Sylvain Foissac

Sylvain Foissac

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Sylvain Foissac

Sylvain Foissac

Publications by authors named "Sylvain Foissac"

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20Publications

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Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

Methods Mol Biol 2017 ;1468:201-19

CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France.

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http://dx.doi.org/10.1007/978-1-4939-4035-6_14DOI Listing
January 2018

Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

Methods Mol Biol 2017 ;1468:E1

CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France.

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http://dx.doi.org/10.1007/978-1-4939-4035-6_17DOI Listing
January 2017

Analysis of alternative splicing events in custom gene datasets by AStalavista.

Methods Mol Biol 2015 ;1269:379-92

UMR1388 GenPhySE, French National Institute for Agricultural Research (INRA), Chemin de Borde Rouge, 31326, Castanet Tolosan, France.

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http://dx.doi.org/10.1007/978-1-4939-2291-8_24DOI Listing
September 2015

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

A general definition and nomenclature for alternative splicing events.

PLoS Comput Biol 2008 Aug 8;4(8):e1000147. Epub 2008 Aug 8.

Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1000147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2467475PMC
August 2008

A combinatorial code for CPE-mediated translational control.

Cell 2008 Feb;132(3):434-48

Centre for Genomic Regulation (CRG), UPF, C/Dr. Aiguader, 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1016/j.cell.2007.12.038DOI Listing
February 2008

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets.

Nucleic Acids Res 2007 Jul 7;35(Web Server issue):W297-9. Epub 2007 May 7.

Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkm311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933205PMC
July 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Integrating alternative splicing detection into gene prediction.

BMC Bioinformatics 2005 Feb 10;6:25. Epub 2005 Feb 10.

Unité de Biométrie et Intelligence Artificielle, INRA, 31326 Castanet Tolosan, France.

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http://dx.doi.org/10.1186/1471-2105-6-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC550657PMC
February 2005

EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences.

Nucleic Acids Res 2003 Jul;31(13):3742-5

Laboratoire de Biométrie et Intelligence Artificielle, INRA, 31326, Castanet Tolosan Cedex, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168992PMC
http://dx.doi.org/10.1093/nar/gkg586DOI Listing
July 2003