Thomas Faraut

127

Documents

Publications

	Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets Jeanlin Jourdain , Harmonie Barasc , Thomas Faraut , Anne Calgaro , Nathalie Bonnet Genome Research, 2023, 33 (6), pp.957-971. ⟨10.1101/gr.277787.123⟩ Article dans une revue hal-04170739v1
	Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions Isaäc J Nijman , Benjamin D Rosen , Philippe Bardou , Thomas Faraut , Tristan Cumer Molecular Ecology, 2022, 17 p. ⟨10.1111/mec.16579⟩ Article dans une revue hal-03722180v1
	Unraveling the history of the genus Gallus through whole genome sequencing Mahendra Mariadassou , Marie Suez , Sanbadam Sathyakumar , Alain Vignal , Mariangela Arca Molecular Phylogenetics and Evolution, 2021, 158, pp.107044. ⟨10.1016/j.ympev.2020.107044⟩ Article dans une revue hal-03155990v1
	Correlation networks provide new insights into the architecture of testicular steroid pathways in pigs Annie Robic , Thomas Faraut , Katia Feve , Sarah Djebali , Armelle Prunier Genes, 2021, 12 (4), pp.1-19. ⟨10.3390/genes12040551⟩ Article dans une revue hal-03222223v1
	Comparative analysis of the circular transcriptome in muscle, liver, and testis in three livestock species Annie Robic , Chloé Cerutti , Christa Kühn , Thomas Faraut Frontiers in Genetics, 2021, 12, ⟨10.3389/fgene.2021.665153⟩ Article dans une revue hal-03264869v1
	VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity Laure Denoyelle , Estelle Talouarn , Philippe Bardou , Licia Colli , Adriana Alberti Genetics Selection Evolution, 2021, 53 (1), 14 p. ⟨10.1186/s12711-021-00659-6⟩ Article dans une revue hal-03480970v1
	Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs Annie Robic , Thomas Faraut , Sarah Djebali , Rosemarie Weikard , Katia Feve RNA Biology, 2019, 16, pp.1-15. ⟨10.1080/15476286.2019.1621621⟩ Article dans une revue hal-02622408v1
	Multi-species annotation of transcriptome and chromatin structure in domesticated animals Sylvain Foissac , Sarah Djebali , Kylie Munyard , Nathalie Vialaneix , Andrea Rau BMC Biology, 2019, 17 (1), 25 p. ⟨10.1186/s12915-019-0726-5⟩ Article dans une revue hal-02437599v1
	Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing Katia Feve , Sylvain Foissac , Alain Pinton , Florence Mompart , Diane Esquerré PLoS ONE, 2017, 12 (11), Non paginé. ⟨10.1371/journal.pone.0187617⟩ Article dans une revue hal-02622330v1
	Accounting for Linkage Disequilibrium in genome scans for selection without individual genotypes: the local score approach Maria Inès Fariello Rico , Simon Boitard , Sabine Mercier , David Robelin , Thomas Faraut Molecular Ecology, 2017, 26 (14), pp.3700-3714. ⟨10.1111/mec.14141⟩ Article dans une revue hal-01607837v1
	The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution Hélène Badouin , Jerome Gouzy , Christopher Grassa , Florent Murat , S Evan Staton Nature, 2017, 546 (7656), pp.148-152. ⟨10.1038/nature22380⟩ Article dans une revue hal-01603287v1
	Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds Magali San Cristobal , Florian Rohart , Christine Lascor , Marcel Bouffaud , Lidwine Trouilh BMC Genomics, 2015, 16, Non paginé. ⟨10.1186/s12864-015-2259-9⟩ Article dans une revue hal-01245970v1
	The sheep genome illuminates biology of the rumen and lipid metabolism Yu Jiang , Min Xie , Wenbin Chen , Richard Talbot , Jillian F. Maddox Science, 2014, 344 (6188), pp.1168-1173. ⟨10.1126/science.1252806⟩ Article dans une revue hal-02635391v1
	Pathways and genes involved in steroid hormone metabolism in male pigs Annie Robic , Thomas Faraut , Armelle Prunier Journal of Steroid Biochemistry and Molecular Biology, 2014, 140, pp.44-55. ⟨10.1016/j.jsbmb.2013.11.001⟩ Article dans une revue hal-01210569v1
	Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011 Erika Sallet , Brice Roux , Laurent Sauviac , M.-F. Jardinaud , S. Carrere DNA Research, 2013, 20 (4), pp.339-353. ⟨10.1093/dnares/dst014⟩ Article dans une revue hal-03082947v1
	The duck genome and transcriptome provide insight into an avian influenza virus reservoir species Yinhua Huang , Yingrui Li , David W Burt , Hualan Chen , Yong Zhang Nature Genetics, 2013, 45 (7), pp.776-783. ⟨10.1038/ng.2657⟩ Article dans une revue hal-02652041v1
	Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus) Yang Dong , Min Xie , Yu Jiang , Nianqing Xiao , Xiaoyong Du Nature Biotechnology, 2013, 31 (2), pp.135-141. ⟨10.1038/nbt.2478⟩ Article dans une revue hal-02651460v1
	Génomique des canards Alain Vignal , Christian Diot , Caroline Molette , Thomas Faraut , Man Rao INRA Productions Animales, 2013, 26 (5), pp.391-402 Article dans une revue hal-01207754v1
	Detecting long tandem duplications in genomic sequences Eric Audemard , Thomas Schiex , Thomas Faraut BMC Bioinformatics, 2012, 13, online (may), Non paginé. ⟨10.1186/1471-2105-13-83⟩ Article dans une revue hal-02650334v1
	High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly Bertrand Servin , Thomas Faraut , Nathalie N. Iannuccelli , Diana Zelenika , Denis Milan BMC Genomics, 2012, 13, online (november), Non paginé. ⟨10.1186/1471-2164-13-585⟩ Article dans une revue hal-02644217v1
	Analyses of pig genomes provide insight into porcine demography and evolution Martien A. M. Groenen , Alan L. Archibald , Hirohide Uenishi , Christopher K. Tuggle , Yasuhiro Takeuchi Nature, 2012, 491 (7426), pp.393-398. ⟨10.1038/nature11622⟩ Article dans une revue cea-00880676v1
	A duck RH panel and its potential for assisting NGS genome assembly Man Rao , Mireille Morisson , Thomas Faraut , Suzanne Bardes , Katia K. Feve BMC Genomics, 2012, 13 (september), Non paginé. ⟨10.1186/1471-2164-13-513⟩ Article dans une revue hal-02646793v1
	Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism. Laurence Liaubet , Valérie Lobjois , Thomas Faraut , Aurélie Tircazes , Francis Benne BMC Genomics, 2011, 12 (november), pp.548. ⟨10.1186/1471-2164-12-548⟩ Article dans une revue hal-00842687v1
	Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Michael Abrouk , Florent Murat , Caroline Pont , Joachim Messing , Scott Jackson Trends in Plant Science, 2010, 15 (9), pp.479-87. ⟨10.1016/j.tplants.2010.06.001⟩ Article dans une revue hal-00681093v1
	Is there a leptin gene in the chicken genome? Lessons from phylogenetics, bioinformatics and genomics Frederique Pitel , Thomas Faraut , Gilles Bruneau , Philippe Monget General and Comparative Endocrinology, 2010, 167 (1), pp.1-5. ⟨10.1016/j.ygcen.2009.10.006⟩ Article dans une revue hal-01129469v1
	The sheep genome reference sequence: a work in progress . The International Sheep Genomics Consortium , A.L. Archibald , N.E. Cockett , B.P. Dalrymple , Thomas Faraut Animal Genetics, 2010, 41 (5), pp.449-453. ⟨10.1111/j.1365-2052.2010.02100.x⟩ Article dans une revue hal-02668022v1
	Statistical confidence measures for genome maps: application to the validation of genome assemblies Bertrand Servin , Simon de Givry , Thomas Faraut Bioinformatics, 2010, 26 (24), pp.3035-3042. ⟨10.1093/bioinformatics/btq598⟩ Article dans une revue hal-02665786v1
	Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals Jerome J. Salse , Michaël M. Abrouk , Stéphanie S. Bolot , Nicolas N. Guilhot , Emmanuel E. Courcelle Proceedings of the National Academy of Sciences of the United States of America, 2009, 106 (35), pp.14908-14913. ⟨10.1073/pnas.0902350106⟩ Article dans une revue hal-00964188v1
	Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals. Thomas Faraut , Simon de Givry , Christophe Hitte , Yvette Lahbib Mansais , Mireille Morisson Cytogenetic and Genome Research, 2009, 126 (1-2), pp.21-33. ⟨10.1159/000245904⟩ Article dans une revue inserm-00442389v1
	The carnitine acetyltransferase gene (CRAT): a characterization of porcine transcripts with insights into the 5'-end variants of mammalian transcripts and their possible sub-cellular localization Annie Robic , Thomas Faraut , Laurence Liaubet , Denis Milan Cellular and Molecular Biology Letters, 2009, 14 (1), pp.90-99. ⟨10.2478/s11658-008-0036-3⟩ Article dans une revue hal-02663909v1
	Narcisse: a mirror view of conserved syntenies Emmanuel E. Courcelle , Yoann Beausse , Sébastien Letort , Olivier Stahl , Julien Fremez Nucleic Acids Research, 2008, 36 (1), pp.D485-D490. ⟨10.1093/nar/gkm805⟩ Article dans une revue hal-02656575v1
	Addressing chromosome evolution in the whole-genome sequence era. Thomas Faraut Chromosome Research, 2008, 16, pp.5-16 Article dans une revue hal-02653333v1
	Characterization of porcine ASB6 gene and transcripts - Comparison of mammalian transcripts Annie Robic , Thomas Faraut , Laurence Liaubet , Juliette Riquet , Denis Milan Animal Biotechnology, 2008, 19, pp.138-143 Article dans une revue hal-02657001v1
	Phylogenetic exploration of bacterial genomic rearrangements. Romain Fremez , Thomas Faraut , Gwennaële Fichant , Jerome Gouzy , Y. Quentin Bioinformatics, 2007, 23, pp.1172-1174 Article dans une revue hal-02653698v1
	Genetic and haplotypic structure in 14 European and African cattle breeds Mathieu M. Gautier , Thomas Faraut , Katayoun Moazami-Goudarzi , Vincent Navratil , Mario Foglio Genetics, 2007, 177, pp.1059-1070 Article dans une revue hal-02660515v1
	Vers une carte comparée des génomes homme / porc hautement résolutive Yvette Lahbib Mansais , Denis Milan , Thomas Faraut , Martine M. Yerle Biofutur, 2007, 26, pp.39-43 Article dans une revue hal-02662738v1
	Alvira: comparative genomics of viral strains. François Enault , Romain Fremez , Eric Baranowski , Thomas Faraut Bioinformatics, 2007, 23, pp.2178-2179 Article dans une revue hal-02654862v1
	A comparative genome approach to marker ordering Thomas Faraut , Simon de Givry , Patrick P. Chabrier , Thomas Derrien , Francis Galibert Bioinformatics, 2007, 23 (2), pp.E50-E56. ⟨10.1093/bioinformatics/btl321⟩ Article dans une revue hal-02667668v1
	Alvira: comparative genomics of viral strains. François Enault , Romain Fremez , Eric Baranowski , Thomas Faraut Bioinformatics, 2007, 23 (16), pp.2178-9. ⟨10.1093/bioinformatics/btm293⟩ Article dans une revue hal-00535599v1
	Evolutionary breakpoints through a high-resolution comparative map between porcine chromosomes 2 and 16 and human chromosomes Yvette Lahbib Mansais , Florence Mompart , Denis Milan , Sophie S. Leroux , Thomas Faraut Genomics, 2006, 88, pp.504-512 Article dans une revue hal-02656467v1
	The rat Toxo1 locus directs toxoplasmosis outcome and controls parasite proliferation and spreading by macrophage-dependent mechanisms. Pierre Cavaillès , Véronique Sergent , Cordelia Bisanz , Olivier Papapietro , Céline Colacios Proceedings of the National Academy of Sciences of the United States of America, 2006, 103 (3), pp.744-9. ⟨10.1073/pnas.0506643103⟩ Article dans une revue hal-00171244v1
	Comparative mapping of genomes. Thomas Faraut Biofutur, 2005, 37, pp.40 Article dans une revue hal-02672330v1
	A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints Yvette Lahbib Mansais , P. Karlskov-Mortensen , Florence Mompart , Denis Milan , C.B. Jorgensen Genomics, 2005, 86, pp.405-413 Article dans une revue hal-02670629v1
	A gene-based radiation hybrid map of chicken microchromosome 14 : comparison to human and alignment to the assembled chicken sequence Mireille Morisson , Sophie S. Leroux , Carine Jiguet-Jiglaire , Sirine Assaf , Frederique Pitel Genetics Selection Evolution, 2005, 37, pp.229-251. ⟨10.1051/gse:2004046⟩ Article dans une revue hal-02670446v1
	Comparison of male and female meiotic segregation patterns in translocation heterozygotes : a case study in an animal model (Sus scrofa domestica L.) Alain Pinton , Thomas Faraut , Martine M. Yerle , Joseph Gruand , F. Pellestor Human Reproduction, 2005, 20, pp.2476-2482 Article dans une revue hal-02674136v1
	A dense comparative gene map between human chromosome 19q13.3 -> q13.4 and a homologous segment of swine chromosome 6. N. Bosak , R. Yamomoto , S. Fujisaki , Thomas Faraut , S. Kiuchi Cytogenetic and Genome Research, 2005, 108, pp.317-321 Article dans une revue hal-02678722v1
	Human cytomegalovirus carries a cell-derived phospholipase A2 required for infectivity. C. Allal , C. Buisson-Brenac , V. Marion , C. Claudel-Renard , Thomas Faraut Journal of Virology, 2004, 78, pp.7717-7726 Article dans une revue hal-02674890v1
	The cyclic genetic code as a constraint satisfaction problem. G. Weil , K. Heus , Thomas Faraut , J. Demongeot Theoretical Computer Science, 2004, 322, pp.313-334 Article dans une revue hal-02673209v1
	Male and female segregation profiles in two reciprocal translocations t(12 ; 14)(q13 ; q21) t(3 ; 15)(q27 ; q13) in the pig species Alain Pinton , A. Ducos , Martine M. Yerle , Thomas Faraut , F. Pellestor Fertility and Sterility, 2004, 82 (Suppl. 2), pp.S272 Article dans une revue hal-02674861v1
	RH mapping in pig to study evolutionary breakpoints between HSA7 and SSC3, 9 and 18 Florence Mompart , Yvette Lahbib Mansais , Thomas Faraut , Denis Milan , Martine M. Yerle Cytogenetic and Genome Research, 2004, 106, pp.18 Article dans une revue hal-02670370v1
	Development of a gene-based radiation hybrid map of chicken Chromosome 7 and comparison to human and mouse. Mireille Morisson , C. Jiguet-Jiglaire , Sophie S. Leroux , Thomas Faraut , Suzanne Bardes Mammalian Genome, 2004, 15, pp.732-739 Article dans une revue hal-02673764v1
	Male and female segregation profiles in two reciprocal translocations t(12;14)(q13;q21) and t(3;15)(q27;q13) in pig Alain Pinton , A. Ducos , Martine M. Yerle , Thomas Faraut , F. Pellestor Cytogenetic and Genome Research, 2004, 106, pp.14-15 Article dans une revue hal-02671512v1
	The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. C. Müller , M. Denis , Laurent Gentzbittel , Thomas Faraut Nucleic Acids Research, 2004, 32, pp.W429-W434 Article dans une revue hal-02675844v1
	A comparative porcine-human RH map for SSC2 focusing on synteny breakpoints with human Yvette Lahbib Mansais , Florence Mompart , Thomas Faraut , Denis Milan , Martine M. Yerle Cytogenetic and Genome Research, 2004, 106, pp.11 Article dans une revue hal-02669950v1
	A comparative porcine-human RH map for SSC2 focusing on synteny breakpoints with human Yvette Lahbib Mansais , Florence Mompart , Thomas Faraut , Denis Milan , Martine M. Yerle Cytogenetic and Genome Research, 2004, 106, pp.11-11 Article dans une revue hal-02673120v1
	Rearranged gene order between pig and human in a QTL region on SSC 7 Olivier O. Demeure , Christine Renard , Martine M. Yerle , Thomas Faraut , Juliette Riquet Mammalian Genome, 2003, 14, pp.71-80. ⟨10.1007/s00335-002-3034-1⟩ Article dans une revue hal-02679052v1
	A radiation hybrid panel and its use in developing a gene map of the chicken Mireille Morisson , C. Jiguet-Jiglaire , Alexis Lemiere , Sophie S. Leroux , Thomas Faraut British Poultry Science, 2003, 44, pp.797-798 Article dans une revue hal-02674651v1
	A new contribution to the integration of human and porcine genome maps: 623 new points of homology Annie Robic , Thomas Faraut , Nathalie N. Iannuccelli , Yvette Lahbib Mansais , V. Cantegrel Cytogenetic and Genome Research, 2003, 102, pp.100-108 Article dans une revue hal-02671887v1
	Construction of a high-resolution comparative gene map between swine chromosome region 6q11 -> q21 and human chromosome 19 q-arm by RH mapping of 51 genes. N. Bosak , Thomas Faraut , S. Mikawa , H. Uenishi , S. Kiuchi Cytogenetic and Genome Research, 2003, 102, pp.109-115 Article dans une revue hal-02676236v1
	Enzyme-specific profiles for genome annotation: PRIAM. C. Claudel-Renard , Claude C. Chevalet , Thomas Faraut , D. Kahn Nucleic Acids Research, 2003, 31, pp.6633-6639 Article dans une revue hal-02676567v1
	A chicken radiation hybrid panel and its use for mapping Mireille Morisson , Thomas Faraut , Martine M. Yerle , Alain Vignal Archiv für Geflügelkunde. Sonderheft, 2002, Special Issue, pp.35 Article dans une revue hal-02675399v1
	Cooperation of selection and meiotic mechanisms in the production of imbalances in reciprocal translocations. Thomas Faraut , M.A. Mermet , J. Demongeot , O. Cohen Cytogenetics and Cell Genetics, 2000, 88, pp.15-21 Article dans une revue hal-02694908v1

	Improvement of the Bos taurus Genome Assembly using New Sequencing Technologies Camille Eché , Carole Iampietro , Clement Birbes , Andreea Dreau , Claire Kuchly Discoveries Roadshow 2023 - PacBio, PacBio, May 2023, Paris, France Communication dans un congrès hal-04096124v1
	Sex differences in recombination maps are associated with differential hotspot usage in sheep Héléna Vassilief , Mohamed Id Bella , Flavie Tortereau , Dominique Hazard , Thomas Faraut World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands. pp.861-864, ⟨10.3920/978-90-8686-940-4_202⟩ Communication dans un congrès hal-04065264v1
	Variations de structure et longues lectures Thomas Faraut Colloque INRAE Genomics, INRAE Genomics, May 2022, Orléans, France Communication dans un congrès hal-04220082v1
	Y-chromosomal haplotypes in domestic and wild goats reveal ancient paternal bottlenecks and recent introgressions Vargoats Consortium , Isaäc J Nijman , Benjamin D Rosen , Thomas Faraut , Philippe Bardou ISGC and IGGC Virtual Meeting, Jun 2021, Toulouse-Dunedin, France Communication dans un congrès hal-03817722v1
	The lariat-derived circRNA from ATXN2L: an outstanding circRNA in pigs Annie Robic , Thomas Faraut , Chloé Cerutti , Julie Demars , Christa Kühn EMBO \| EMBL Symposium: The Non-Coding Genome, Oct 2021, virtual, Germany Communication dans un congrès hal-03445759v1
	Circular RNAs detection and cross-species conservation Chloé Cerutti , Annie Robic , Thomas Faraut JOBIM 2020 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2020, virtual meeting, France Communication dans un congrès hal-03703612v1
	Pig transcriptome analysis suggests a global regulation mechanism enabling temporary bursts of circular RNAs Annie Robic , Katia Feve , Thomas Faraut , Sarah Djebali , R. Weikard 37. International Society for Animal Genetics Conference (ISAG), Jul 2019, Lleida, Spain Communication dans un congrès hal-02788077v1
	Chromatin accessibility conservation across four livestock species Sarah Djebali Quelen , Sylvain Foissac , Nathalie Vialaneix , Kylie Munyard , Andrea Rau Conference of the International Society for Animal Genetics (ISAG 2019), Jul 2019, Llieda, Spain Communication dans un congrès hal-02788732v1
	Meiotic and gene expression analyses in a case of t(1;15) azoospermic boar Alain Pinton , Anne Calgaro , Nicolas Mary , Harmonie Barasc , Nathalie Bonnet 23. International Colloquium on Animal Cytogenetics and Genomics (23 ICACG), Jun 2018, Saint-Pétersburg, Russia. 360 p Communication dans un congrès hal-02737986v1
	VarGoats: first results of an international 1000-genome project Gwenola Tosser-Klopp , Philippe Bardou , Laure Denoyelle , Thomas Faraut , Francois Pompanon International Symposium on Environmental and Agronomical Genomics, Nov 2018, Paris, France Communication dans un congrès hal-02785613v1
	Vers une meilleure compréhension des fonctions & des interactions des ARN circulaires Annie Robic , Sarah Djebali Quelen , Thomas Faraut Journées Scientifiques du Département Génétique Animale - La Génétique Animale et les Interactions, Oct 2018, Dienné, France Communication dans un congrès hal-02785651v1
	The analysis of sheep and goat genomes reveals new biological mechanisms explaining the variation of Mendelian and complex phenotypes Gwenola Tosser-Klopp , Julie Demars , Laurence Drouilhet , Stéphane Fabre , Thomas Faraut Séminaire mensuel (CRAG), Nov 2018, Barcelone, Spain Communication dans un congrès hal-02785242v1
	Effects of balanced chromosome translocations on boar fertility and cell reprogramming Annabelle Congras , Harmonie Barasc , Valentine Marquet , Kamila Canale-Tabet , Emeline Lhuillier 22. International Colloquium on Animal Cytogenetics and Genomics (ICACG), Jul 2016, Toulouse, France. 116p Communication dans un congrès hal-02738753v1
	Genome structural variability in the light of NGS Thomas Faraut 22. International Colloquium on Animal Cytogenetics and Genomics (ICACG), Jul 2016, Toulouse, France. 116 p Communication dans un congrès hal-01602943v1
	De novo Assembly of the Chinese Bamboo-Partridge Genome and Comparison with Chicken Gabriel Rognon , Diane Esquerre , Sylvain Foissac , Alain Vignal , Jean-Luc Coville Plant and Animal Genome (PAG), Jan 2015, San Diego, United States Communication dans un congrès hal-01194054v1
	Improving the Pig Genome Assembly with Mate-Pair Sequencing Sylvain Foissac , Diane D. Esquerre , Katia K. Feve , Juliette Riquet , Thomas Faraut Plant and Animal Genome (PAG), Jan 2014, San Diego, United States Communication dans un congrès hal-02739253v1
	Numerous interchromosomal rearrangements in spite of high synteny conservation between duck and chicken Valerie Fillon , Man Rao , Thomas Faraut , Daren Griffin , Mireille Morisson 21. International Colloquium on Animal Cytogenetics and Gene Mapping, Jun 2014, Ischia, Italy Communication dans un congrès hal-02793231v1
	Local score based method on pool-sequenced behaviour-divergent quail lines precisely detected selection signatures related to autism Simon S. Boitard , Maria Inès M. I. Fariello Rico , Sabine Mercier , David Robelin , Thomas Faraut 35. Colloque du Petit Pois Déridé, Aug 2013, Marseille, France Communication dans un congrès hal-02810860v1
	Detection de SNP chez la caille : production d'un outil commum pour des programmes scientifiques multiples Sophie Leroux , Patrice Dehais , Alain Vignal , Olivier Bouchez , Thomas Faraut 10. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, Institut Technique de l'Aviculture et des Elevages de Petits Animaux (ITAVI). Nouzilly, FRA. Institut National de la Recherche Agronomique (INRA). Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), FRA., Mar 2013, La Rochelle, France Communication dans un congrès hal-01190264v1
	Mapping by RH sequencing: organizing NGS scaffolds into chromosomes Man Rao , Mireille Morisson , Valerie Fillon , Sophie S. Leroux , Emeline Lhuillier 21. P!ant and animal genome meeting (PAG XXI), Jan 2013, San Diego, Californie, United States Communication dans un congrès hal-02749835v1
	Goat genome assembly, availability of an international 50K SNP chip and RH panel: an update of the international goat genome consortium projects Gwenola Tosser-Klopp , Cédric Cabau , Andre Eggen , Thomas Faraut , Henri Heuven 20. Conference of the Plant & Animal Genome, Plant & Animal Genome (PAG). USA., Jan 2012, San Diego, United States. 28 diapositives Communication dans un congrès hal-01019243v1
	Towards a high density SNP International Goat Chip Gwenola Tosser-Klopp , Abdullah Johari Jiken , Philippe Bardou , Cédric Cabau , Patrice Dehais Plant and Animal Genome, Jan 2011, San Diégo, United States Communication dans un congrès hal-01194170v1
	Modelling RH maps uncertainty and application to the validation of whole genome assemblies. Bertrand Servin , Sebastien Givry , Thomas Faraut 9th World Congress on Genetics Applied to Livestock Production, 2010, Leipzig, pp.Inconnu Communication dans un congrès hal-02813656v1
	Détection de régions génomiques homologues par un algorithme de flots avec coûts Eric Audemard , Thomas Faraut , Thomas Schiex Congrès ROADEF'2010, Société Française de Recherche Opérationnelle et d'Aide à la Décision (SFROAD). FRA., Feb 2010, Toulouse, France. 2 p Communication dans un congrès hal-02752130v1
	Utilisation dune puce 60 000 SNP pour cartographier finement des QTL affectant des caractères de production, de résistance aux maladies et de comportement chez les ovins Carole Moreno-Romieux Moreno , Bertrand Servin , Thomas Faraut , Christophe C. Klopp , Rachel Rupp 16. Rencontres autour des Recherches sur les Ruminants, Dec 2009, Paris, France Communication dans un congrès hal-02755058v1
	D'Iccare à Narcisse, une promenade parmi les mythes de la bioinformatique animale. Thomas Faraut , E. Courcelle , Jerome Gouzy Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau Communication dans un congrès hal-02756487v1
	Deux exemples d'épissage alternatif (ASB6 et CRAT) pour montrer l'intérêt de l'étude de ce phénomène chez les espèces d'élevage Annie Robic , Thomas Faraut , Laurence Liaubet Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau Communication dans un congrès hal-02752629v1
	Modéliser l'incertitude des cartes d'hybrides irradiés : application à la validation d'assemblage de génomes complets. Bertrand Servin , Thomas Faraut , Sebastien Givry Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau Communication dans un congrès hal-02754669v1
	High resolution chicken radiation hybrid maps using the IlluminaTM technology. Alain Vignal , Caroline Hourcade , Thomas Faraut , Sophie S. Leroux , Marine M. Douaud 31st Conference of the International Society of Animal Genetics (ISAG), 2008, Amsterdam, pp.Inconnu Communication dans un congrès hal-02815790v1
	Présentation du projet ANR 2008 SheepSNPQTL : utilisation de la puce 60 000 SNP pour la cartographie fine de QTL chez les ovins. Carole Moreno-Romieux Moreno , Andres Legarra , David Robelin , Christèle Robert-Granié , Rachel Rupp Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau, France Communication dans un congrès hal-02813290v1
	ArcAnGe, annotating, representing and comparing animal genomes. Thomas Faraut , E. Courcelle , Jerome Gouzy Séminaire AGENAE, La Rochelle, Oct 2008, France, pp.Inconnu Communication dans un congrès hal-02815778v1
	A SNP detection project using one million reads from WGS libraries produced from one pig from seven different breeds. Patrice Dehais , Denis Milan , Thomas Faraut , C. Dossat , Patrick Wincker International Plant & Animal Genomes XV Conference, San Diego, 2007, California, France Communication dans un congrès hal-02751166v1
	Chromosomal rearrangements and comparative mapping. Thomas Faraut Séminaire Cytogénétique des plantes Clermont-Ferrand, Apr 2007, France, pp.Inconnu Communication dans un congrès hal-02811665v1
	High resolution mapping of evolutionary breakpoints in pigs Yvette Lahbib Mansais , Florence Mompart , Denis Milan , Thomas Faraut , Martine M. Yerle 17. European Colloquium on Animal Cytogenetics and Gene mapping, June 18-21, 2006, Lisbonne, Portugal Communication dans un congrès hal-02813597v1
	The rat Toxo1 locus directs toxoplasmosis outcome and controls parasite proliferation and spreading by macrophage-dependent mechanisms P. Cavaillès , V. Sergent , C. Bisanz , O. Papapietro , C. Colacios Inconnu, 2006, Inconnu Communication dans un congrès hal-02752628v1
	A comparative radiation hybrid map of SSC17 and human homologous chromosomes HSA 20, 8 and 4 Yvette Lahbib Mansais , M.P. Karlskov , Florence Mompart , Jan Gorodkin , Thomas Faraut 29. International Conference on International Society of Animla Genetics, Sep 2004, Tokyo, Japan Communication dans un congrès hal-02761544v1
	A comparative porcine-human RH map for SSC2 focusing on synteny breakpoints with human Yvette Lahbib Mansais , Florence Mompart , Thomas Faraut , Denis Milan , Martine M. Yerle 16. European Colloquium on Animal Cytogenetics and Gene Mapping, 2004, Jouy-en-Josas, France Communication dans un congrès hal-02826042v1
	RH mapping in pig to study evolutionary breakpoints between HSA7 and SSC3, 9 and 18 Florence Mompart , Yvette Lahbib Mansais , Thomas Faraut , Denis Milan , Martine M. Yerle 16. European Colloquium on Animal Cytogenetics and Gene Mapping, 2004, Jouy-en-Josas, France Communication dans un congrès hal-02827995v1
	Reciprocal translocations in pigs: frequency in the French populations and analysis of their consequences on reproduction abilities of carrier animals Alain Pinton , Martine M. Yerle , Thomas Faraut , F. Pellestor , H.M. Berland 11th Internnational Congress on Biotechnology in Animal Reproduction, Sep 2004, Rapotin, pp.Inconnu Communication dans un congrès hal-02827383v1
	Male and female segregation profiles in two reciprocal translocations t(12;14)(q13;q21) and t(3;15)(q27;q13) in pig Alain Pinton , A. Ducos , Martine M. Yerle , Thomas Faraut , F. Pellestor 16th European Colloquium on Animal Cytogenetics and Gene Mapping, 2004, Jouy-en-Josas, France Communication dans un congrès hal-02829792v1
	Male and female segregation profiles in two reciprocal translocations t(12;14)(q13;q21) and t(3;15)(q27;q13) in the pig species Alain Pinton , A. Ducos , Martine M. Yerle , Thomas Faraut , F. Pellestor 60th Annual Meeting of the American Society for Reproductive Medicine, Oct 2004, Philadelphia, pp.Inconnu Communication dans un congrès hal-02831758v1
	Un panel d'hybrides irradiés et son utilisation pour développer une carte des gènes de la poule Mireille Morisson , C. Jiguet-Jiglaire , Alexis Lemiere , Sophie S. Leroux , Thomas Faraut 5èmes Journées de la Recherche Avicole, 2003, Tours, France Communication dans un congrès hal-02761067v1
	A radiation hybrid panel and its use in developing a gene map of the chicken Mireille Morisson , C. Jiguet-Jiglaire , Alexis Lemiere , Sophie S. Leroux , Thomas Faraut 2003 Spring Meeting of the WPSA French Branch., 2003, Inconnu Communication dans un congrès hal-02826038v1
	Promises and lessons from complete genome sequences for comparative mapping. Thomas Faraut International Workshop on Major Genes and QTL in Sheep and Goat, 2003, Toulouse Communication dans un congrès hal-02760525v1
	Integration des cartes humaines et porcines : 623 nouveaux points d'homologie Annie Robic , Thomas Faraut , Nathalie N. Iannuccelli , Patrick Chardon , Denis Milan Colloque Génomique des animaux d'élevage, Seignosse-le-Penon, May 2003, Seignosse-le-Peignon Communication dans un congrès hal-02762328v1
	A chicken radiation hybrid panel and its use for mapping Mireille Morisson , Thomas Faraut , Martine M. Yerle , Alain Vignal 11th European Poultry Conference, Sep 2002, Bremen, Germany Communication dans un congrès hal-02825614v1

	Major contribution to the bovine pangenome: whole genome sequences, SNPs, and structural variants of 154 bulls from 14 breeds Amandine Suin , Camille Marcuzzo , Camille Eché , Andreea Dréau , Clément Birbes Plant and Genome San Diego 2024, Jan 2024, San Diego, United States Poster de conférence hal-04432840v1
	Combiner analyse d’association et génomique fonctionnelle pour la recherche de gènes candidats Sarah Djebali , Sophie Leroux , Katia Feve , Yann Labrune , Catherine Larzul Journées scientifiques Département Génétique animale, Sep 2022, Bordeaux, France Poster de conférence hal-03936070v1
	Rétrogènes et variation du nombre de copies chez les ruminants Carine Genet , Stéphane Fabre , Thomas Faraut Journées scientifiques Département Génétique Animale, Sep 2022, Bordeaux, France Poster de conférence hal-04225788v1
	Structural variants detection and de novo genome assembly of a maize line Carole Iampietro , Camille Eché , Clément Birbes , Arnaud Di Franco , Andreea Dréau Plant & Animal Genome Conference (PAG) 2022, Jan 2022, San Diego, United States Poster de conférence hal-03541379v1
	Quelques résultats du programme VarGoats : « 1000 génomes caprins » L Denoyelle , M Amills , Philippe Bardou , Maxime Ben Braiek , Thomas Faraut Journées Scientifiques du Département de Génétique Animale, Sep 2022, Bordeaux, France Poster de conférence hal-03812438v1
	De novo assembly of bovine genome using PacBio applications Camille Eché , Clément Birbes , Carole Iampietro , Andreea Dréau , Claire Kuchly SMRT Leiden 2021 – Young Investigator Virtual Conference, May 2021, virtuel, Netherlands Poster de conférence hal-03541224v1
	De novo assembling 19 maize inbred lines of the European germplasm Carole Iampietro , Camille Eché , Clement Birbes , Andreea Dreau , Erwan Denis 63rd Annual Maize Genetics Meeting, Mar 2021, virtuel, United States Poster de conférence hal-03539396v1
	Structural variants detection and de novo genome assembly of a Maize line Camille Eché , Clement Birbes , Carole Iampietro , Arnaud Di Franco , Andreea Dreau SMRT Leiden 2021 – Young Investigator Virtual Conference, May 2021, virtuel, Netherlands Poster de conférence hal-03541316v1
	The importance of annotations (reference genome and parent gene) for the study of circRNAs Annie Robic , Thomas Faraut , Chloé Cerutti , Julie Demars , Christa Kühn ISAG 2021- virtual conference of the International Society for Animal Genetics, Jul 2021, virtual, South Africa. Poster de conférence hal-03445792v1
	A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis Carole Iampietro , Camille Eché , Adrien Castinel , Rémy-Félix Serre , Christophe C. Klopp PAG XXVIII, Plant and Animal Genome, Jan 2020, San Diego, United States. 2020 Poster de conférence hal-02947690v1
	the ability to produce exonic circularRNA appears to be mainly linked to the genomic structure of genes Annie Robic , Sarah Djebali , Rosemarie Weikard , Christa Kuehn , Thomas Faraut RNAtoul 2019, Jun 2019, Toulouse, France. 2019 Poster de conférence hal-02788016v1
	Integrative analyses of chromosome conformation, chromatin accessibility and gene expression in human and livestock genomes Camille Mestre , Sarah Djebali Quelen , Thomas Faraut , Nathalie Vialaneix , Andrea Rau European Conference on Computational Biology (ECCB 2018), Sep 2018, Athènes, Greece. , 2018 Poster de conférence hal-02784857v1
	Présentation et premiers résultats du programme 1000 génomes caprins : VarGoats Philippe Bardou , Céline Bourdon , Laure Denoyelle , Thomas Faraut , Estelle Talouarn Journées Scientifiques du Département de Génétique Animale, Oct 2018, Dienné, France Poster de conférence hal-03817570v1
	Local Score Based Method On Pool-Sequenced Behavior-Divergent Quail Lines Precisely Detected Selection Signatures Related To Autism Maria Inès Fariello Rico , Simon Boitard , S. Mercier , David Robelin , Thomas Faraut 10. World Congress on Genetics Applied to Livestock Production (WCGALP), Aug 2014, Vancouver, Canada. American Society of Animal Science, 2014, 10th Word Congress on Genetics Applied to Livestock Production Poster de conférence hal-01194042v1
	Local Score Based Method On Pool-Sequenced Behavior-Divergent Quail Lines Precisely Detected Selection Signatures Related To Autism Maria Inès Fariello Rico , Cécile Arnould , Simon Boitard , Patrice Dehais , Thomas Faraut Journée Régionale de Bioinformatique et Biostatistique, Génopole Toulouse, Jun 2014, Toulouse, France. 2014 Poster de conférence hal-01194044v1
	Evaluation of the porcine Sscrofa10.2 assembly and associated annotations. Annie Robic , Laurence Liaubet , Agnès Bonnet , Thomas Faraut 25. International Conference Genetic Days, Sep 2012, Wroclaw, Poland. 2012 Poster de conférence hal-02804016v1

	RH mapping by sequencing: chromosome-scale assembly of the duck genome Man Rao , Alain Vignal , Mireille Morisson , Valérie Fillon , Sophie Leroux 2019 Pré-publication, Document de travail hal-02955250v1
	A new local score based method applied to behavior-divergent quail lines sequenced in pools precisely detects selection signatures on genes related to autism Maria Inès Fariello Rico , Simon Boitard , Sabine Mercier , David Robelin , Thomas Faraut 2015 Pré-publication, Document de travail hal-01194146v1

	Comparaison et visualisation de graphes de pangénomes Siegfried Dubois , Claire Lemaitre , Thomas Faraut , Matthias Zytnicki Université de rennes. 2023, pp.1-38 Rapport hal-04213245v1

Thomas Faraut

Publications

Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets

Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Unraveling the history of the genus Gallus through whole genome sequencing

Correlation networks provide new insights into the architecture of testicular steroid pathways in pigs

Comparative analysis of the circular transcriptome in muscle, liver, and testis in three livestock species

VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing

Accounting for Linkage Disequilibrium in genome scans for selection without individual genotypes: the local score approach

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds

The sheep genome illuminates biology of the rumen and lipid metabolism

Pathways and genes involved in steroid hormone metabolism in male pigs

Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Génomique des canards

Detecting long tandem duplications in genomic sequences

High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

Analyses of pig genomes provide insight into porcine demography and evolution

A duck RH panel and its potential for assisting NGS genome assembly

Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism.

Palaeogenomics of plants: synteny-based modelling of extinct ancestors.

Is there a leptin gene in the chicken genome? Lessons from phylogenetics, bioinformatics and genomics

The sheep genome reference sequence: a work in progress

Statistical confidence measures for genome maps: application to the validation of genome assemblies

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals.

The carnitine acetyltransferase gene (CRAT): a characterization of porcine transcripts with insights into the 5'-end variants of mammalian transcripts and their possible sub-cellular localization

Narcisse: a mirror view of conserved syntenies

Addressing chromosome evolution in the whole-genome sequence era.

Characterization of porcine ASB6 gene and transcripts - Comparison of mammalian transcripts

Phylogenetic exploration of bacterial genomic rearrangements.

Genetic and haplotypic structure in 14 European and African cattle breeds

Vers une carte comparée des génomes homme / porc hautement résolutive

Alvira: comparative genomics of viral strains.

A comparative genome approach to marker ordering

Alvira: comparative genomics of viral strains.

Evolutionary breakpoints through a high-resolution comparative map between porcine chromosomes 2 and 16 and human chromosomes

The rat Toxo1 locus directs toxoplasmosis outcome and controls parasite proliferation and spreading by macrophage-dependent mechanisms.

Comparative mapping of genomes.

A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints

A gene-based radiation hybrid map of chicken microchromosome 14 : comparison to human and alignment to the assembled chicken sequence

Comparison of male and female meiotic segregation patterns in translocation heterozygotes : a case study in an animal model (Sus scrofa domestica L.)

A dense comparative gene map between human chromosome 19q13.3 -> q13.4 and a homologous segment of swine chromosome 6.

Human cytomegalovirus carries a cell-derived phospholipase A2 required for infectivity.

The cyclic genetic code as a constraint satisfaction problem.

Male and female segregation profiles in two reciprocal translocations t(12 ; 14)(q13 ; q21) t(3 ; 15)(q27 ; q13) in the pig species

RH mapping in pig to study evolutionary breakpoints between HSA7 and SSC3, 9 and 18

Development of a gene-based radiation hybrid map of chicken Chromosome 7 and comparison to human and mouse.

Male and female segregation profiles in two reciprocal translocations t(12;14)(q13;q21) and t(3;15)(q27;q13) in pig

The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species.

A comparative porcine-human RH map for SSC2 focusing on synteny breakpoints with human

A comparative porcine-human RH map for SSC2 focusing on synteny breakpoints with human

Rearranged gene order between pig and human in a QTL region on SSC 7

A radiation hybrid panel and its use in developing a gene map of the chicken

A new contribution to the integration of human and porcine genome maps: 623 new points of homology

Construction of a high-resolution comparative gene map between swine chromosome region 6q11 -> q21 and human chromosome 19 q-arm by RH mapping of 51 genes.

Enzyme-specific profiles for genome annotation: PRIAM.

A chicken radiation hybrid panel and its use for mapping

Cooperation of selection and meiotic mechanisms in the production of imbalances in reciprocal translocations.

Improvement of the Bos taurus Genome Assembly using New Sequencing Technologies

Sex differences in recombination maps are associated with differential hotspot usage in sheep

Variations de structure et longues lectures

Y-chromosomal haplotypes in domestic and wild goats reveal ancient paternal bottlenecks and recent introgressions

The lariat-derived circRNA from ATXN2L: an outstanding circRNA in pigs

Circular RNAs detection and cross-species conservation

Pig transcriptome analysis suggests a global regulation mechanism enabling temporary bursts of circular RNAs

Chromatin accessibility conservation across four livestock species

Meiotic and gene expression analyses in a case of t(1;15) azoospermic boar

VarGoats: first results of an international 1000-genome project

Vers une meilleure compréhension des fonctions & des interactions des ARN circulaires

The analysis of sheep and goat genomes reveals new biological mechanisms explaining the variation of Mendelian and complex phenotypes

Effects of balanced chromosome translocations on boar fertility and cell reprogramming

Genome structural variability in the light of NGS

De novo Assembly of the Chinese Bamboo-Partridge Genome and Comparison with Chicken

Improving the Pig Genome Assembly with Mate-Pair Sequencing