Alain Viari Alain Puisieux Patrick Goudot Chloé Bertolus Nicolas Foray Youlia Kirova Pierre Verrelle Pierre Saintigny

BMC Med 2017 09 1;15(1):165. Epub 2017 Sep 1.

Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, F-69008, France.

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http://dx.doi.org/10.1186/s12916-017-0929-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580222PMC
September 2017

Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency.

Authors:
Helen Davies Sandro Morganella Colin A Purdie Se Jin Jang Elin Borgen Hege Russnes Dominik Glodzik Xueqing Zou Alain Viari Andrea L Richardson Anne-Lise Børresen-Dale Alastair Thompson Jorunn E Eyfjord Gu Kong Michael R Stratton Serena Nik-Zainal

Cancer Res 2017 09;77(18):4755-4762

Wellcome Trust Sanger Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1083DOI Listing
September 2017

BCL2 mutations do not confer adverse prognosis in follicular lymphoma patients treated with rituximab.

Authors:
Sarah Huet Edith Szafer-Glusman Bruno Tesson Luc Xerri Wayne J Fairbrother Kiran Mukhyala Chris Bolen Elizabeth Punnoose Laurie Tonon Catherine Chassagne-Clément Pierre Feugier Alain Viari Fabrice Jardin Gilles Salles Pierre Sujobert

Am J Hematol 2017 Jun 24;92(6):515-519. Epub 2017 Mar 24.

Service d'hématologie biologique, Hospices Civils de Lyon, 69495, Pierre Bénite cedex, France.

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http://dx.doi.org/10.1002/ajh.24701DOI Listing
June 2017

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Authors:
Helen Davies Dominik Glodzik Sandro Morganella Lucy R Yates Johan Staaf Xueqing Zou Manasa Ramakrishna Sancha Martin Sandrine Boyault Anieta M Sieuwerts Peter T Simpson Tari A King Keiran Raine Jorunn E Eyfjord Gu Kong Åke Borg Ewan Birney Hendrik G Stunnenberg Marc J van de Vijver Anne-Lise Børresen-Dale John W M Martens Paul N Span Sunil R Lakhani Anne Vincent-Salomon Christos Sotiriou Andrew Tutt Alastair M Thompson Steven Van Laere Andrea L Richardson Alain Viari Peter J Campbell Michael R Stratton Serena Nik-Zainal

Nat Med 2017 Apr 13;23(4):517-525. Epub 2017 Mar 13.

Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/nm.4292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833945PMC
April 2017

[Contribution and challenges of Big Data in oncology].

Authors:
Pierre Saintigny Jean-Philippe Foy Anthony Ferrari Philippe Cassier Alain Viari Alain Puisieux

Bull Cancer 2017 Mar 25;104(3):281-287. Epub 2016 Nov 25.

Université Lyon, université Claude-Bernard Lyon 1, centre Léon-Bérard, centre de recherche en cancérologie de Lyon, CNRS 5286, Inserm 1052, 69008 Lyon, France.

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http://dx.doi.org/10.1016/j.bulcan.2016.10.020DOI Listing
March 2017

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

Authors:
Dominik Glodzik Sandro Morganella Helen Davies Peter T Simpson Yilong Li Xueqing Zou Javier Diez-Perez Johan Staaf Ludmil B Alexandrov Marcel Smid Arie B Brinkman Inga Hansine Rye Hege Russnes Keiran Raine Colin A Purdie Sunil R Lakhani Alastair M Thompson Ewan Birney Hendrik G Stunnenberg Marc J van de Vijver John W M Martens Anne-Lise Børresen-Dale Andrea L Richardson Gu Kong Alain Viari Douglas Easton Gerard Evan Peter J Campbell Michael R Stratton Serena Nik-Zainal

Nat Genet 2017 Mar 23;49(3):341-348. Epub 2017 Jan 23.

Wellcome Trust Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/ng.3771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988034PMC
March 2017

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.

Authors:
Young Seok Ju Inigo Martincorena Moritz Gerstung Mia Petljak Ludmil B Alexandrov Raheleh Rahbari David C Wedge Helen R Davies Manasa Ramakrishna Anthony Fullam Sancha Martin Christopher Alder Nikita Patel Steve Gamble Sarah O'Meara Dilip D Giri Torril Sauer Sarah E Pinder Colin A Purdie Åke Borg Henk Stunnenberg Marc van de Vijver Benita K T Tan Carlos Caldas Andrew Tutt Naoto T Ueno Laura J van 't Veer John W M Martens Christos Sotiriou Stian Knappskog Paul N Span Sunil R Lakhani Jórunn Erla Eyfjörd Anne-Lise Børresen-Dale Andrea Richardson Alastair M Thompson Alain Viari Matthew E Hurles Serena Nik-Zainal Peter J Campbell Michael R Stratton

Nature 2017 03 22;543(7647):714-718. Epub 2017 Mar 22.

Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature21703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169740PMC
March 2017

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.

Authors:
Marcel Smid F Germán Rodríguez-González Anieta M Sieuwerts Roberto Salgado Wendy J C Prager-Van der Smissen Michelle van der Vlugt-Daane Anne van Galen Serena Nik-Zainal Johan Staaf Arie B Brinkman Marc J van de Vijver Andrea L Richardson Aquila Fatima Kim Berentsen Adam Butler Sancha Martin Helen R Davies Reno Debets Marion E Meijer-Van Gelder Carolien H M van Deurzen Gaëtan MacGrogan Gert G G M Van den Eynden Colin Purdie Alastair M Thompson Carlos Caldas Paul N Span Peter T Simpson Sunil R Lakhani Steven Van Laere Christine Desmedt Markus Ringnér Stefania Tommasi Jorunn Eyford Annegien Broeks Anne Vincent-Salomon P Andrew Futreal Stian Knappskog Tari King Gilles Thomas Alain Viari Anita Langerød Anne-Lise Børresen-Dale Ewan Birney Hendrik G Stunnenberg Mike Stratton John A Foekens John W M Martens

Nat Commun 2016 Sep 26;7:12910. Epub 2016 Sep 26.

Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.

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http://www.nature.com/articles/ncomms12910
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http://dx.doi.org/10.1038/ncomms12910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052682PMC
September 2016

A phenotypic and mechanistic perspective on heterogeneity of HER2-positive breast cancers.

Authors:
Anthony Ferrari Anne-Sophie Sertier Anne Vincent-Salomon Xavier Pivot Iris Pauporté Pierre Saintigny Daniel Birnbaum Alain Viari

Mol Cell Oncol 2016 12;3(6):e1232186. Epub 2016 Sep 12.

Synergie Lyon Cancer, Plateforme de Bioinformatique 'Gilles Thomas' Centre Léon Bérard, Lyon, France; INRIA Grenoble-Rhône-Alpes, Montbonnot-Saint Martin, France.

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http://dx.doi.org/10.1080/23723556.2016.1232186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5160388PMC
September 2016

A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers.

Authors:
Anthony Ferrari Anne Vincent-Salomon Xavier Pivot Anne-Sophie Sertier Emilie Thomas Laurie Tonon Sandrine Boyault Eskeatnaf Mulugeta Isabelle Treilleux Gaëtan MacGrogan Laurent Arnould Janice Kielbassa Vincent Le Texier Hélène Blanché Jean-François Deleuze Jocelyne Jacquemier Marie-Christine Mathieu Frédérique Penault-Llorca Frédéric Bibeau Odette Mariani Cécile Mannina Jean-Yves Pierga Olivier Trédan Thomas Bachelot Hervé Bonnefoi Gilles Romieu Pierre Fumoleau Suzette Delaloge Maria Rios Jean-Marc Ferrero Carole Tarpin Catherine Bouteille Fabien Calvo Ivo Glynne Gut Marta Gut Sancha Martin Serena Nik-Zainal Michael R Stratton Iris Pauporté Pierre Saintigny Daniel Birnbaum Alain Viari Gilles Thomas

Nat Commun 2016 07 13;7:12222. Epub 2016 Jul 13.

Synergie Lyon Cancer, Plateforme de bioinformatique 'Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France.

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http://dx.doi.org/10.1038/ncomms12222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947184PMC
July 2016

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Authors:
Serena Nik-Zainal Helen Davies Johan Staaf Manasa Ramakrishna Dominik Glodzik Xueqing Zou Inigo Martincorena Ludmil B Alexandrov Sancha Martin David C Wedge Peter Van Loo Young Seok Ju Marcel Smid Arie B Brinkman Sandro Morganella Miriam R Aure Ole Christian Lingjærde Anita Langerød Markus Ringnér Sung-Min Ahn Sandrine Boyault Jane E Brock Annegien Broeks Adam Butler Christine Desmedt Luc Dirix Serge Dronov Aquila Fatima John A Foekens Moritz Gerstung Gerrit K J Hooijer Se Jin Jang David R Jones Hyung-Yong Kim Tari A King Savitri Krishnamurthy Hee Jin Lee Jeong-Yeon Lee Yilong Li Stuart McLaren Andrew Menzies Ville Mustonen Sarah O'Meara Iris Pauporté Xavier Pivot Colin A Purdie Keiran Raine Kamna Ramakrishnan F Germán Rodríguez-González Gilles Romieu Anieta M Sieuwerts Peter T Simpson Rebecca Shepherd Lucy Stebbings Olafur A Stefansson Jon Teague Stefania Tommasi Isabelle Treilleux Gert G Van den Eynden Peter Vermeulen Anne Vincent-Salomon Lucy Yates Carlos Caldas Laura van't Veer Andrew Tutt Stian Knappskog Benita Kiat Tee Tan Jos Jonkers Åke Borg Naoto T Ueno Christos Sotiriou Alain Viari P Andrew Futreal Peter J Campbell Paul N Span Steven Van Laere Sunil R Lakhani Jorunn E Eyfjord Alastair M Thompson Ewan Birney Hendrik G Stunnenberg Marc J van de Vijver John W M Martens Anne-Lise Børresen-Dale Andrea L Richardson Gu Kong Gilles Thomas Michael R Stratton

Nature 2016 06 2;534(7605):47-54. Epub 2016 May 2.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nature17676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910866PMC
June 2016

Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito.

Authors:
Laurence Després Renaud Stalinski Frédéric Faucon Vincent Navratil Alain Viari Margot Paris Guillaume Tetreau Rodolphe Poupardin Muhammad Asam Riaz Aurélie Bonin Stéphane Reynaud Jean-Philippe David

Biol Lett 2014 Dec;10(12):20140716

Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine UMR 5553, BP53, Grenoble 38041, France CNRS, Laboratoire d'Ecologie Alpine UMR 5553, BP53, Grenoble 38041, France.

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http://rsbl.royalsocietypublishing.org/cgi/doi/10.1098/rsbl.
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http://dx.doi.org/10.1098/rsbl.2014.0716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298186PMC
December 2014

Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.

Authors:
Veasna Duong Cameron Simmons Laurent Gavotte Alain Viari Sivuth Ong Ngan Chantha Niall J Lennon Bruce W Birren Sirenda Vong Jeremy J Farrar Matthew R Henn Vincent Deubel Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 2;15:59-68. Epub 2011 Jul 2.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

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http://dx.doi.org/10.1016/j.meegid.2011.06.019DOI Listing
April 2013

Biased mutational pattern and quasispecies hypothesis in H5N1 virus.

Authors:
Ramona Alikiiteaga Gutiérrez Alain Viari Bernard Godelle Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 29;15:69-76. Epub 2011 Oct 29.

Virology Unit, Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong blvd, PO Box 983, Phnom Penh, Cambodia.

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https://linkinghub.elsevier.com/retrieve/pii/S15671348110037
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http://dx.doi.org/10.1016/j.meegid.2011.10.019DOI Listing
April 2013

Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters.

Authors:
Veasna Duong Matthew R Henn Cameron Simmons Chantha Ngan Bunthin Y Laurent Gavotte Alain Viari Sivuth Ong Rekol Huy Niall J Lennon Sowath Ly Sirenda Vong Bruce W Birren Jeremy J Farrar Vincent Deubel Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 5;15:77-86. Epub 2012 Jun 5.

Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.

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http://dx.doi.org/10.1016/j.meegid.2012.05.012DOI Listing
April 2013

Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade.

Authors:
San Sorn Touch Sok Sovann Ly Sareth Rith Nguyen Tung Alain Viari Laurent Gavotte Davun Holl Heng Seng Nima Asgari Beat Richner Denis Laurent Nora Chea Veasna Duong Tetsuya Toyoda Chadwick Y Yasuda Paul Kitsutani Paul Zhou Sun Bing Vincent Deubel Ruben Donis Roger Frutos Philippe Buchy

Infect Genet Evol 2013 Apr 7;15:87-94. Epub 2012 Jun 7.

Virology Unit/National Influenza Centre, Institut Pasteur in Cambodia, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia.

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http://dx.doi.org/10.1016/j.meegid.2012.05.013DOI Listing
April 2013

[Big Data in biology].

Authors:
Alain Viari

Med Sci (Paris) 2012 Dec 21;28(12):1027-8. Epub 2012 Dec 21.

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http://dx.doi.org/10.1051/medsci/20122812001DOI Listing
December 2012

The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

Authors:
Adam Alexander Thil Smith Eugeni Belda Alain Viari Claudine Medigue David Vallenet

PLoS Comput Biol 2012 May 31;8(5):e1002540. Epub 2012 May 31.

CEA DSV IG, Genoscope, Evry, France.

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http://dx.doi.org/10.1371/journal.pcbi.1002540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364942PMC
May 2012

UniPathway: a resource for the exploration and annotation of metabolic pathways.

Authors:
Anne Morgat Eric Coissac Elisabeth Coudert Kristian B Axelsen Guillaume Keller Amos Bairoch Alan Bridge Lydie Bougueleret Ioannis Xenarios Alain Viari

Nucleic Acids Res 2012 Jan 18;40(Database issue):D761-9. Epub 2011 Nov 18.

Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1093/nar/gkr1023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245108PMC
January 2012

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.

Authors:
Tiayyba Riaz Wasim Shehzad Alain Viari François Pompanon Pierre Taberlet Eric Coissac

Nucleic Acids Res 2011 Nov 19;39(21):e145. Epub 2011 Sep 19.

Laboratoire d'Ecologie Alpine, CNRS UMR 5553 2233, Université Joseph Fourrier, BP 53, 38041 Grenoble Cedex-9, France.

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https://academic.oup.com/nar/article/39/21/e145/1105558
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http://dx.doi.org/10.1093/nar/gkr732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241669PMC
November 2011

Bacterial syntenies: an exact approach with gene quorum.

Authors:
Yves-Pol Deniélou Marie-France Sagot Frédéric Boyer Alain Viari

BMC Bioinformatics 2011 May 24;12:193. Epub 2011 May 24.

INRIA Grenoble-Rhône-Alpes, Team BAMBOO, 655 Avenue de l'Europe, 38334 Montbonnot Cedex, France.

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http://dx.doi.org/10.1186/1471-2105-12-193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121647PMC
May 2011

Innovative approach for transcriptomic analysis of obligate intracellular pathogen: selective capture of transcribed sequences of Ehrlichia ruminantium.

Authors:
Loïc Emboulé France Daigle Damien F Meyer Bernard Mari Valérie Pinarello Christian Sheikboudou Virginie Magnone Roger Frutos Alain Viari Pascal Barbry Dominique Martinez Thierry Lefrançois Nathalie Vachiéry

BMC Mol Biol 2009 Dec 24;10:111. Epub 2009 Dec 24.

UMR 15 CIRAD-INRA, Contrôle des maladies animales exotiques et émergentes, Site de Duclos, Prise d'Eau 97170, Petit Bourg, Guadeloupe.

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http://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-21
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http://dx.doi.org/10.1186/1471-2199-10-111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806407PMC
December 2009

Emergence and potential of high-throughput and integrative approaches in pathology.

Authors:
Roger Frutos Alain Viari Nathalie Vachiéry Frédéric Boyer Thierry Lefrançois Dominique Martinez

Ann N Y Acad Sci 2008 Dec;1149:62-5

Cirad, TA A-15/G, Campus International de Baillarguet, Montpellier, France.

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http://dx.doi.org/10.1196/annals.1428.060DOI Listing
December 2008

Differential strain-specific diagnosis of the heartwater agent: Ehrlichia ruminantium.

Authors:
Nathalie Vachiery Gael Maganga Thierry Lefrançois Yane Kandassamy Frédéric Stachurski Hassane Adakal Conchita Ferraz Anne Morgat Albert Bensaid Eric Coissac Frédéric Boyer Jacques Demaille Alain Viari Dominique Martinez Roger Frutos

Infect Genet Evol 2008 Jul 19;8(4):459-66. Epub 2007 Jun 19.

CIRAD TA A-15/G, Campus International de Baillarguet, 34398, Montpellier Cedex 05, France.

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http://linkinghub.elsevier.com/retrieve/pii/S156713480700094
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http://dx.doi.org/10.1016/j.meegid.2007.06.001DOI Listing
July 2008

PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences.

Authors:
Myriam Ferro Marianne Tardif Erwan Reguer Romain Cahuzac Christophe Bruley Thierry Vermat Estelle Nugues Marielle Vigouroux Yves Vandenbrouck Jérôme Garin Alain Viari

J Proteome Res 2008 May 19;7(5):1873-83. Epub 2008 Mar 19.

CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, Grenoble, F-38054, France.

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https://www.researchgate.net/profile/Yves_Vandenbrouck/publi
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http://pubs.acs.org/doi/abs/10.1021/pr070415k
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http://dx.doi.org/10.1021/pr070415kDOI Listing
May 2008

Ehrlichia ruminantium: genomic and evolutionary features.

Authors:
Roger Frutos Alain Viari Nathalie Vachiery Frédéric Boyer Dominique Martinez

Trends Parasitol 2007 Sep 24;23(9):414-9. Epub 2007 Jul 24.

Centre de coopération internationale en recherche agronomique pour le développement (Cirad), TA30/G, Campus International de Baillarguet, 34398 Montpellier Cedex 05, France.

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http://dx.doi.org/10.1016/j.pt.2007.07.007DOI Listing
September 2007

Repseek, a tool to retrieve approximate repeats from large DNA sequences.

Authors:
Guillaume Achaz Frédéric Boyer Eduardo P C Rocha Alain Viari Eric Coissac

Bioinformatics 2007 Jan 11;23(1):119-21. Epub 2006 Oct 11.

Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris 6 12, rue Cuvier, 75005 Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btl519DOI Listing
January 2007

Genepi: a blackboard framework for genome annotation.

Authors:
Stéphane Descorps-Declère Danielle Ziébelin François Rechenmann Alain Viari

BMC Bioinformatics 2006 Oct 12;7:450. Epub 2006 Oct 12.

GENOME express, Meylan, France.

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http://dx.doi.org/10.1186/1471-2105-7-450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626490PMC
October 2006

Comparative genomics of three strains of Ehrlichia ruminantium: a review.

Authors:
Roger Frutos Alain Viari Conchita Ferraz Albert Bensaid Anne Morgat Frederic Boyer Eric Coissac Nathalie Vachiéry Jacques Demaille Dominique Martinez

Ann N Y Acad Sci 2006 Oct;1081:417-33

CIRAD, Emvt Department, TA30/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.

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http://dx.doi.org/10.1196/annals.1373.061DOI Listing
October 2006

Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity.

Authors:
Roger Frutos Alain Viari Conchita Ferraz Anne Morgat Sophie Eychenié Yane Kandassamy Isabelle Chantal Albert Bensaid Eric Coissac Nathalie Vachiery Jacques Demaille Dominique Martinez

J Bacteriol 2006 Apr;188(7):2533-42

CIRAD TA30/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.

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http://jb.asm.org/content/188/7/2533.full.pdf
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http://jb.asm.org/cgi/doi/10.1128/JB.188.7.2533-2542.2006
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http://dx.doi.org/10.1128/JB.188.7.2533-2542.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1428390PMC
April 2006

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins.

Authors:
Patrick Durand Laurent Labarre Alain Meil Jean-Louis Divo Yves Vandenbrouck Alain Viari Jérôme Wojcik

BMC Bioinformatics 2006 Jan 17;7:21. Epub 2006 Jan 17.

Hybrigenics SA, 3-5 Impasse Reille, 75014 Paris, France.

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http://dx.doi.org/10.1186/1471-2105-7-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1382257PMC
January 2006

Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.

Authors:
Frédéric Boyer Anne Morgat Laurent Labarre Joël Pothier Alain Viari

Bioinformatics 2005 Dec 10;21(23):4209-15. Epub 2005 Oct 10.

INRIA Rhône-Alpes, HELIX Group 655 avenue de l'Europe, 38334 Montbonnot Cedex, France.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti711DOI Listing
December 2005

Ab initio reconstruction of metabolic pathways.

Authors:
Frédéric Boyer Alain Viari

Bioinformatics 2003 Oct;19 Suppl 2:ii26-34

LSR-IMAG, Saint Martin d'Hères Cedex, France.

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http://dx.doi.org/10.1093/bioinformatics/btg1055DOI Listing
October 2003

Integration of data and methods for genome analysis.

Authors:
Patrick Durand Claudine Médigue Anne Morgat Yves Vandenbrouck Alain Viari François Rechenmann

Curr Opin Drug Discov Devel 2003 May;6(3):346-52

Hybrigenics 3-5 Impasse Reille, 75014 Paris, France.

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May 2003