Accéder directement au contenu
DT

Derrien Thomas

62
Documents

Publications

Image document

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 hal-03467210v1
Image document

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 Dubos
Current Biology - CB, 2022, 32 (4), pp.889-897.e9. ⟨10.1016/j.cub.2021.12.036⟩
Article dans une revue hal-03555249v1
Image document

Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets

Anais Prouteau , Stephanie Mottier , Aline Primot , Edouard Cadieu , Laura Bachelot
Cancers, 2022, 14 (2), pp.276. ⟨10.3390/cancers14020276⟩
Article dans une revue hal-03555450v1
Image document

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 Derrien
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
Image document

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 Derrien
Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-020-80332-y⟩
Article dans une revue hal-03110876v1
Image document

Identification of common predisposing loci to hematopoietic cancers in four dog breeds

Benoit Hedan , Edouard Cadieu , Maud Rimbault , Amaury Vaysse , Caroline Dufaure de Citres
PLoS Genetics, 2021, 17 (4), pp.e1009395. ⟨10.1371/journal.pgen.1009395⟩
Article dans une revue hal-03215819v1
Image document

An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

Frédéric Jehl , Kévin Muret , Maria Bernard , Morgane Boutin , Laetitia Lagoutte
Scientific Reports, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩
Article dans une revue hal-03039897v1
Image document

Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma

Anaïs Prouteau , Florian Chocteau , Clotilde de Brito , Edouard Cadieu , Aline Primot
Veterinary and Comparative Oncology, 2020, 18 (2), pp.214-223. ⟨10.1111/vco.12536⟩
Article dans une revue hal-02280596v1
Image document

PTPN11 mutations in canine and human disseminated histiocytic sarcoma

Benoit Hedan , Mélanie Rault , Jérôme Abadie , Ronan Ulvé , Nadine Botherel
International Journal of Cancer, 2020, 147 (6), pp.1657-1665. ⟨10.1002/ijc.32991⟩
Article dans une revue hal-02534873v1
Image document

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 Letko
Genes, 2019, 10 (5), pp.E386. ⟨10.3390/genes10050386⟩
Article dans une revue hal-02153481v1
Image document

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
Image document

Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas

Christophe Hitte , Céline Le Béguec , Edouard Cadieu , Valentin Wucher , Aline Primot
Genes, 2019, 10 (6), pp.E:477. ⟨10.3390/genes10060477⟩
Article dans une revue hal-02179210v1
Image document

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo , Corinne Cruaud , Corinne da Silva , Audric Cologne , Marion Dubarry
Scientific Reports, 2019, 9 (1), pp.14908. ⟨10.1038/s41598-019-51470-9⟩
Article dans une revue hal-02335574v1
Image document

Characterisation and functional predictions of canine long non-coding RNAs

Celine Le Beguec , Valentin Wucher , Laetitia Lagoutte , Edouard Cadieul , Nadine Botherel
Scientific Reports, 2018, 8 (1), pp.13444. ⟨10.1038/s41598-018-31770-2⟩
Article dans une revue hal-01888670v1

Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis

Sarah Djebali , Valentin Wucher , Sylvain Foissac , Christophe Hitte , Erwan Corre
Methods in Molecular Biology, 2017, 1468, pp.E1. ⟨10.1007/978-1-4939-4035-6_17⟩
Article dans une revue hal-01439359v1
Image document

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. Mugford
Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩
Article dans une revue hal-01588181v1
Image document

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 Wucher
New Phytologist, 2017, 214 (1), pp.219-232. ⟨10.1111/nph.14321⟩
Article dans une revue hal-03145812v1
Image document

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 Lagoutte
Nucleic Acids Research, 2017, 45 (8), pp.12. ⟨10.1093/nar/gkw1306⟩
Article dans une revue hal-01532061v1
Image document

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. Mugford
Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩
Article dans une revue hal-01500475v1
Image document

An exome sequencing based approach for genome-wide association studies in the dog

Bart J. G. Broeckx , Thomas Derrien , Stephanie Mottier , Valentin Wucher , Edouard Cadieu
Scientific Reports, 2017, 7 (1), pp.15680. ⟨10.1038/s41598-017-15947-9⟩
Article dans une revue hal-01659287v1
Image document

Long noncoding RNA repertoire in chicken liver and adipose tissue

Kévin Muret , Christophe C. Klopp , Valentin Wucher , Diane Esquerré , Fabrice Legeai
Genetics Selection Evolution, 2017, 49 (1), pp.6. ⟨10.1186/s12711-016-0275-0⟩
Article dans une revue hal-01431420v1
Image document

Discovery of Human-Similar Gene Fusions in Canine Cancers

Ronan Ulvé , Mélanie Rault , Mathieu Bahin , Laetitia Lagoutte , Jérôme Abadie
Cancer Research, 2017, 77 (21), pp.5721-5727. ⟨10.1158/0008-5472.CAN-16-2691⟩
Article dans une revue hal-01647128v1

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 Guaguère
PLoS Genetics, 2016, 12 (12), pp.e1006482. ⟨10.1371/journal.pgen.1006482⟩
Article dans une revue hal-01439364v1
Image document

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. Guaguere
Bulletin de l'Académie Vétérinaire de France, 2016, 21 (3), pp.289--290. ⟨10.4267/2042/61953⟩
Article dans une revue hal-01415930v1
Image document

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 Keulenaer
Scientific Reports, 2015, 5 (1), pp.12810. ⟨10.1038/srep12810⟩
Article dans une revue hal-01187322v1
Image document

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 hal-01240461v1

Assessment of transcript reconstruction methods for RNA-seq.

Tamara Steijger , Josep F Abril , Pär G Engström , Felix Kokocinski , Martin Akerman
Nature Methods, 2013, 10 (12), pp.1177-1184. ⟨10.1038/nmeth.2714⟩
Article dans une revue hal-00909081v1

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
Image document

Landscape of transcription in human cells

Sarah Djebali , Carrie A. Davis , Angelika Merkel , Alex Dobin , Timo Lassmann
Nature, 2012, 489 (7414), pp.101-108. ⟨10.1038/nature11233⟩
Article dans une revue hal-01216755v1
Image document

Fast computation and applications of genome mappability.

Thomas Derrien , Jordi Estellé , Santiago Marco Sola , David G. Knowles , Emanuele Raineri
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 Djebali
Genome Research, 2012, 22, pp.1775-1789. ⟨10.1101/gr.132159.111⟩
Article dans une revue hal-01205054v1
Image document

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
Image document

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

Amaury Vaysse , Abhirami Ratnakumar , Thomas Derrien , Erik Axelsson , Gerli Rosengren Pielberg
PLoS Genetics, 2011, 7 (10), pp.e1002316. ⟨10.1371/journal.pgen.1002316⟩
Article dans une revue inserm-00638834v1
Image document

Long noncoding RNAs with enhancer-like function in human cells

Thomas Derrien , Malte Beringer , Kiranmai Gumireddy , Alessandro Gardini , Giovanni Bussotti
Cell, 2010, 143 (1), pp.46-58. ⟨10.1016/j.cell.2010.09.001⟩
Article dans une revue hal-02668720v1
Image document

Revisiting the missing protein-coding gene catalog of the domestic dog.

Thomas Derrien , Julien Thézé , Amaury Vaysse , Catherine André , Elaine A. Ostrander
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 Galibert
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 Vilboux
BMC Veterinary Research, 2006, 2, pp.9. ⟨10.1186/1746-6148-2-9⟩
Article dans une revue hal-01068391v1
Image document

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 Acloque
PAG XXVII - Plant & Animal Genome Conference, Jan 2019, San Diego, United States
Communication dans un congrès hal-02790912v1

Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid

Valentin Wucher , Fabrice Legeai , Lucas Bourneuf , Thomas Derrien , Aurore Gallot
10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States
Communication dans un congrès hal-01566438v1

Pig chromosome X long non-coding RNA annotation and expression

Sarah Djebali , Oana Palasca , Christian Anton , Thomas Derrien , Ole Madsen
PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Communication dans un congrès hal-02788116v1

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 Brito
International Conference on Malignant Lymphoma, Jun 2015, Lugano, Switzerland. pp.245, ⟨10.1002/hon.2229⟩
Communication dans un congrès hal-01163617v1
Image document

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 Trionnaire
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 Rosenfeld
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

Study on laser-induced periodic structures and photovoltaic application

R. Torres , T.E. Itina , V. Vervisch , Mathieu Halbwax , Thomas Derrien
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

Characterization of black silicon structural and electrical properties for photovoltaics applications

R. Torres , Thomas Derrien , V. Vervisch , Mathieu Halbwax , F. Torregrosa
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 Audouard
SPIE, High Power Laser Ablation, Apr 2010, Santa Fe, United States
Communication dans un congrès ujm-00487302v1
Image document

Evaluation of Luminosity Reduction in the ILC Head-on Scheme from Parasitic Collisions

J. Brossard , P. Bambade , P. Dadoun , Thomas Derrien , M.C. Alabau-Pons
22nd Particle Accelerator Conference 07 (PAC'07), Jun 2007, Albuquerque, United States. pp.THPMN008
Communication dans un congrès in2p3-00170819v1
Image document

Storing the declaration of human rights on one data DNA molecule

Gouenou Coatrieux , Chloé Berton , Elsa Dupraz , Belaid Hamoum , Thomas Derrien
CominLabs day 2022, Oct 2022, Rennes, France. pp.1-1
Poster de conférence hal-03817852v1

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
Image document

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 Blanc
36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book
Poster de conférence hal-01608449v1

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 Rau
36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book
Poster de conférence hal-01603033v1
Image document

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 C. Klopp
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 C. Klopp , Valentin Wucher , Diane Esquerre , Fabrice Legeai
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

Long-non coding RNAs repertoire in liver and adipose tissue in chicken

Kévin Muret , Christophe C. Klopp , Valentin Wucher , Diane D. Esquerre , Fabrice Legeai
XXIV International Plant & Animal Genome (Pag), Jan 2016, San Diego, United States. 2016
Poster de conférence hal-02799305v1

nBioinformatics Pipeline for Transcriptome Sequencing Analysis

Sarah Djebali , Valentin Wucher , Sylvain Foissac , Christophe Hitte , Erwan Corre
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 Corre
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