Thomas DERRIEN

Information

Staff scientist

Catherine ANDRÉ Group

+33 (0)2 23 23 65 34

Villejean campus / Building 4 / Room 212

Responsibilities

  • Member of the FAANG consortium (Functional Annotation of Animal Genomes)
  • Member of the Fr-AgENCODE consortium
  • Development and maintenance of bioinformatic tools:

         - AutoGRAPH (autograph.genouest.org): a web server for comparative genomic
         - FEELnc (https://github.com/tderrien/FEELnc) : FlExible Extraction of Long non-coding RNAs

Education

  • Teaching bioinformatics in Master BiG (BioInformatic and Génomic) of Rennes1
  • Teaching molecular biology (genome annotation) at the faculty of Pharmacy at Rennes1
  • Teaching biostatistics in L3 Biology of Rennes1

Shared responsibilities

  • Member of the IGDR social events group

In a few words

I’m a researcher in biology/bioinformatics specialized in genome annotation which aims at identifying functional elements of the genome (protein-coding genes, ncRNAs…). During my PhD, I have developed methods in comparative genomics based on gene order conservation between species. This approach highlighted the multiple conserved segments between dogs and others mammals and allowed us to annotate many novel canine genes in the genome.

 

Then in 2008, I moved to Barcelona- Spain as postdoctoral researcher in Pr. R.Guigó’s team where I worked on the analysis of Next generation Sequencing (NGS) data within the ENCODE project (ENCyclopedia Of Dna Elements). More particularly, using whole transcriptome sequencing (RNA-Seq), I characterized a catalogue of 15,000 human long non-coding RNAs and analyzed their correlations of expression with mRNAs partners.

 

I was hired by CNRS in 2012 in the dog genetics team (Dr. Catherine André) where I’m now developing new bioinformatic tools to facilitate the automatic annotation of lncRNAs based on machine learning techniques and using RNA-Seq. This tool has been used on multiple species including dogs, chicken, aphids and algae.

Major publications

    •  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. 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).

     

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