Philippe Bardou

Publications

Article dans une revue (34)

Inferring Domestic Goat Demographic History Through Ancient Genome Imputation Jolijn Erven,Alice Etourneau,Marjan Mashkour,Mahesh Neupane,Phillipe Bardouet al. Genome Biology and Evolution, 2025, 17 (11), ⟨10.1093/gbe/evaf181⟩ Article dans une revue hal-05393593v1
Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker Sarah Maman,Philippe Bardou,Emilien Lasguignes,Faustine Oudin,Floréal Cabanetteset al. Journal of Open Source Software, 2024, 9 (103), pp.6272. ⟨10.21105/joss.06272⟩ Article dans une revue hal-04792598v1
Whole genome sequencing reveals signals of adaptive admixture in Creole cattle Slim Ben-Jemaa,Gabriele Adam,Mekki Boussaha,Philippe Bardou,Christophe Kloppet al. Scientific Reports, 2023, 13 (1), pp.12155. ⟨10.1038/s41598-023-38774-7⟩ Article dans une revue hal-04186791v1
Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens Florian Herry,Frédéric Herault,Frédéric Lecerf,Laetitia Lagoutte,Mathilde Doubletet al. BMC Genomics, 2023, 24 (1), pp.271. ⟨10.1186/s12864-023-09321-5⟩ Article dans une revue hal-04131807v1
A Nonsense Variant in CCDC65 Gene Causes Respiratory Failure Associated with Increased Lamb Mortality in French Lacaune Dairy Sheep Maxime Ben Braiek,Carole Moreno-Romieux,Charlotte Allain,Philippe Bardou,Arnaud Bordeset al. Genes, 2022, 13 (1), pp.45. ⟨10.3390/genes13010045⟩ Article dans une revue hal-03525204v1
An open-source tool to assess the carbon footprint of research Jérôme Mariette,Odile Blanchard,Olivier Berné,Olivier Aumont,Julian Carreyet al. Environmental Research: Infrastructure and Sustainability, 2022, 2 (3), pp.035008. ⟨10.1088/2634-4505/ac84a4⟩ Article dans une revue hal-03796807v3
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 Cumeret al. Molecular Ecology, 2022, 17 p. ⟨10.1111/mec.16579⟩ Article dans une revue hal-03722180v1
FishmiRNA: An evolutionarily supported microRNA annotation and expression database for ray-finned fishes Thomas Desvignes,Philippe Bardou,Jérôme Montfort,Jason Sydes,Cervin Guyomaret al. Molecular Biology and Evolution, 2022, 39 (2), pp.msac004. ⟨10.1093/molbev/msac004⟩ Article dans une revue hal-03528022v1
Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae Aurélie Allais-Bonnet,Aurélie Hintermann,Marie-Christine Deloche,Raphael Cornette,Philippe Bardouet al. Molecular Biology and Evolution, 2021, ⟨10.1093/molbev/msab021⟩ Article dans une revue hal-03164832v1
RNA-Seq Data for Reliable SNP Detection and Genotype Calling Frédéric Jehl,Fabien Degalez,Frédéric Lecerf,Maria Bernard,Laetitia Lagoutteet al. Frontiers in Genetics, 2021, 12, pp.655707. ⟨10.3389/fgene.2021.655707⟩ Article dans une revue hal-03276149v1
VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity Laure Denoyelle,Estelle Talouarn,Philippe Bardou,Licia Colli,Adriana Albertiet al. Genetics Selection Evolution, 2021, 53 (1), 14 p. ⟨10.1186/s12711-021-00659-6⟩ Article dans une revue hal-03480970v1
In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets Céline Bourdon,Mekki Boussaha,Philippe Bardou,Marie-Pierre Sanchez,Sandrine Le Guillouet al. Scientific Reports, 2021, 11, ⟨10.1038/s41598-021-98639-9⟩ Article dans une revue hal-03371440v1
MINTIA: a metagenomic INserT integrated assembly and annotation tool Philippe Bardou,Sandrine Laguerre,Sarah Maman Haddad,Sabrina Legoueix,Elisabeth Lavilleet al. PeerJ, 2021, 9, 13 p. ⟨10.7717/peerj.11885⟩ Article dans une revue hal-03407218v1
Using sequence variants of a QTL region improves the accuracy of genomic evaluation in French Saanen goats Estelle Talouarn,Marc Teissier,Philippe Bardou,Hélène Larroque,Virginie Clémentet al. Journal of Dairy Science, 2021, 104 (1), pp.588-601. ⟨10.3168/jds.2020-18837⟩ Article dans une revue hal-03146844v1
Le projet « Mille Génomes Gallus » : partager les données de séquences pour mieux les utiliser Michèle Tixier-Boichard,Frédéric Lecerf,Frédéric Herault,Philippe Bardou,Christophe Klopp INRAE Productions Animales, 2020, 33 (3), pp.189-202. ⟨10.20870/productions-animales.2020.33.3.4564⟩ Article dans une revue hal-03103324v1
Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats Estelle Talouarn,Philippe Bardou,Isabelle Palhiere,Claire Oget,Virginie Clémentet al. BMC Genetics, 2020, 21 (1), ⟨10.1186/s12863-020-0826-9⟩ Article dans une revue hal-02548369v1
RumimiR: a detailed microRNA database focused on ruminant species Céline Bourdon,Philippe Bardou,Etienne Aujean,Sandrine Le Guillou,Gwenola Tosser-Kloppet al. Database - The journal of Biological Databases and Curation, 2019, 2019, pp.1-10. ⟨10.1093/database/baz099⟩ Article dans une revue hal-02627384v1
Multi-species annotation of transcriptome and chromatin structure in domesticated animals Sylvain Foissac,Sarah Djebali,Kylie Munyard,Nathalie Vialaneix,Andrea Rauet al. BMC Biology, 2019, 17 (1), 25 p. ⟨10.1186/s12915-019-0726-5⟩ Article dans une revue hal-02437599v1
Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep Julie Demars,Margarita Cano,Laurence Drouilhet,Florence Plisson-Petit,Philippe Bardouet al. Molecular Biology and Evolution, 2017, 34 (7), pp.1722-1729. ⟨10.1093/molbev/msx114⟩ Article dans une revue hal-01608205v1
Author correction : A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content Pauline Martin,Isabelle Palhiere,Cyrielle Maroteau,Philippe Bardou,Kamila Canale-Tabetet al. Scientific Reports, 2017, 8, ⟨10.1038/s41598-018-22118-x⟩ Article dans une revue hal-02622800v1
A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content Pauline Martin,Isabelle Palhiere,Cyrielle Maroteau,Philippe Bardou,Kamila Canale-Tabetet al. Scientific Reports, 2017, 7 (1), Non paginé. ⟨10.1038/s41598-017-02052-0;⟩ Article dans une revue hal-01605655v1
Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing Amélie Juanchich,Philippe Bardou,Olivier Rué,Jean-Charles Gabillard,Christine Gaspinet al. BMC Genomics, 2016, 17:164 (1), pp.1-12. ⟨10.1186/s12864-016-2505-9⟩ Article dans une revue hal-01509042v1
Jflow: a workflow management system for web applications Jérôme J. Mariette,Frédéric Escudié,Philippe Bardou,Ibouniyamine Ibrahime,Céline Noirotet al. Bioinformatics, 2016, 32 (3), pp.456-458. ⟨10.1093/bioinformatics/btv589⟩ Article dans une revue hal-02631131v1
Correction : Design and Characterization of a 52K SNP Chip for Goats Gwenola Tosser-Klopp,Philippe Bardou,Olivier Bouchez,Cédric Cabau,Richard Crooijmanset al. PLoS ONE, 2016, 11 (3), pp.Non Paginé. ⟨10.1371/journal.pone.0152632⟩ Article dans une revue hal-01602260v1
The BioMart community portal: an innovative alternative to large, centralized data repositories Damian Smedley,Syed Haider,Steffen Durinck,Luca Pandini,Paolo Proveroet al. Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩ Article dans une revue hal-01146849v1
RNAbrowse: RNA-Seq de novo assembly results browser. Jérôme J. Mariette,Céline Noirot,Ibouniyamine Nabihoudine,Philippe Bardou,Claire Hoedeet al. PLoS ONE, 2014, 9 (5), 7 p. ⟨10.1371/journal.pone.0096821⟩ Article dans une revue hal-02636622v1
Design and characterization of a 52K SNP chip for goats Gwenola Tosser-Klopp,Philippe Bardou,Olivier Bouchez,Cédric Cabau,Richard Crooijmanset al. PLoS ONE, 2014, 9, online (1), Non paginé. ⟨10.1371/journal.pone.0086227⟩ Article dans une revue hal-01019568v1
jvenn: an interactive Venn diagram viewer Philippe Bardou,Jérôme J. Mariette,Frédéric Escudié,Christophe Djemiel,Christophe Klopp BMC Bioinformatics, 2014, 15 (1), pp.293. ⟨10.1186/1471-2105-15-293⟩ Article dans une revue hal-02640484v1
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Camille Berthelot,Frédéric Brunet,Domitille Chalopin,Amélie Juanchich,Maria Bernardet al. Nature Communications, 2014, 5, pp.1-10. ⟨10.1038/ncomms4657⟩ Article dans une revue hal-01193812v1
The Highly Prolific Phenotype of Lacaune Sheep Is Associated with an Ectopic Expression of the B4GALNT2 Gene within the Ovary. Laurence Drouilhet,Camille Mansanet,Julien Sarry,Kamila Canale-Tabet,Philippe Bardouet al. PLoS Genetics, 2013, 9 (9), pp.e1003809. ⟨10.1371/journal.pgen.1003809⟩ Article dans une revue hal-01129778v1
The Medicago genome provides insight into the evolution of rhizobial symbioses Nevin D. Young,Frederic Debellé,Giles E. D. Oldroyd,Rene Geurts,Steven Cannonet al. Nature, 2011, 480 (7378), pp.520-524. ⟨10.1038/nature10625⟩ Article dans une revue hal-02652790v1
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. Marie-Josée Cros,Antoine de Monte,Jérôme J. Mariette,Philippe Bardou,Benjamin Grenier-Boleyet al. RNA, 2011, 17 (11), pp.1947-56. ⟨10.1261/rna.2844911⟩ Article dans une revue hal-00639174v1
Interoperability with Moby 1.0--it's better than sharing your toothbrush! M.D. Wilkinson,M. Senger,E. Kawas,R. Bruskiewich,Jerome Gouzyet al. Briefings in Bioinformatics, 2008, 9, pp.220-231 Article dans une revue hal-02654526v1
EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences Sylvain Foissac,Philippe Bardou,Annick Moisan,Marie-Josée Cros,Thomas Schiex Nucleic Acids Research, 2003, 31 (13), pp.3742-3745. ⟨10.1093/nar/gkg586⟩ Article dans une revue hal-02675508v1

Logiciel (5)

IntronSeeker Sarah Maman,Philippe Bardou,Emilien Lasguignes,Faustine Oudin,Floréal Cabanetteset al. 2025, ⟨swh:1:dir:4c5875115428c349f7c5a90c510ce91fe8981071;origin=https://github.com/Bios4Biol/intronSeeker;visit=swh:1:snp:94a8406f83eb30a1bc86b1b01052f48c6bcf0c19;anchor=swh:1:rev:0ad12c9965c843c625470af4d35caad1023fa434⟩ Logiciel hal-05058489v1
Jflow: a workflow management system for web applications Jérôme J. Mariette,Frédéric Escudié,Philippe Bardou,Ibouniyamine Ibrahime,Céline Noirotet al. 2016 Logiciel hal-02795849v1
jvenn: an interactive Venn diagram viewer Philippe Bardou,Jérôme J. Mariette,Frédéric Escudié,Christophe Djemiel,Christophe Klopp 2014 Logiciel hal-02795848v1
RNAbrowse: RNA-Seq de novo assembly results browser Jérôme J. Mariette,Céline Noirot,Ibouniyamine Nabihoudine,Philippe Bardou,Claire Hoedeet al. 2014 Logiciel hal-02795847v1
RNAspace Marie-Josée Cros,Antoine de Monte,Jérôme J. Mariette,Philippe Bardou,Benjamin Grenier-Boleyet al. 2010 Logiciel hal-02819286v1

Poster de conférence (11)

Quelques résultats du programme VarGoats : « 1000 génomes caprins » L Denoyelle,M Amills,Philippe Bardou,Maxime Ben Braiek,Thomas Farautet al. Journées Scientifiques du Département de Génétique Animale, Sep 2022, Bordeaux, France Poster de conférence hal-03812438v1
Interest of Genotyping-by-Sequencing technologies as an alternative to low density SNP chips for genomic selection in layer chicken Florian Herry,Frédéric Herault,David Picard Druet,Philippe Bardou,Camille Echéet al. XIth European symposium on poultry genetics (ESPG), Oct 2019, Prague, Czech Republic. Guarant International spol. s r.o., 2019, Proceedings of the XIth European symposium on Poultry Genetics Poster de conférence hal-02460147v1
Accuracy of whole-genome sequence genotype imputation in a layer line Sophie Allais,Florian Herry,Frédéric Herault,David Picard Druet,Philippe Bardouet al. XIth European symposium on poultry genetics (ESPG), Oct 2019, Prague, Czech Republic. Guarant International spol. s r.o., 2019, Proceedings of the XIth European symposium on Poultry Genetics Poster de conférence hal-02500398v1
Using sequence data to refine QTL mapping in French dairy goats Estelle Talouarn,Philippe Bardou,Gwenola Tosser-Klopp,Rachel Rupp,Christèle Robert-Granié 70. Annual Meeting of the European Association for Animal Production (EAAP), Aug 2019, Ghent, Belgium. Wageningen Academic Publishers, Annual Meeting of the European Association for Animal Production, 25 (1ère Ed.), 717 p., 2019, Book of the Abstracts of the 70th Annual Meeting of the European Association for Animal Production (EAAP) Poster de conférence hal-02737623v1
Analysis of whole genome sequence data on a tropical admixed cattle breed, the Creole cattle of Guadeloupe Gabrièle Adam,Diane Esquerré,Olivier Bouchez,Philippe Bardou,Christophe Kloppet al. International Symposium on environmental and agronomical genomics, Nov 2018, Paris, France. , 2018 Poster de conférence hal-02786834v1
Présentation et premiers résultats du programme 1000 génomes caprins : VarGoats Philippe Bardou,Céline Bourdon,Laure Denoyelle,Thomas Faraut,Estelle Talouarnet al. Journées Scientifiques du Département de Génétique Animale, Oct 2018, Dienné, France Poster de conférence hal-03817570v1
Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project] Sylvain Foissac,Sarah Djebali Quelen,Hervé Acloque,Philippe Bardou,Fany Blancet al. 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book Poster de conférence hal-01608449v1
E-formations en bioinformatique Sarah Maman Haddad,Frédérique F. Malipier,Catherine Herry,Philippe Bardou Les journées Bioinformatique de l'Inra, Mar 2016, Toulouse, France. , 1p, 2016 Poster de conférence hal-02800765v1
RNAspace: an integrated environment for the prediction, annotation and analysis of non-coding RNA Marie-Josée Cros,Antoine de Monte,Jérôme J. Mariette,Philippe Bardou,Daniel Gautheretet al. 12.Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2011, Jun 2011, Paris, France. 2011 Poster de conférence hal-02810153v1
rnaspace.org - a web application for noncoding RNA identification Marie-Josée Cros,Antoine de Monte,Jérôme J. Mariette,Philippe Bardou,Daniel Gautheretet al. JOBIM 2010 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France. 2010 Poster de conférence hal-02819250v1
RNAspace: non-coding RNA annotation web platform Philippe Bardou,Marie-Josée Cros,Christine Gaspin,Daniel Gautheret,Benjamin Grenier-Boleyet al. JOBIM 2009 : 10. Journées Ouvertes Biologie Informatique Mathématiques, Jun 2009, Nantes, France. 2009 Poster de conférence hal-02819249v1

Communication dans un congrès (14)

A recessive stop-gain mutation in CCDC65 is associated with lamb mortality in French Lacaune dairy sheep Maxime Ben Braiek,Carole Moreno-Romieux,Charlotte Allain,Philippe Bardou,Arnaud Bordeset al. International Sheep Genomics and the International Goat Genome Consortiums combined virtual meeting, Jun 2021, Online, France Communication dans un congrès hal-03360133v1
Using sequence variants to better characterize a QTL region and improve the accuracy of genomic evaluation in Saanen goats Estelle Talouarn,Isabelle Palhière,Marc Teissier,Philippe Bardou,Hélène Larroqueet al. ISGC and IGGC Virtual Meeting, Jun 2021, Toulouse-Dunedin, France Communication dans un congrès hal-03817609v1
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 Bardouet 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-03817722v1
Unsing sequence data to refine QTL mapping in French dairy goats Christèle Robert-Granié,Estelle Talouarn,Philippe Bardou,Gwenola Tosser-Klopp,Rachel Rupp European federation of Animal Science EAAP, https://meetings.eaap.org/wp-content/uploads/2021/09/2019-ghent-book-of-abstracts.pdf, Aug 2019, Ghent, Belgium. pp.125 Communication dans un congrès hal-04809337v1
RumimiR: a detailed microRNA database focused on ruminant species Céline Bourdon,Philippe Bardou,Etienne Aujean,Sandrine Le Guillou,Fabienne Le Provostet al. 70. Annual Meeting of the European Federation of Animal Science (EAAP), European Federation of Animal Science (EAAP). INT., Aug 2018, Gand, Belgium Communication dans un congrès hal-02738039v1
Analysis of whole genome sequence data on a tropical admixed cattle breed: the creole cattle of Guadeloupe. Gabrièle Adam,Diane Esquerre,Olivier Bouchez,Philippe Bardou,Christophe Kloppet al. Caribbean Science ans Innovation Meeting 2019, Oct 2019, Pointe-à-Pitre, Guadeloupe Communication dans un congrès hal-02423161v1
Imputation from CaprineSNP50 BeadChip to sequence : a case-study in French Alpine and Saanen data from the VarGoats project Estelle Talouarn,Philippe Bardou,Gwenola Tosser,Rachel Rupp,Christèle Robert-Granié PAG XXVII - Plant and Animal Genome Conference, Jan 2019, San Diego, United States Communication dans un congrès hal-02790419v1
Le projet mille génomes gallus : comment partager les données de séquences pour mieux les utiliser Michèle Tixier-Boichard,Frédéric Lecerf,Philippe Bardou,Christophe Klopp 13.Journées de la recherche avicole et des palmipèdes à foie gras, Mar 2019, Tours, France Communication dans un congrès hal-02737429v1
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
Recherche d'associations entre microARNs, variants génétiques et QTL laitiers chez les bovins caprins et ovins Céline Bourdon,Mekki Boussaha,Rachel Rupp,Marie-Pierre Sanchez,Thierry Triboutet al. 24. Rencontres Recherches Ruminants (3R), Dec 2018, Paris, France Communication dans un congrès hal-02734423v1
Construction d'une puce 50000 SNP pour l'espèce caprine Gwenola Tosser-Klopp,Philippe Bardou Séminaire NGS, organisé par Illumina et la plate-forme Get-PlaGe, Jun 2016, Auzeville, France Communication dans un congrès hal-02801438v1
Classification non supervisée d'un graphe de co-expression avec des méta-données pour la détection de micro-ARNs Florian Brunet,Jérôme J. Mariette,Christine Cierco-Ayrolles,Christine Gaspin,Philippe Bardouet al. MARAMI (Modèles et l'Analyse des Réseaux : Approches Mathématiques et Informatiques) 2013, Oct 2013, Saint-Étienne, France. pp.SI-1 Communication dans un congrès hal-00877561v1
Towards a high density SNP International Goat Chip Gwenola Tosser-Klopp,Abdullah Johari Jiken,Philippe Bardou,Cédric Cabau,Patrice Dehaiset al. Plant and Animal Genome, Jan 2011, San Diégo, United States Communication dans un congrès hal-01194170v1
Development of genomic resources for &lt;em&gt;Medicago truncatula&lt;/em&gt; and related legume crops Frederic Debellé,Marion Verdenaud,Anne-Marie Dudez,Nicolas Samson,Olivier Sauratet al. Model Legume Congress 2011, Institut National Polytechnique (Toulouse) (Toulouse INP). Castanet Tolosan, FRA., May 2011, Sainte Maxime, France Communication dans un congrès hal-02746654v1

Pré-publication, Document de travail (2)

Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 to Determine the Number and Topology of Horns in Bovidae Aurélie Allais-Bonnet,Aurélie Hintermann,Marie-Christine Deloche,Raphaël Cornette,Philippe Bardouet al. 2025 Pré-publication, Document de travail hal-04426679v1
Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig Sylvain Foissac,Sarah Djebali,Kylie Munyard,Nathalie Vialaneix,Andrea Rauet al. 2018 Pré-publication, Document de travail (preprint/prepublication) hal-02791029v1

Cours (1)

Initiation à la plateforme de traitement bioinformatique Galaxy - Instance Sigenae / BioInfo Genotoul Sarah Maman Haddad,Philippe Bardou,Sabrina Legoueix Master. Formation Master 2 Bioinformatique (Initiation à la plateforme de traitement bioinformatique Galaxy - Instance Sigenae / BioInfo Genotoul - Cours et TP.), 2016 Cours hal-02801693v1