Matthieu Muffato

Matthieu Muffato

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Matthieu Muffato

Matthieu Muffato

Publications by authors named "Matthieu Muffato"

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30Publications

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Advances and Applications in the Quest for Orthologs.

Mol Biol Evol 2019 10;36(10):2157-2164

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA.

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http://dx.doi.org/10.1093/molbev/msz150DOI Listing
October 2019

Ensembl comparative genomics resources.

Database (Oxford) 2016 20;2016. Epub 2016 Feb 20.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA,

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http://dx.doi.org/10.1093/database/bav096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110PMC
October 2016

ncRNA orthologies in the vertebrate lineage.

Database (Oxford) 2016 15;2016. Epub 2016 Mar 15.

European Molecular Biology Laboratory, European Bioinformatics Institute UCL Cancer Institute, University College London, London WC1E 6BT, UK.

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http://dx.doi.org/10.1093/database/bav127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792531PMC
October 2016

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Syst Biol 2015 Sep 1;64(5):778-91. Epub 2015 Jun 1.

University College London, Gower St, London WC1E 6BT, UK; and European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK;

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http://dx.doi.org/10.1093/sysbio/syv033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538881PMC
September 2015

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Genome Biol Evol 2015 Jul 1;7(7):1988-99. Epub 2015 Jul 1.

Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evv121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524488PMC
July 2015

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.

Nucleic Acids Res 2015 Jan 6;43(Database issue):D682-9. Epub 2014 Nov 6.

Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris F-75005, France Inserm U1024, Paris F-75005, France CNRS, UMR 8197, Paris F-75005, France.

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http://dx.doi.org/10.1093/nar/gku1112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383929PMC
January 2015

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.

BMC Bioinformatics 2014 Aug 8;15:268. Epub 2014 Aug 8.

Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, 46 rue d'Ulm, 75005 Paris, France.

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http://dx.doi.org/10.1186/1471-2105-15-268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155083PMC
August 2014

TreeFam v9: a new website, more species and orthology-on-the-fly.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D922-5. Epub 2013 Nov 4.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkt1055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965059PMC
January 2014

The zebrafish reference genome sequence and its relationship to the human genome.

Authors:
Kerstin Howe Matthew D Clark Carlos F Torroja James Torrance Camille Berthelot Matthieu Muffato John E Collins Sean Humphray Karen McLaren Lucy Matthews Stuart McLaren Ian Sealy Mario Caccamo Carol Churcher Carol Scott Jeffrey C Barrett Romke Koch Gerd-Jörg Rauch Simon White William Chow Britt Kilian Leonor T Quintais José A Guerra-Assunção Yi Zhou Yong Gu Jennifer Yen Jan-Hinnerk Vogel Tina Eyre Seth Redmond Ruby Banerjee Jianxiang Chi Beiyuan Fu Elizabeth Langley Sean F Maguire Gavin K Laird David Lloyd Emma Kenyon Sarah Donaldson Harminder Sehra Jeff Almeida-King Jane Loveland Stephen Trevanion Matt Jones Mike Quail Dave Willey Adrienne Hunt John Burton Sarah Sims Kirsten McLay Bob Plumb Joy Davis Chris Clee Karen Oliver Richard Clark Clare Riddle David Elliot David Eliott Glen Threadgold Glenn Harden Darren Ware Sharmin Begum Beverley Mortimore Beverly Mortimer Giselle Kerry Paul Heath Benjamin Phillimore Alan Tracey Nicole Corby Matthew Dunn Christopher Johnson Jonathan Wood Susan Clark Sarah Pelan Guy Griffiths Michelle Smith Rebecca Glithero Philip Howden Nicholas Barker Christine Lloyd Christopher Stevens Joanna Harley Karen Holt Georgios Panagiotidis Jamieson Lovell Helen Beasley Carl Henderson Daria Gordon Katherine Auger Deborah Wright Joanna Collins Claire Raisen Lauren Dyer Kenric Leung Lauren Robertson Kirsty Ambridge Daniel Leongamornlert Sarah McGuire Ruth Gilderthorp Coline Griffiths Deepa Manthravadi Sarah Nichol Gary Barker Siobhan Whitehead Michael Kay Jacqueline Brown Clare Murnane Emma Gray Matthew Humphries Neil Sycamore Darren Barker David Saunders Justene Wallis Anne Babbage Sian Hammond Maryam Mashreghi-Mohammadi Lucy Barr Sancha Martin Paul Wray Andrew Ellington Nicholas Matthews Matthew Ellwood Rebecca Woodmansey Graham Clark James D Cooper James Cooper Anthony Tromans Darren Grafham Carl Skuce Richard Pandian Robert Andrews Elliot Harrison Andrew Kimberley Jane Garnett Nigel Fosker Rebekah Hall Patrick Garner Daniel Kelly Christine Bird Sophie Palmer Ines Gehring Andrea Berger Christopher M Dooley Zübeyde Ersan-Ürün Cigdem Eser Horst Geiger Maria Geisler Lena Karotki Anette Kirn Judith Konantz Martina Konantz Martina Oberländer Silke Rudolph-Geiger Mathias Teucke Christa Lanz Günter Raddatz Kazutoyo Osoegawa Baoli Zhu Amanda Rapp Sara Widaa Cordelia Langford Fengtang Yang Stephan C Schuster Nigel P Carter Jennifer Harrow Zemin Ning Javier Herrero Steve M J Searle Anton Enright Robert Geisler Ronald H A Plasterk Charles Lee Monte Westerfield Pieter J de Jong Leonard I Zon John H Postlethwait Christiane Nüsslein-Volhard Tim J P Hubbard Hugues Roest Crollius Jane Rogers Derek L Stemple

Nature 2013 Apr 17;496(7446):498-503. Epub 2013 Apr 17.

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

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http://dx.doi.org/10.1038/nature12111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703927PMC
April 2013

Genomicus: five genome browsers for comparative genomics in eukaryota.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D700-5. Epub 2012 Nov 27.

Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, France.

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http://dx.doi.org/10.1093/nar/gks1156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531091PMC
January 2013

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes.

Bioinformatics 2010 Apr 24;26(8):1119-21. Epub 2010 Feb 24.

Dyogen Group, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Santé et de la Recherche Médicale U1024, 75005 Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btq079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686PMC
April 2010

Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time.

Bioessays 2008 Feb;30(2):122-34

Ecole Normale Supérieure, Dyogen Group, Paris, France.

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http://dx.doi.org/10.1002/bies.20707DOI Listing
February 2008