Thomas Derrien

Publications

Article dans une revue (38)

Long non-coding RNAs in dogs: comparative insights across species and breeds Nicolaï Hoffmann,Aurore Besson,Christophe Hitte,Jocelyn Plassais,Thomas Derrien Annual Review of Animal Biosciences, 2025, ⟨10.1146/annurev-animal-030424-073201⟩ Article dans une revue (article de synthèse) hal-05239477v1
Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids Jocelyn Plassais,Bridgett M Vonholdt,Heidi G Parker,Alberto Carmagnini,Nicolas Duboset al. Current Biology, 2022, 32 (4), pp.889-897.e9. ⟨10.1016/j.cub.2021.12.036⟩ Article dans une revue hal-03555249v1
Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets Anais Prouteau,Stephanie Mottier,Aline Primot,Edouard Cadieu,Laura Bachelotet al. Cancers, 2022, 14 (2), pp.276. ⟨10.3390/cancers14020276⟩ Article dans une revue hal-03555450v1
LncRNAs in domesticated animals: from dog to livestock species Sandrine Lagarrigue,Matthias Lorthiois,Fabien Degalez,David Gilot,Thomas Derrien Mammalian Genome, 2022, 33 (2), pp.248-270. ⟨10.1007/s00335-021-09928-7⟩ Article dans une revue (article de synthèse) hal-03467210v1
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes Julia Halo,Amanda L. Pendleton,Feichen Shen,Aurelien J. Doucet,Thomas Derrienet al. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (11), ⟨10.1073/pnas.2016274118⟩ Article dans une revue hal-03206721v1
Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma Anaïs Prouteau,Jérôme Alexandre Denis,Pauline de Fornel,Edouard Cadieu,Thomas Derrienet al. Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-020-80332-y⟩ Article dans une revue hal-03110876v1
Identification of common predisposing loci to hematopoietic cancers in four dog breeds Benoit Hedan,Edouard Cadieu,Maud Rimbault,Amaury Vaysse,Caroline Dufaure de Citreset al. PLoS Genetics, 2021, 17 (4), pp.e1009395. ⟨10.1371/journal.pgen.1009395⟩ Article dans une revue hal-03215819v1
Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma Anaïs Prouteau,Florian Chocteau,Clotilde de Brito,Edouard Cadieu,Aline Primotet al. Veterinary and Comparative Oncology, 2020, 18 (2), pp.214-223. ⟨10.1111/vco.12536⟩ Article dans une revue hal-02280596v1
PTPN11 mutations in canine and human disseminated histiocytic sarcoma Benoit Hedan,Mélanie Rault,Jérôme Abadie,Ronan Ulvé,Nadine Botherelet al. International Journal of Cancer, 2020, 147 (6), pp.1657-1665. ⟨10.1002/ijc.32991⟩ Article dans une revue hal-02534873v1
An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues Frédéric Jehl,Kévin Muret,Maria Bernard,Morgane Boutin,Laetitia Lagoutteet al. Scientific Reports, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩ Article dans une revue hal-03039897v1
Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs Benoit Hedan,Edouard Cadieu,Nadine Botherel,Caroline Dufaure de Citres,Anna Letkoet al. Genes, 2019, 10 (5), pp.E386. ⟨10.3390/genes10050386⟩ Article dans une revue hal-02153481v1
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
Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules Camille Sessegolo,Corinne Cruaud,Corinne da Silva,Audric Cologne,Marion Dubarryet al. Scientific Reports, 2019, 9 (1), pp.14908. ⟨10.1038/s41598-019-51470-9⟩ Article dans une revue hal-02335574v1
Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas Christophe Hitte,Céline Le Béguec,Edouard Cadieu,Valentin Wucher,Aline Primotet al. Genes, 2019, 10 (6), pp.E:477. ⟨10.3390/genes10060477⟩ Article dans une revue hal-02179210v1
Characterisation and functional predictions of canine long non-coding RNAs Celine Le Beguec,Valentin Wucher,Laetitia Lagoutte,Edouard Cadieul,Nadine Botherelet al. Scientific Reports, 2018, 8 (1), pp.13444. ⟨10.1038/s41598-018-31770-2⟩ Article dans une revue hal-01888670v1
Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus Alexandre Cormier,Komlan Avia,Lieven Sterck,Thomas Derrien,Valentin Wucheret al. New Phytologist, 2017, 214 (1), pp.219-232. ⟨10.1111/nph.14321⟩ Article dans une revue hal-03145812v1
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome Valentin Wucher,Fabrice Legeai,Benoit Hedan,Guillaume Rizk,Laëtitia Lagoutteet al. Nucleic Acids Research, 2017, 45 (8), pp.12. ⟨10.1093/nar/gkw1306⟩ Article dans une revue hal-01532061v1
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species Thomas C. Mathers,Yazhou Chen,Gemy Kaithakottil,Fabrice Legeai,Sam T. Mugfordet al. Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩ Article dans une revue hal-01500475v1
Long noncoding RNA repertoire in chicken liver and adipose tissue Kévin Muret,Christophe Klopp,Valentin Wucher,Diane Esquerré,Fabrice Legeaiet al. Genetics Selection Evolution, 2017, 49 (1), pp.6. ⟨10.1186/s12711-016-0275-0⟩ Article dans une revue hal-01431420v1
An exome sequencing based approach for genome-wide association studies in the dog Bart J. G. Broeckx,Thomas Derrien,Stephanie Mottier,Valentin Wucher,Edouard Cadieuet al. Scientific Reports, 2017, 7 (1), pp.15680. ⟨10.1038/s41598-017-15947-9⟩ Article dans une revue hal-01659287v1
Discovery of Human-Similar Gene Fusions in Canine Cancers Ronan Ulvé,Mélanie Rault,Mathieu Bahin,Laetitia Lagoutte,Jérôme Abadieet al. Cancer Research, 2017, 77 (21), pp.5721-5727. ⟨10.1158/0008-5472.CAN-16-2691⟩ Article dans une revue hal-01647128v1
Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis Sarah Djebali,Valentin Wucher,Sylvain Foissac,Christophe Hitte,Erwan Correet al. Methods in Molecular Biology, 2017, 1468, pp.E1. ⟨10.1007/978-1-4939-4035-6_17⟩ Article dans une revue hal-01439359v1
Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species Thomas C. Mathers,Yazhou Chen,Gemy Kaithakottil,Fabrice Legeai,Sam T. Mugfordet al. Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩ Article dans une revue hal-01588181v1
A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies Jocelyn Plassais,Laetitia Lagoutte,Solenne Correard,Manon Paradis,Eric Guaguèreet al. PLoS Genetics, 2016, 12 (12), pp.e1006482. ⟨10.1371/journal.pgen.1006482⟩ Article dans une revue hal-01439364v1
A DOG SPONTANEOUS MODEL FOR HUMAN SENSORY NEUROPATHIES: IDENTIFICATION OF A MUTATION IN THE UPSTREAM REGION OF A NEUROTROPHIC FACTOR S. Correard,J. Plassais,L. Lagoutte,M. Paradis,E. Guaguereet al. Bulletin de l'Académie Vétérinaire de France, 2016, 21 (3), pp.289--290. ⟨10.4267/2042/61953⟩ Article dans une revue hal-01415930v1
Identification of long non-coding RNAs in insects genomes Fabrice Legeai,Thomas Derrien Current Opinion in Insect Science, 2015, 7, pp.37 - 44. ⟨10.1016/j.cois.2015.01.003⟩ Article dans une revue (article de synthèse) hal-01240461v1
Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes Bart J. G. Broeckx,Christophe Hitte,Frank Coopman,Geert E. C. Verhoeven,Sarah de Keulenaeret al. Scientific Reports, 2015, 5 (1), pp.12810. ⟨10.1038/srep12810⟩ Article dans une revue hal-01187322v1
Assessment of transcript reconstruction methods for RNA-seq. Tamara Steijger,Josep F Abril,Pär G Engström,Felix Kokocinski,Martin Akermanet al. Nature Methods, 2013, 10 (12), pp.1177-1184. ⟨10.1038/nmeth.2714⟩ Article dans une revue hal-00909081v1
Fast computation and applications of genome mappability. Thomas Derrien,Jordi Estellé,Santiago Marco Sola,David G. Knowles,Emanuele Raineriet al. PLoS ONE, 2012, 7 (1), pp.e30377. ⟨10.1371/journal.pone.0030377⟩ Article dans une revue inserm-00664289v1
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression Thomas Derrien,Rory Johnson,Giovanni Bussotti,Andrea Tanzer,Sarah Djebaliet al. Genome Research, 2012, 22, pp.1775-1789. ⟨10.1101/gr.132159.111⟩ Article dans une revue hal-01205054v1
Annotation of the domestic dog genome sequence: finding the missing genes. Thomas Derrien,Amaury Vaysse,Catherine André,Christophe Hitte Mammalian Genome, 2012, 23 (1-2), pp.124-31. ⟨10.1007/s00335-011-9372-0⟩ Article dans une revue inserm-00643182v1
Landscape of transcription in human cells Sarah Djebali,Carrie A. Davis,Angelika Merkel,Alex Dobin,Timo Lassmannet al. Nature, 2012, 489 (7414), pp.101-108. ⟨10.1038/nature11233⟩ Article dans une revue hal-01216755v1
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. Amaury Vaysse,Abhirami Ratnakumar,Thomas Derrien,Erik Axelsson,Gerli Rosengren Pielberget al. PLoS Genetics, 2011, 7 (10), pp.e1002316. ⟨10.1371/journal.pgen.1002316⟩ Article dans une revue inserm-00638834v1
Des longs ARN non codants humains activateurs de la transcription des gènes. [Long non-coding RNAs with enhancer-like function in human cells]. Thomas Derrien,Roderic Guigó Médecine/Sciences, 2011, 27 (4), pp.359-61. ⟨10.1051/medsci/2011274009⟩ Article dans une revue inserm-00589934v1
Long noncoding RNAs with enhancer-like function in human cells Thomas Derrien,Malte Beringer,Kiranmai Gumireddy,Alessandro Gardini,Giovanni Bussottiet al. Cell, 2010, 143 (1), pp.46-58. ⟨10.1016/j.cell.2010.09.001⟩ Article dans une revue hal-02668720v1
Revisiting the missing protein-coding gene catalog of the domestic dog. Thomas Derrien,Julien Thézé,Amaury Vaysse,Catherine André,Elaine A. Ostranderet al. BMC Genomics, 2009, 10 (1), pp.62. ⟨10.1186/1471-2164-10-62⟩ Article dans une revue inserm-00366111v1
A comparative genome approach to marker ordering Thomas Faraut,Simon de Givry,Patrick P. Chabrier,Thomas Derrien,Francis Galibertet al. Bioinformatics, 2007, 23 (2), pp.E50-E56. ⟨10.1093/bioinformatics/btl321⟩ Article dans une revue hal-02667668v1
Coat colour in dogs: identification of the merle locus in the Australian shepherd breed Benoit Hédan,Sébastien Corre,Christophe Hitte,Stéphane Dréano,Thierry Vilbouxet al. BMC Veterinary Research, 2006, 2, pp.9. ⟨10.1186/1746-6148-2-9⟩ Article dans une revue hal-01068391v1

Communication dans un congrès (12)

Abstract 6494: Genetically characterized canine tumoral cell lines are relevant models to test the efficacy of new targeted therapies: Example of anti-MDM2 targeted therapy Pierre Montagne,Ulrich Jarry,Caroline Confais,Edouard Cadieu,Aline Primotet al. AACR Annual Meeting 2025, American Association for Cancer Research, Apr 2025, Chicago, United States. pp.6494-6494, ⟨10.1158/1538-7445.am2025-6494⟩ Communication dans un congrès hal-05069080v1
Advancing genome annotation with long-read RNA sequencing: Insights from the IGDRion Facility Edouard Cadieu,Aurore Besson,Matthias Lorthiois,Victor Le Bars,Armel Houelet al. JOBIM, Jun 2024, Toulouse, France Communication dans un congrès hal-04768303v1
An atlas of chicken long non-coding RNAs gathering multiple sources : gene models and expression across more than twenty tissues Frédéric Jehl,Kévin Muret,Maria Bernard,Diane Esquerré,Hervé Acloqueet al. PAG XXVII - Plant & Animal Genome Conference, Jan 2019, San Diego, United States Communication dans un congrès hal-02790912v1
Pig chromosome X long non-coding RNA annotation and expression Sarah Djebali,Oana Palasca,Christian Anton,Thomas Derrien,Ole Madsenet al. PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States Communication dans un congrès hal-02788116v1
Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid Valentin Wucher,Fabrice Legeai,Lucas Bourneuf,Thomas Derrien,Aurore Gallotet al. 10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States Communication dans un congrès hal-01566438v1
292 Lymphomas in dogs: spontaneous models to decipher the genetics of lymphomagenesis and new therapeutic options in dogs and humans R. Ulvé,B. Hédan,M. Bahin,Thomas Derrien,C. De Britoet al. International Conference on Malignant Lymphoma, Jun 2015, Lugano, Switzerland. pp.245, ⟨10.1002/hon.2229⟩ Communication dans un congrès hal-01163617v1
Long non-­‐coding RNA in the pea aphid; identification and comparative expression in sexual and asexual embryos Fabrice Legeai,Thomas Derrien,Valentin Wucher,David Audrey,Gaël Le Trionnaireet al. Arthropod Genomics Symposium, Jun 2014, Urbana, United States Communication dans un congrès hal-01091304v1
Numerical Analysis of LIPSS Coverage of Silicon Upon Irradiation with Multiple Double-fs-Pulse Sequences: The Impact of Carriers and Cumulative Effects Thomas Derrien,J. Krüger,Tatiana Itina,S. Höhm,Arkadi Rosenfeldet al. 12th International Conference on Laser Ablation, COLA 2013, Ischia, Italy 6-11 October 2013, Oct 2013, Ischia, Italy. page 126 O-49 Communication dans un congrès ujm-00878679v1
Characterization of black silicon structural and electrical properties for photovoltaics applications R. Torres,Thomas Derrien,V. Vervisch,Mathieu Halbwax,F. Torregrosaet al. European Materials Research Society Spring Meeting, E-MRS Spring 2010, Symposium I : Advanced silicon materials research for electronic and photovoltaic applications II, 2010, Strasbourg, France Communication dans un congrès hal-00574120v1
Laser Applications for Nanotechnology : Insights From Numerical Modeling Tatiana Itina,Nikita Shcheblanov,Jean-Philippe Colombier,Razvan Stoian,Eric Audouardet al. SPIE, High Power Laser Ablation, Apr 2010, Santa Fe, United States Communication dans un congrès ujm-00487302v1
Study on laser-induced periodic structures and photovoltaic application R. Torres,T.E. Itina,V. Vervisch,Mathieu Halbwax,Thomas Derrienet al. International Symposium on High-Power Laser Ablation, HPLA 2010, 2010, United States. pp.576-581, ⟨10.1063/1.3507149⟩ Communication dans un congrès hal-00568639v1
Evaluation of Luminosity Reduction in the ILC Head-on Scheme from Parasitic Collisions J. Brossard,P. Bambade,P. Dadoun,Thomas Derrien,M.C. Alabau-Ponset al. 22nd Particle Accelerator Conference 07 (PAC'07), Jun 2007, Albuquerque, United States. pp.THPMN008 Communication dans un congrès in2p3-00170819v1

Pré-publication, Document de travail (6)

Facilitating genome annotation using ANNEXA and long-read RNA sequencing Nicolaï Hoffmann,Aurore Besson,Christophe Hitte,Jocelyn Plassais,Thomas Derrien 2025 Pré-publication, Document de travail hal-05357761v1
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes Julia Halo,Amanda Pendleton,Feichen Shen,Aurélien Doucet,Thomas Derrienet al. 2020 Pré-publication, Document de travail hal-03007309v1
The tree that hides the forest: identification of common predisposing loci in several hematopoietic cancers and several dog breeds Benoit Hédan,Edouard Cadieu,Maud Rimbault,Amaury Vaysse,Patrick Devauchelleet al. 2020 Pré-publication, Document de travail hal-03007317v1
Interest of circulating tumor DNA as a biomarker for canine cancers: illustration in histiocytic sarcoma, oral malignant melanoma and multicentric lymphoma Anaïs Prouteau,Jérôme Alexandre Denis,Pauline de Fornel,Edouard Cadieu,Thomas Derrienet al. 2020 Pré-publication, Document de travail hal-03007320v1
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
A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters Thomas Mathers,Yazhou Chen,Gemy Kaithakottil,Fabrice Legeai,Sam Mugfordet al. 2020 Pré-publication, Document de travail (preprint/prepublication) hal-02936181v1

Proceedings/Recueil des communications (1)

Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework Anastasia Rusakovich,Sebastien Corre,Edouard Cadieu,Rose-Marie Fraboulet,Marie-Dominique Galibertet al. JOBIM, Jul 2025, Bordeaux, France. 2025, ⟨10.1101/2025.04.17.649290⟩ Proceedings/Recueil des communications hal-05402684v1

Poster de conférence (8)

Storing the declaration of human rights on one data DNA molecule Gouenou Coatrieux,Chloé Berton,Elsa Dupraz,Belaid Hamoum,Thomas Derrienet al. CominLabs day 2022, Oct 2022, Rennes, France. pp.1-1 Poster de conférence hal-03817852v1
Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules Jean-Marc Aury,Camille Sessegolo,Corinne Cruaud,Corinne Da Silva,Audric Cologneet al. Advances in Genome Biology and Technology General Meeting - AGBT, Feb 2020, Marco Island, FL, United States Poster de conférence hal-04443472v1
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 Rauet al. European Conference on Computational Biology (ECCB 2018), Sep 2018, Athènes, Greece. , 2018 Poster de conférence hal-02784857v1
Integrative and differential analysis of transcriptomes and chromatin accessibility regions reveals regulatory mechanisms involved in pig immune and metabolic functions Sarah Djebali Quelen,Kylie Munyard,Nathalie Villa-Vialaneix,Cédric Cabau,Andrea Rauet al. 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book Poster de conférence hal-01603033v1
Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species Kévin Muret,Sarah Djebali Quelen,Thomas Derrien,Cédric Cabau,Christophe Kloppet al. 36. Conference of the International Society for Animal Genetics (ISAG), Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book Poster de conférence hal-01621915v1
Une nouvelle facette du génome de poule : les genes “longs non-codants Kévin Muret,Christophe Klopp,Valentin Wucher,Diane Esquerre,Fabrice Legeaiet al. 12. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Apr 2017, Tours, France. ITAVI - Institut Technique de l'Aviculture, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, 2017, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras Poster de conférence hal-01605848v1
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
Long-non coding RNAs repertoire in liver and adipose tissue in chicken Kévin Muret,Christophe Klopp,Valentin Wucher,Diane D. Esquerre,Fabrice Legeaiet al. XXIV International Plant & Animal Genome (Pag), Jan 2016, San Diego, United States. 2016 Poster de conférence hal-02799305v1

Chapitre d'ouvrage (2)

nBioinformatics Pipeline for Transcriptome Sequencing Analysis Sarah Djebali,Valentin Wucher,Sylvain Foissac,Christophe Hitte,Erwan Correet al. Enhancer RNAs : Methods and Protocols, 1468 (Chapter 14), Humana Press Inc., 2017, Methods in Molecular Biology, 978-1-4939-4033-2. ⟨10.1007/978-1-4939-4035-6_14⟩ Chapitre d'ouvrage hal-02788591v1
Bioinformatics Pipeline for Transcriptome Sequencing Analysis Sarah Djebali,Valentin Wucher,Sylvain Foissac,Christophe Hitte,Erwan Correet al. Enhancer RNAs - Methods and Protocols, 1468, Editions Springer, pp.E1-E1, 2017, Methods in Molecular Biology, 978-1-4939-4035-6. ⟨10.1007/978-1-4939-4035-6⟩ Chapitre d'ouvrage hal-02789209v1

Thèse (1)

L'analyse comparée des génomes : applications à l'identification de nouveaux gènes canins Thomas Derrien Bio-informatique [q-bio.QM]. Université Rennes 1, 2007. Français. ⟨NNT : ⟩ Thèse tel-00656330v1