Sarah Djebali Quelen
AgreenSkills session, year: 1st session, 2015
Receiving laboratory: GenPhySE, Toulouse
Country of origin : Spain
Functional annotation of livestock genomes using functional genomics data and comparative genomics approaches
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 will 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 will be made available to the scientific community to enable advances in livestock research, and one particular focus one could explore would be to try and combine this functional annotation with genomic evaluation data, in order to investigate the genetic architecture of complex traits in livestock.
Initially trained in computer science (ENSEIRB Engineering school, Bordeaux, France), I moved to computational Biology and Bioinformatics during my 2nd master in 2001 (DEA AMIB, Evry, France), since I always liked biology and genetics. I then did my phD in computational biology at ENS Paris and Université d’Evry, where I developed the Exogean program to identify genes in eukaryotic genomes using comparative genomics and heuristic rules, which was ranked 1st at the transcript level at the EGASP’05 competition (Djebali et al., Genome Biology, 2006). Convinced that computer science and data analysis were essential in Biology given the exponentially increasing amount of data being generated, I decided to become involved in large scale functional genomics consortia such as ENCODE, as a postdoc with in “postdoc in Professor R. Guigo” (CRG, Barcelona), from October 2006. During this postdoc I had the great opportunity to collaborate with Pr. Thomas Gingeras (Affymetrix and CSHL), and to work on transcript annotation and pervasive transcription in human. In the production phase of ENCODE, I was also responsible for the coordination of all transcriptomics analyses done within the consortium, which ended up with the ENCODE transcriptome paper publication in September 2012 (Djebali et al., Nature, 2012). In the context of the mouseENCODE project, I recently contributed to the large-scale comparison of mouse and human transcriptomes (Pervouchine*, Djebali*, Breschi*, Davis* et al, Nature Communications, 2015). I am generally interested in functional genomic annotation of animal genomes, and its application to the understanding of complex traits in livestock.
• Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA, 2016, A benchmark for RNA-seq quantification pipelines, Genome Biol,17(1):74
• Pervouchine DD*, Djebali S*, Breschi A*, Davis CA*, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR, 2015, Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression, Nat Commun, 6:5903.*
• Durán E, Djebali S, González S, Flores O, Mercader JM, Guigó R, Torrents D, Soler-López M, Orozco M, 2013, Unravelling the hidden DNA structural/physical code provides novel insights on promoter location, Nucleic Acids Res. 41(15):7220-30.
• Derrien T*, Johnson R*, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R, 2012, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res, 9:1775-89.
• Djebali S*, Davis CA*, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, 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, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR, 2012, Evidence for transcript networks composed of chimeric RNAs in human cells, PLoS One, 7(1):e28213.
• Djebali S*, Kapranov P*, Foissac S*, Lagarde J*, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, Harrow J, Makrythanasis P, Vidal M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigó R, 2008, Efficient targeted transcript discovery via array-based normalization of RACE libraries, Nat Methods, 7:629-35.
The 3rd prize Vanguardia de la Ciencia in May 2013 (together with Pr. Roderic Guigó) for Landscape of Transcription in human cells, published in Nature in 2012