Mots-Clés
Multi-omics
liver pathophysiology
cell identity
transcriptional regulation
Description
Presentation of the recruiting organization and scientific context
Our team “Integrated transcriptional analysis of liver diseases” (https://u1011.pasteur-lille.fr/5/the-unit/theme-4-integrated-molecular-analysis-of-gene-expression-in-liver-diseases/) is part of UMR Inserm 1011 (headed by Prof Bart Staels) hosting 6 teams with research interests ranging from metabolic, inflammatory and cardiac pathologies to epigenomic and transcriptomic characterization of disease progression. Our laboratory is part of the Université de Lille (70,000 students, the largest in France), Institut Pasteur de Lille (IPL, an independent non-profit private foundation created by Louis Pasteur in 1894) and the European Genomic Institute
for Diabetes (EGID, "Laboratory of Excellence”).
The recruited post-doctoral fellow will work under the supervision of Dr Jérôme Eeckhoute (CNRS DR; https://cvscience.aviesan.fr/cv/479/jerome-eeckhoute) and will benefit from a highly collaborative and international environment including both bioinformaticians (Dr Julie Dubois-Chevalier) and biologists. The successful candidate will conduct a project dedicated to
the understanding and in-depth characterization of pathophysiological liver cell plasticity through mining omics data including bulk and single-cell epigenomic and transcriptomic datasets.
Candidate profile and responsibilities
We are seeking a highly motivated post-doctoral fellow with strong and proven expertise in (multi-)omics data mining (transcriptomics and additional genome-wide approaches to study gene transcriptional regulation). The successful candidate should have a PhD in bioinformatics or a solid and proven background in running bioinformatical analyses. Experience with omics data and functional genomics is required.
Expected skills:
- Program coding skills (R, python)
- skills in multivariate methods and machine learning in high dimension, dimension reduction methods (data modelling, inferential statistics...)
- ability to work independently within a pluridisciplinary team environment in tight interaction with biologists
Responsibilities of the successful candidate:
- bioinformatical and statistical analysis of omics data to monitor cell plasticity at the transcriptomic level
- infer pathways and transcriptional regulators driving modulation to the cellular transcriptome
- define strategies for integrative analysis of heterogeneous omics datasets
- present results at lab meetings and conferences, write scientific articles and contribute to grant writing
Selected recent publications from the host team
An extended transcription factor regulatory network controls hepatocyte identity.
Dubois-Chevalier J, Gheeraert C, Berthier A, Boulet C, Dubois V, Guille L, Fourcot M, Marot G, Gauthier K, Dubuquoy L, Staels B, Lefebvre P, Eeckhoute J. EMBO Rep. 2023 Sep 6;24(9):e57020. doi: 10.15252/embr.202357020.
Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis.
Bobowski-Gerard M, Boulet C, Zummo FP, Dubois-Chevalier J, Gheeraert C, Bou Saleh M, Strub JM, Farce A, Ploton M, Guille L, Vandel J, Bongiovanni A, Very N, Woitrain E, Deprince A, Lalloyer F, Bauge E, Ferri L, Ntandja-Wandji LC, Cotte AK, Grangette C, Vallez E, Cianférani S, Raverdy V, Caiazzo R, Gnemmi V, Leteurtre E, Pourcet B, Paumelle R, Ravnskjaer K, Lassailly G, Haas JT, Mathurin P, Pattou F, Dubuquoy L, Staels B, Lefebvre P, Eeckhoute J. Nat Commun. 2022 Sep 10;13(1):5324. doi: 10.1038/s41467-022-33063-9.
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver.
Dubois V, Gheeraert C, Vankrunkelsven W, Dubois-Chevalier J, Dehondt H, Bobowski-Gerard M, Vinod M, Zummo FP, Güiza F, Ploton M, Dorchies E, Pineau L, Boulinguiez A, Vallez E, Woitrain E, Baugé E, Lalloyer F, Duhem C, Rabhi N, van Kesteren RE, Chiang CM, Lancel S, Duez H, Annicotte JS, Paumelle R, Vanhorebeek I, Van den Berghe G, Staels B, Lefebvre P, Eeckhoute J
Mol Syst Biol. 2020 May;16(5):e9156.
Hepatic molecular signatures highlight the Non-Alcoholic SteatoHepatitis (NASH) sexual dimorphism.
Vandel J, Dubois-Chevalier J, Gheeraert C, Derudas B, Raverdy V, Thuillier D, Van Gaal L, Francque S, Pattou F, Staels B, Eeckhoute J, Lefebvre P. Hepatology. 2020 Mar;73(3):920-936. doi: 10.1002/hep.31312