Thomas DERRIEN

Equipe Génétique du Chien

Email : thomas [dot] derrien [at] univ-rennes1 [dot] fr

Phone : +33 (0)2 23 23 65 34

Office number : Villejean / Bât 4 / 10 (RdC)

In a few words

I am a biologist-bioinformatician and I am particularly interested in genome annotation, i.e. the identification of functional genomic elements (genes, non-coding RNAs, etc.) combining complentary strategies such as  high-throughput sequencing and bioinformatics.

During my thesis on dog genetics, I developed a method for comparing genomes based on the conservation of gene order between species (AutoGRAPH). This approach highlighted the evolutionarily conserved segments between the dog and other mammals and improved the annotation of its genome by identifying several hundred new canine genes.

During my post-doctorate at the CRG (Barcelona), I was interested in new methods for identifying human functional elements by high-throughput sequencing (or NGS) in the framework of the international consortium ENCODE (ENCyclopedia Of Dna Elements). Through the exploitation of transcriptome sequencing data (RNA-Seq), I characterised a catalogue of ~15,000 long non-coding RNAs (lncRNAs) involved in the regulation of mRNA expression.

I was recruited as a research fellow at CNRS in 2012.  I now use and develop bioinformatics tools based on machine learning methods (e.g. FEELnc: Wucher et al.) for the annotation of genomes of model and/or domesticated organisms (dog, chicken...).

Since 2019, I am also the scientific leader of the "long-read" IGDR sequencing facility using the Oxford Nanopore technology. In this context, we use and develop bioinformatics tools dedicated to long-read data to identify lncRNAs (Matthias Lorthiois, Aurore Besson) and genomic structural variations (Céline Le Béguec, Stéphanie Mottier) in dogs and humans.

We are also developing deep learning strategies (CNN, transformers) applied to genomic/transcriptomic data in order to predict gene expression and the impact of non-coding mutations (Camille Kergal's thesis). 

 

Responsibilities

  • Co-leader of the bioinformatics group Bioinfog of the dog genetics team. 

  • Scientific leader of the IGDRion "long-read" IGDR sequencing facility using the Oxford Nanopore technology.

  • Nominated member of the CNRS section 21 (2020-2025).

  • Nominated member of the CSS MISTI of INRAE: Commission Scientifique Spécialisée Mathématique, Informatique, Sciences et Technologies du numérique, Intelligence artificielle et Robotique (MISTI) (2020 - 2025).

  • Elected member of the Laboratory Council (college C/EC) of the IGDR (2017-2021)

  • Development and maintenance of the following bioinformatics tools:

    • AutoGRAPH : Comparative genomics server

    • FEELnc : Long non-coding RNA annotation tool

Selected Publications

(full-list here)

  • Prouteau, A., Mottier, S., Primot, A., Cadieu, E., Bachelot, L., Botherel, N., Cabillic, F., Houel, A., Cornevin, L., Kergal, C., Corre, S., Abadie, J., Hitte, C., Gilot, D., Lindblad-Toh, K., André, C., Derrien, T., & Hedan, B. (2022). Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. Cancers14(2), 276. https://doi.org/10.3390/cancers14020276

  • Lagarrigue, S., Lorthiois, M., Degalez, F., Gilot, D., & Derrien, T. (2021). LncRNAs in domesticated animals : From dog to livestock species. Mammalian Genome.

  • Hédan B, Rault M, Abadie J, Ulvé R, Botherel N, Devauchelle P, Copie-Bergman C, Cadieu E, Parrens M, Alten J, Zalcman EL, Cario G, Damaj G, Mokhtari K, Le Loarer F, Coulomb-Lhermine A, Derrien T, Hitte C, Bachelot L, Breen M, Gilot D, Blay JY, Donadieu J, André C. PTPN11 mutations in canine and human disseminated histiocytic sarcoma. Int J Cancer. 2020 Sep 15;147(6):1657-1665. doi: 10.1002/ijc.32991. Epub 2020 Apr 8. PMID: 32212266.

  • Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, Pinard-Van der Laan MH, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, Giuffra E. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol. 2019 Dec 30;17(1):108. doi: 10.1186/s12915-019-0726-5. PMID: 31884969; PMCID: PMC6936065.

  • Sessegolo C, Cruaud C, Da Silva C, Cologne A, Dubarry M, Derrien T, Lacroix V, Aury JM. Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules. Sci Rep. 2019 Oct 17;9(1):14908. doi: 10.1038/s41598-019-51470-9. PMID: 31624302; PMCID: PMC6797730.

  • Prouteau A, Chocteau F, de Brito C, Cadieu E, Primot A, Botherel N, Degorce F, Cornevin L, Lagadic MA, Cabillic F, de Fornel-Thibaud P, Devauchelle P, Derrien T, Abadie J, André C, Hédan B.

  • Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma. Vet Comp Oncol. 2020 Jun;18(2):214-223. doi: 10.1111/vco.12536. Epub 2019 Sep 13. PMID: 31461207.

  • Hitte C, Le Béguec C, Cadieu E, Wucher V, Primot A, Prouteau A, Botherel N, Hédan B, Lindblad-Toh K, André C, Derrien T. Genome-Wide Analysis of Long Non- Coding RNA Profiles in Canine Oral Melanomas. Genes (Basel). 2019 Jun 23;10(6):477. doi: 10.3390/genes10060477. PMID: 31234577; PMCID: PMC6628375.

  • Hédan B, Cadieu E, Botherel N, Dufaure de Citres C, Letko A, Rimbault M, Drögemüller C, Jagannathan V, Derrien T, Schmutz S, Leeb T, André C. Identification of a Missense Variant in <i>MFSD12</i> Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs. Genes (Basel). 2019 May 21;10(5):386. doi: 10.3390/genes10050386. PMID: 31117290; PMCID: PMC6562630.

  • Le Béguec C., et al. Characterisation and functional predictions of canine long non-coding RNAs. Sci Rep,  8:13444 (2018). Wucher, V. et al. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res gkw1306 (2017). doi:10.1093/nar/gkw1306

  • Plassais, J. et al. A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies. PLoS Genet 12, e1006482 (2016).

  • Broeckx B. J. G. et al. Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Scientific Reports 5, 12810 (2015).
    Derrien T, Estellé J, Sola SM, Knowles DG, Raineri E, Guigó R, et al. Fast Computation and Applications of Genome Mappability. PLoS One. (2012);7. 

  • Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22, 1775–1789 (2012).

  • Djebali, S. et al. Landscape of transcription in human cells. Nature 488, 101–108 (2012).
    Ørom U et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010).

  • Derrien T., André, C., Galibert, F. & Hitte, C. AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. Bioinformatics 23, 498–499 (2007)

Responsabilités partagées

  • Membre du groupe de cohésion sociale de l’IGDR