Bioinformatics core facility

Bioinformatics core facility - Activities

• Analysis of (epi)genomic / transcriptomic sequencing data (WGS / WES / TGS, RNA-seq, ChIP / ATAC-seq, Single-Cell, Long Reads)
• Data management (recovery, centralization, organization, labeling, provision / sharing)
• Support to bioinformaticians, biologists, and clinicians from Gustave Roussy
• Publication assistance (material and methods, figures, deposit of data on public databases such as GEO / SRA / EGA / dbGAP)
• Co-supervision of junior bioinformaticians (trainees, PhD students…)
• Dissemination of knowledge and skills for all audiences (internal teaching sessions, national training, massive open online course)

Equipments

• Calculation cluster (1500 CPUs, 9 GPUs, 5To RAM, 2Po storage)

Bioinformatics core facility - Major publications

• Nguyen-Khac, F. et al. Acquisition of TCF3 and CCND3 Mutations and Transformation to Burkitt Lymphoma in a Case of B-Cell Prolymphocytic Leukemia. Hemasphere 5, e563 (2021).
• Mazzi, S. et al. Dual role of EZH2 on megakaryocyte differentiation. Blood blood.2019004638 (2021) doi:10.1182/blood.2019004638.
• Kuksin, M. et al. Applications of single-cell and bulk RNA sequencing in onco-immunology. Eur J Cancer 149, 193–210 (2021).
• Kasperek, A. et al. Therapeutic potential of the human endogenous retroviral envelope protein HEMO: a pan-cancer analysis. Mol Oncol (2021) doi:10.1002/1878-0261.13069.
• Carré, T. et al. Selection of tumor‑resistant variants following sustained natural killer cell‑mediated immune stress. Oncol Rep 45, 582–594 (2021).
• Buart, S. et al. The Most Common VHL Point Mutation R167Q in Hereditary VHL Disease Interferes with Cell Plasticity Regulation. Cancers (Basel) 13, 3897 (2021).
• Baloche, V. et al. Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model. Sci Rep 11, 5227 (2021).

• Vielh, P. et al. DNA FISH Diagnostic Assay on Cytological Samples of Thyroid Follicular Neoplasms. Cancers (Basel) 12, E2529 (2020).
• Stefanovska, B. et al. Rapalog-Mediated Repression of Tribbles Pseudokinase 3 Regulates Pre-mRNA Splicing. Cancer Res 80, 2190–2203 (2020).
• Silvin, A. et al. Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19. Cell 182, 1401-1418.e18 (2020).
• Laurent, A. P. et al. Constitutive Activation of RAS/MAPK Pathway Cooperates with Trisomy 21 and Is Therapeutically Exploitable in Down Syndrome B-cell Leukemia. Clin Cancer Res 26, 3307–3318 (2020).
• Hassan Venkatesh, G. et al. Hypoxia increases mutational load of breast cancer cells through frameshift mutations. Oncoimmunology 9, 1750750 (2020).
• Guillem, F. et al. XPO1 regulates erythroid differentiation and is a new target for the treatment of β-thalassemia. Haematologica 105, 2240–2249 (2020).
• Desbois, M. et al. IL-15 superagonist RLI has potent immunostimulatory properties on NK cells: implications for antimetastatic treatment. J Immunother Cancer 8, e000632 (2020).
• Corgnac, S. et al. CD103+CD8+ TRM Cells Accumulate in Tumors of Anti-PD-1-Responder Lung Cancer Patients and Are Tumor-Reactive Lymphocytes Enriched with Tc17. Cell Rep Med 1, 100127 (2020).
• Beke, A. et al. Multilayer intraclonal heterogeneity in chronic myelomonocytic leukemia. Haematologica 105, 112–123 (2020).
• Auguste, A. et al. Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. Cells 9, E1496 (2020).

Bioinformatics core facility - Lab members

• Head of the bioinformatics core facility: Marc Deloger (marc.deloger@gustaveroussy.fr)

• "Core Service" bioinformaticians (permanent employees): Thibault Dayris, M’boyba Diop, Bastien Job, Gérôme Jules-Clement, Franck Le-Layo.

• "Core Service" bioinformaticians (non-permanent employees) : Marine Aglave, Edi Tihic

• "Core Service" bioinformaticians in training:  
  • Affiliated bioinformaticians working exclusively for a specific research team: Aziza Caidi, Windy Rondof, Alicia Tran Dien
  • Other bioinformaticians (hosted by the bioinformatics core facility): Baptiste Audinot, Robin Droit, Antonin Marchais, Hanane Zair, Thierno Balde