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Predictive biology in livestock production is essential, however it would greatly benefit from a better functional annotation of livestock genomes. To this end, the scientific community is undertaking a coordinated international action with FAANG, the Functional Annotation of ANimal Genomes project. Within FAANG, the FR-AgENCODE French initiative is producing functional genomics data including expression data (RNA-seq) and chromatin conformation data (Hi-C), in 4 livestock species (cow, pig, goat, chicken). My project aims at identifying functional genomics elements in these 4 livestock species, based on the FR-AgENCODE data, but also on comparative genomics approaches, which serve both to transfer functional annotation from model species (such as human and mouse) to livestock species, but also to produce sets of orthologous and species-specific functional elements across the 4 livestock species. These functional maps and correspondences are made available to the scientific community to enable advances in livestock research.One particular focus we will consider is to combine this functional annotation with genomic evaluation data, in order to investigate the genetic architecture of complex traits in livestock.
Initially trained incomputerscience,Imovedtocomputational biology and bioinformatics during my 2nd master in 2001. I then did my phD in computational biology at ENS Paris and Univ Evry, where I developed the Exogean program to identify genes in eukaryotic genomes using comparative genomics and heuristic rules. This program was ranked 1st at the transcript level at the EGASP’05 competition. Convinced that computer science and data analysis were essential in biology, I decided to become involved in large scale functional genomics consortia such as ENCODE, as a postdoc in Pr. Roderic Guigo (CRG, Barcelona), from 2006. I then had the opportunity to collaborate with Pr. Thomas Gingeras (Affymetrix and CSHL), and to work on transcript annotation and pervasive transcription in human and mouse. In the production phase of ENCODE, I was also responsible for the coordination of all transcriptomics analyses done within the consortium. In the context of the mouse ENCODE project, I recently contributed to the large- scale comparison of mouse and human transcriptomes. I am generally interested in functional genomic annotation of animal genomes, and its application to the understanding of complex traits in livestock.
Breschi A, Djebali S, Gillis J, Pervouchine DD, Dobin A, Davis CA, Gingeras TR, Guigó R., 2016. Gene-specific patterns of expression variation across organs and species, Genome Biol., 17(1):151.
Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH et al., 2015. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression, Nat Commun, 6:5903.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al., 2012. Landscape of transcription in human cells, Nature, 489(7414):101-8.
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al 2012, Evidence for transcript networks composed of chimeric RNAs in human cells, PLoS One, 7(1):e28213.
Djebali S, Delaplace F, Roest Crollius H, 2006, Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA, Genome Biol, 7 Suppl 1:S7.110.