Thomas Faraut

138
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Publications

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A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats

Marie Verneret , Caroline Leroux , Thomas Faraut , Vincent Navratil , Emmanuelle Lerat et al.
Mobile DNA, 2025, 16 (1), pp.4. ⟨10.1186/s13100-024-00337-6⟩
Article dans une revue hal-04963611 v1
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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 et al.
Genome Research, 2023, 33 (6), pp.957-971. ⟨10.1101/gr.277787.123⟩
Article dans une revue hal-04170739 v1
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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 et al.
Molecular Ecology, 2022, 17 p. ⟨10.1111/mec.16579⟩
Article dans une revue hal-03722180 v1
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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 et al.
Genetics Selection Evolution, 2021, 53 (1), 14 p. ⟨10.1186/s12711-021-00659-6⟩
Article dans une revue hal-03480970 v1
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Correlation networks provide new insights into the architecture of testicular steroid pathways in pigs

Annie Robic , Thomas Faraut , Katia Feve , Sarah Djebali , Armelle Prunier et al.
Genes, 2021, 12 (4), pp.1-19. ⟨10.3390/genes12040551⟩
Article dans une revue hal-03222223 v1
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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-03264869 v1
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Unraveling the history of the genus Gallus through whole genome sequencing

Mahendra Mariadassou , Marie Suez , Sanbadam Sathyakumar , Alain Vignal , Mariangela Arca et al.
Molecular Phylogenetics and Evolution, 2021, 158, pp.107044. ⟨10.1016/j.ympev.2020.107044⟩
Article dans une revue hal-03155990 v1

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 et al.
RNA Biology, 2019, 16, pp.1-15. ⟨10.1080/15476286.2019.1621621⟩
Article dans une revue hal-02622408 v1
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Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Sylvain Foissac , Sarah Djebali , Kylie Munyard , Nathalie Vialaneix , Andrea Rau et al.
BMC Biology, 2019, 17 (1), 25 p. ⟨10.1186/s12915-019-0726-5⟩
Article dans une revue hal-02437599 v1
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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Hélène Badouin , Jerome Gouzy , Christopher Grassa , Florent Murat , S Evan Staton et al.
Nature, 2017, 546 (7656), pp.148-152. ⟨10.1038/nature22380⟩
Article dans une revue hal-01603287 v1

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 et al.
Molecular Ecology, 2017, 26 (14), pp.3700-3714. ⟨10.1111/mec.14141⟩
Article dans une revue hal-01607837 v1
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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 et al.
PLoS ONE, 2017, 12 (11), Non paginé. ⟨10.1371/journal.pone.0187617⟩
Article dans une revue hal-02622330 v1
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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 et al.
BMC Genomics, 2015, 16, Non paginé. ⟨10.1186/s12864-015-2259-9⟩
Article dans une revue hal-01245970 v1
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The sheep genome illuminates biology of the rumen and lipid metabolism

Yu Jiang , Min Xie , Wenbin Chen , Richard Talbot , Jillian F. Maddox et al.
Science, 2014, 344 (6188), pp.1168-1173. ⟨10.1126/science.1252806⟩
Article dans une revue hal-02635391 v1

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-01210569 v1

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 et al.
Nature Genetics, 2013, 45 (7), pp.776-783. ⟨10.1038/ng.2657⟩
Article dans une revue hal-02652041 v1
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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 et al.
DNA Research, 2013, 20 (4), pp.339-353. ⟨10.1093/dnares/dst014⟩
Article dans une revue hal-03082947 v1
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Génomique des canards

Alain Vignal , Christian Diot , Caroline Molette , Thomas Faraut , Man Rao et al.
INRA Productions Animales, 2013, 26 (5), pp.391-402
Article dans une revue hal-01207754 v1

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 et al.
Nature Biotechnology, 2013, 31 (2), pp.135-141. ⟨10.1038/nbt.2478⟩
Article dans une revue hal-02651460 v1
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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-02644217 v1

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 et al.
Nature, 2012, 491 (7426), pp.393-398. ⟨10.1038/nature11622⟩
Article dans une revue cea-00880676 v1
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A duck RH panel and its potential for assisting NGS genome assembly

Man Rao , Mireille Morisson , Thomas Faraut , Suzanne Bardes , Katia K. Feve et al.
BMC Genomics, 2012, 13 (september), Non paginé. ⟨10.1186/1471-2164-13-513⟩
Article dans une revue hal-02646793 v1
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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-02650334 v1
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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 et al.
BMC Genomics, 2011, 12 (november), pp.548. ⟨10.1186/1471-2164-12-548⟩
Article dans une revue hal-00842687 v1

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 istex hal-01129469 v1

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 et al.
Animal Genetics, 2010, 41 (5), pp.449-453. ⟨10.1111/j.1365-2052.2010.02100.x⟩
Article dans une revue istex hal-02668022 v1

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-02665786 v1

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

Michael Abrouk , Florent Murat , Caroline Pont , Joachim Messing , Scott Jackson et al.
Trends in Plant Science, 2010, 15 (9), pp.479-87. ⟨10.1016/j.tplants.2010.06.001⟩
Article dans une revue istex hal-00681093 v1

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 et al.
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-00964188 v1

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals.

Thomas Faraut , Simon de Givry , Christophe Hitte , Yvette Lahbib Mansais , Mireille Morisson et al.
Cytogenetic and Genome Research, 2009, 126 (1-2), pp.21-33. ⟨10.1159/000245904⟩
Article dans une revue inserm-00442389 v1

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-02663909 v1
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Narcisse: a mirror view of conserved syntenies

Emmanuel E. Courcelle , Yoann Beausse , Sébastien Letort , Olivier Stahl , Julien Fremez et al.
Nucleic Acids Research, 2008, 36 (1), pp.D485-D490. ⟨10.1093/nar/gkm805⟩
Article dans une revue hal-02656575 v1

Addressing chromosome evolution in the whole-genome sequence era.

Thomas Faraut
Chromosome Research, 2008, 16, pp.5-16
Article dans une revue hal-02653333 v1

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

Annie Robic , Thomas Faraut , Laurence Liaubet , Juliette Riquet , Denis Milan et al.
Animal Biotechnology, 2008, 19, pp.138-143
Article dans une revue hal-02657001 v1

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-00535599 v1

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-02662738 v1

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-02653698 v1

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-02654862 v1

A comparative genome approach to marker ordering

Thomas Faraut , Simon de Givry , Patrick P. Chabrier , Thomas Derrien , Francis Galibert et al.
Bioinformatics, 2007, 23 (2), pp.E50-E56. ⟨10.1093/bioinformatics/btl321⟩
Article dans une revue hal-02667668 v1
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Genetic and haplotypic structure in 14 European and African cattle breeds

Mathieu M. Gautier , Thomas Faraut , Katayoun Moazami-Goudarzi , Vincent Navratil , Mario Foglio et al.
Genetics, 2007, 177, pp.1059-1070
Article dans une revue hal-02660515 v1

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 et al.
Genomics, 2006, 88, pp.504-512
Article dans une revue hal-02656467 v1

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 et al.
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-00171244 v1
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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 et al.
Genetics Selection Evolution, 2005, 37, pp.229-251. ⟨10.1051/gse:2004046⟩
Article dans une revue hal-02670446 v1

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 et al.
Genomics, 2005, 86, pp.405-413
Article dans une revue hal-02670629 v1

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 et al.
Cytogenetic and Genome Research, 2005, 108, pp.317-321
Article dans une revue hal-02678722 v1

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

Alain Pinton , Thomas Faraut , Martine M. Yerle , Joseph Gruand , F. Pellestor et al.
Human Reproduction, 2005, 20, pp.2476-2482
Article dans une revue hal-02674136 v1

Comparative mapping of genomes.

Thomas Faraut
Biofutur, 2005, 37, pp.40
Article dans une revue hal-02672330 v1

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 et al.
Mammalian Genome, 2004, 15, pp.732-739
Article dans une revue hal-02673764 v1

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-02673120 v1

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-02671512 v1
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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-02675844 v1

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-02669950 v1

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

C. Allal , C. Buisson-Brenac , V. Marion , C. Claudel-Renard , Thomas Faraut et al.
Journal of Virology, 2004, 78, pp.7717-7726
Article dans une revue hal-02674890 v1

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-02670370 v1

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-02674861 v1

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-02673209 v1

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 et al.
Cytogenetic and Genome Research, 2003, 102, pp.100-108
Article dans une revue hal-02671887 v1

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 et al.
Cytogenetic and Genome Research, 2003, 102, pp.109-115
Article dans une revue hal-02676236 v1

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 et al.
British Poultry Science, 2003, 44, pp.797-798
Article dans une revue hal-02674651 v1

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 et al.
Mammalian Genome, 2003, 14, pp.71-80. ⟨10.1007/s00335-002-3034-1⟩
Article dans une revue istex hal-02679052 v1
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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-02676567 v1

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-02675399 v1

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-02694908 v1

Illustration of a deep learning approach to identify key genomic sequence features of 3D genome organisation

Thomas Faraut , Nicolas Mary , Anne-Laure Valton , Harmonie Barasc , Anne Calgaro et al.
25th International Colloquium on Animal Cytogenetics and Genomics, Vincenzo Peretti, Leopoldo Iannuzzi, Andrea Scaloni, Francesca Ciotola, Sara Albarella, Alessandra Iannuzzi, Angela Perucatti, Jun 2024, Naples (Italie), Italy
Communication dans un congrès hal-04651656 v1

Detection and characterization of cytogenetic defects in cattle using large genotypic and phenotypic data sets generated for genomic evaluation

Jeanlin Jourdain , Harmonie Barasc , Sébastien Fritz , Clémentine Escouflaire , Anne Barbat et al.
25th International Colloquium on Animal Cytogenetics and Genomics (ICACG), Jun 2024, Naples, Italy
Communication dans un congrès hal-04726165 v1
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Improvement of the Bos taurus Genome Assembly using New Sequencing Technologies

Camille Eché , Carole Iampietro , Clement Birbes , Andreea Dreau , Claire Kuchly et al.
Discoveries Roadshow 2023 - PacBio, PacBio, May 2023, Paris, France
Communication dans un congrès hal-04096124 v1
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Variations de structure et longues lectures

Thomas Faraut
Colloque INRAE Genomics, INRAE Genomics, May 2022, Orléans, France
Communication dans un congrès hal-04220082 v1

A first step towards the characterization of endogenous retroviruses’ evolutionary history and impact on small ruminant genomes

Marie Verneret , Caroline Leroux , Vincent Navratil , Thomas Faraut , Emmanuelle Lerat et al.
CNET 2023 : 24th National Congress on Transposable Elements 2023, The French research community working on transposable elements (CNET), Jul 2023, Perpignan, France
Communication dans un congrès hal-04728744 v1
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Sex differences in recombination maps are associated with differential hotspot usage in sheep

Héléna Vassilief , Mohamed Id Bella , Flavie Tortereau , Dominique Hazard , Thomas Faraut et al.
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-04065264 v1
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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-03445759 v1
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Y-chromosomal haplotypes in domestic and wild goats reveal ancient paternal bottlenecks and recent introgressions

J.A. Lenstra , Vargoats Consortium , I.J. Nijman , B.D. Rosen , Philippe Bardou et al.
ISGC and IGGC Virtual Meeting, Jun 2021, Toulouse-Dunedin, France. pp.886-889, ⟨10.3920/978-90-8686-940-4_208⟩
Communication dans un congrès hal-03817722 v1
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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-03703612 v1

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

Annie Robic , Katia Feve , Thomas Faraut , Sarah Djebali , R. Weikard et al.
37. International Society for Animal Genetics Conference (ISAG), Jul 2019, Lleida, Spain
Communication dans un congrès hal-02788077 v1

Chromatin accessibility conservation across four livestock species

Sarah Djebali Quelen , Sylvain Foissac , Nathalie Vialaneix , Kylie Munyard , Andrea Rau et al.
Conference of the International Society for Animal Genetics (ISAG 2019), Jul 2019, Llieda, Spain
Communication dans un congrès hal-02788732 v1
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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-02785651 v1

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 et al.
Séminaire mensuel (CRAG), Nov 2018, Barcelone, Spain
Communication dans un congrès hal-02785242 v1

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

Alain Pinton , Anne Calgaro , Nicolas Mary , Harmonie Barasc , Nathalie Bonnet et al.
23. International Colloquium on Animal Cytogenetics and Genomics (23 ICACG), Jun 2018, Saint-Pétersburg, Russia. 360 p
Communication dans un congrès hal-02737986 v1

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-02785613 v1

Effects of balanced chromosome translocations on boar fertility and cell reprogramming

Annabelle Congras , Harmonie Barasc , Valentine Marquet , Kamila Canale-Tabet , Emeline Lhuillier et al.
22. International Colloquium on Animal Cytogenetics and Genomics (ICACG), Jul 2016, Toulouse, France. 116p
Communication dans un congrès hal-02738753 v1

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-01602943 v1
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De novo Assembly of the Chinese Bamboo-Partridge Genome and Comparison with Chicken

Gabriel Rognon , Diane Esquerre , Sylvain Foissac , Alain Vignal , Jean-Luc Coville et al.
Plant and Animal Genome (PAG), Jan 2015, San Diego, United States
Communication dans un congrès hal-01194054 v1

Numerous interchromosomal rearrangements in spite of high synteny conservation between duck and chicken

Valerie Fillon , Man Rao , Thomas Faraut , Daren Griffin , Mireille Morisson et al.
21. International Colloquium on Animal Cytogenetics and Gene Mapping, Jun 2014, Ischia, Italy
Communication dans un congrès hal-02793231 v1

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-02739253 v1
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Mapping by RH sequencing: organizing NGS scaffolds into chromosomes

Man Rao , Mireille Morisson , Valerie Fillon , Sophie S. Leroux , Emeline Lhuillier et al.
21. P!ant and animal genome meeting (PAG XXI), Jan 2013, San Diego, Californie, United States
Communication dans un congrès hal-02749835 v1
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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 et al.
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-01190264 v1

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 et al.
35. Colloque du Petit Pois Déridé, Aug 2013, Marseille, France
Communication dans un congrès hal-02810860 v1

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 et al.
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-01019243 v1
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Towards a high density SNP International Goat Chip

Gwenola Tosser-Klopp , Abdullah Johari Jiken , Philippe Bardou , Cédric Cabau , Patrice Dehais et al.
Plant and Animal Genome, Jan 2011, San Diégo, United States
Communication dans un congrès hal-01194170 v1
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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-02752130 v1

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-02813656 v1

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 , Bertrand Servin , Thomas Faraut , Christophe Klopp , Rachel Rupp et al.
16. Rencontres autour des Recherches sur les Ruminants, Dec 2009, Paris, France
Communication dans un congrès hal-02755058 v1

High resolution chicken radiation hybrid maps using the IlluminaTM technology.

Alain Vignal , Caroline Hourcade , Thomas Faraut , Sophie S. Leroux , Marine M. Douaud et al.
31st Conference of the International Society of Animal Genetics (ISAG), 2008, Amsterdam, pp.Inconnu
Communication dans un congrès hal-02815790 v1

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-02754669 v1

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-02815778 v1

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 , Andres Legarra , David Robelin , Christèle Robert-Granié , Rachel Rupp et al.
Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau, France
Communication dans un congrès hal-02813290 v1

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-02752629 v1

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-02756487 v1

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 et al.
International Plant & Animal Genomes XV Conference, San Diego, 2007, California, France
Communication dans un congrès hal-02751166 v1

Chromosomal rearrangements and comparative mapping.

Thomas Faraut
Séminaire Cytogénétique des plantes Clermont-Ferrand, Apr 2007, France, pp.Inconnu
Communication dans un congrès hal-02811665 v1

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 et al.
Inconnu, 2006, Inconnu
Communication dans un congrès hal-02752628 v1

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-02813597 v1

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 et al.
29. International Conference on International Society of Animla Genetics, Sep 2004, Tokyo, Japan
Communication dans un congrès hal-02761544 v1

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-02831758 v1

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-02827995 v1

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-02826042 v1

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 et al.
11th Internnational Congress on Biotechnology in Animal Reproduction, Sep 2004, Rapotin, pp.Inconnu
Communication dans un congrès hal-02827383 v1

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-02829792 v1

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-02760525 v1

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 et al.
2003 Spring Meeting of the WPSA French Branch., 2003, Inconnu
Communication dans un congrès hal-02826038 v1

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-02762328 v1

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 et al.
5èmes Journées de la Recherche Avicole, 2003, Tours, France
Communication dans un congrès hal-02761067 v1

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-02825614 v1

Exploring endogenous retroviruses in ruminant genomes: They might not be all dead after all

Marie Verneret , Caroline Leroux , Thomas Faraut , Vincent Navratil , Emmanuelle Lerat et al.
Bioinformatics and Evolutionary Genomics (ALPHY = ALignments and PHYlogeny), Feb 2025, Villeurbane, France
Poster de conférence hal-04965269 v1

Hi-C for the detection and characterization of chromosomal rearrangements in cattle

Nicolas Mary , Anne-Laure Valton , Harmonie Barasc , Anne Calgaro , Christelle Marrauld et al.
25th International Colloquium on Animal Cytogenetics and Genomics, Jun 2024, Naples (Italie), Italy.
Poster de conférence hal-04651644 v1
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Small ruminants versus endogenous retroviruses: an evolutive showdown still in progress in the domestic goat genome

Marie Verneret , Caroline Leroux , Vincent Navratil , Thomas Faraut , Jocelyn Turpin et al.
International congress on transposable elements, Apr 2024, Saint Malo (FR), France
Poster de conférence hal-04727644 v1
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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 et al.
Plant and Genome San Diego 2024, Jan 2024, San Diego, United States
Poster de conférence hal-04432840 v1
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Structural variants detection and de novo genome assembly of a maize line

Carole Iampietro , Camille Eché , Clément Birbes , Arnaud Di Franco , Andreea Dréau et al.
Plant & Animal Genome Conference (PAG) 2022, Jan 2022, San Diego, United States
Poster de conférence hal-03541379 v1
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Quelques résultats du programme VarGoats : « 1000 génomes caprins »

L Denoyelle , M Amills , Philippe Bardou , Maxime Ben Braiek , Thomas Faraut et al.
Journées Scientifiques du Département de Génétique Animale, Sep 2022, Bordeaux, France
Poster de conférence hal-03812438 v1
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Combiner analyse d’association et génomique fonctionnelle pour la recherche de gènes candidats

Sarah Djebali , Sophie Leroux , Katia Feve , Yann Labrune , Catherine Larzul et al.
Journées scientifiques Département Génétique animale, Sep 2022, Bordeaux, France
Poster de conférence hal-03936070 v1
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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-04225788 v1
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De novo assembly of 90 bovines genomes using PacBio CLR application comparison and optimization

Camille Marcuzzo , Amandine Suin , Camille Eché , Andreea Dreau , Clément Birbes et al.
Assemblée générale France Génomique, Jun 2022, Paris, France
Poster de conférence hal-04590746 v1
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De novo assembling 19 maize inbred lines of the European germplasm

Carole Iampietro , Camille Eché , Clement Birbes , Andreea Dreau , Erwan Denis et al.
63rd Annual Maize Genetics Meeting, Mar 2021, virtuel, United States
Poster de conférence hal-03539396 v1
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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-03445792 v1
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Structural variants detection and de novo genome assembly of a Maize line

Camille Eché , Clement Birbes , Carole Iampietro , Arnaud Di Franco , Andreea Dreau et al.
SMRT Leiden 2021 – Young Investigator Virtual Conference, May 2021, virtuel, Netherlands
Poster de conférence hal-03541316 v1
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De novo assembly of bovine genome using PacBio applications

Camille Eché , Clément Birbes , Carole Iampietro , Andreea Dréau , Claire Kuchly et al.
SMRT Leiden 2021 – Young Investigator Virtual Conference, May 2021, virtuel, Netherlands
Poster de conférence hal-03541224 v1
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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 Klopp et al.
PAG XXVIII, Plant and Animal Genome, Jan 2020, San Diego, United States. 2020
Poster de conférence hal-02947690 v1
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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-02788016 v1

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 et al.
European Conference on Computational Biology (ECCB 2018), Sep 2018, Athènes, Greece. , 2018
Poster de conférence hal-02784857 v1
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Présentation et premiers résultats du programme 1000 génomes caprins : VarGoats

Philippe Bardou , Céline Bourdon , Laure Denoyelle , Thomas Faraut , Estelle Talouarn et al.
Journées Scientifiques du Département de Génétique Animale, Oct 2018, Dienné, France
Poster de conférence hal-03817570 v1

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 et al.
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-01194042 v1
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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 et al.
Journée Régionale de Bioinformatique et Biostatistique, Génopole Toulouse, Jun 2014, Toulouse, France. 2014
Poster de conférence hal-01194044 v1

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-02804016 v1
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Organisation linéaire du génome et ses variations

Thomas Faraut
Sciences du Vivant [q-bio]. Université Toulouse 3, 2019
HDR tel-04975276 v1