Thomas Derrien

Thomas Derrien

Researcher CNRS

CNRS - IGDR

Biography

I’m CNRS researcher at IGDR in the Canine Genetics Team. I’m particularly interested in transcritpome sequencing (short and long reads), lncRNAs annotation with the FEELnc program and deep learning for genomics.

Interests

  • Transcriptome sequencing using short (SR-RNASeq) and long (LR-RNASeq) sequencing technologies
  • Long non-coding RNAs (lncRNAs) in human and domesticated species
  • Machine Learning
  • Canine genomics

Education

  • Postdoctoral researcher in Prof Roderic Guigó s team, 2008-2011

    CRG (Barcelonan, SP)

  • PhD in comparative genomics, 2004-2007

    UMR6061 (Rennes, FR)

  • Master in bioinformatics, 2002 - 2004

    Master Bioinformatic (Rouen - FR)

Posts

News

  • We have a new engineer position for working on lncRNAs, CRISPR and cancers (2021)!! If you are interested in Nanopore sequencing and lncRNA annotation from both dry (bioinformatic) and wet (molecular biology) lab aspects, please see here for more details.
  • Feel free to contact us if your are interested in bioinformatics and long read sequencing strategies.

Projects

Genome Annotation

Genome Annotation

  • LncRNA Annotation and classification with FEELnc.
  • LncRNAs characterisation in canine cancers.
  • Long-read sequencing with Oxford Nanopore Technologies (ONT) at IGDR LR sequencing.

Deep Learning for genomics

NGS analysis for canine cancers

  • Mutations and CNAs analysis for mucosal melanoma (MM) and Hystiocytic Sarcoma (HS)).
  • Unsupervised clustering of dog patients using NMF method.
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All FEELnc Nanopore Sequencing Deep Learning Dog NGS

Recent Publications

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Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma

Circulating tumor DNA (ctDNA) has become an attractive biomarker in human oncology, and its use may be informative in canine cancer. …
Anäis Prouteau, Jérôme Alexandre Denis, Pauline De Fornel, Edouard Cadieu, Thomas Derrien, Camille Kergal, Nadine Botherel, Ronan Ulvé, Mélanie Rault, Amira Bouzidi, Romain François, Laetitia Dorso, Alexandra Lespagnol, Patrick Devauchelle, Jérôme Abadie, Catherine André, Benoît Hédan
PDF DOI

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

Histiocytic sarcoma (HS) is a rare but aggressive cancer in both humans and dogs. The spontaneous canine model, which has clinical, …
Benoît Hédan, Édouard Cadieu, Maud Rimbault, Amaury Vaysse, Caroline Dufaure de Citres, Patrick Devauchelle, Nadine Botherel, Jérôme Abadie, Pascale Quignon, Thomas Derrien, Catherine André
DOI

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

textlessptextgreaterTechnological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- …
Julia V. Halo, Amanda L. Pendleton, Feichen Shen, Aurélien J. Doucet, Thomas Derrien, Christophe Hitte, Laura E. Kirby, Bridget Myers, Elzbieta Sliwerska, Sarah Emery, John V. Moran, Adam R. Boyko, Jeffrey M. Kidd
PDF DOI

PTPN11 mutations in canine and human disseminated histiocytic sarcoma

Benoit Hédan, Mélanie Rault, Jérôme Abadie, Ronan Ulvé, Nadine Botherel, Patrick Devauchelle, Christiane Copie‐Bergman, Edouard Cadieu, Marie Parrens, Julia Alten, Emmanuelle L. Zalcman, Gunnar Cario, Gandhi Damaj, Karima Mokhtari, Francois Le Loarer, Aurore Coulomb‐Lhermine, Thomas Derrien, Christophe Hitte, Laura Bachelot, Matthew Breen, David Gilot, Jean Y. Blay, Jean Donadieu, Catherine André
PDF DOI

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

BACKGROUND: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, …
Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kevin Muret, Diane Esquerre, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cedric Cabau, Elisa Crisci, Sophie Dhorne-Pollet, Francoise Drouet, Thomas Faraut, Ignacio Gonzalez, Adeline Goubil, Sonia Lacroix-Lamande, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaelle Momal-Leisenring, Florence Mompart, Pascale Quere, David Robelin, Magali San Cristobal, Gwenola Tosser-Klopp, Silvia Vincent-Naulleau, Stephane Fabre, Marie-Helene Pinard-Van der Laan, Christophe Klopp, Michele Tixier-Boichard, Herve Acloque, Sandrine Lagarrigue, Elisabetta Giuffra
DOI
See all publications

Animation/Formation

INRAE MISTI

INRAE Nominated member Oct 2020
INRAE Researcher evaluation

CNRS section 21

CNRS Nominated member Oct 2020 – Jun 2021
See certificate

IGDR laboratory Council

Elected member Jan 2017
See certificate

Contact

  • (+33)2 23 23 65 34
  • Université Rennes1, IGDR, 2 av Leon Bernard, Rennes, 35043
  • Enter Building 4 and take the stairs to Office 212 on Floor 2
  • DM Me