Python Job: Bio-informatician - A 5-year contract (H-F)

Votre Mission :

A 5-year position for an experienced bio-informatician, is open at Gustave Roussy Cancer Center. Position can be adapted to the experience of the candidate. The position is part of an institutional effort to build a large data center and promote analyses and integration of patients and model-generated data. This effort aims at generating multi-omics data from tumor samples for integration and analyses by artificial intelligence.

The project aims at analyzing the molecular mechanisms underlying hematopoietic transformation and resistance to treatment. It will be centered on the analyses of lymphomaand acute myeloid leukemia-related data, for which bulk NGS (RNA-seq, CHIP-seq, ATACseq,...) and single cell expression data are already available. An important goal of the work will be to generate or organize appropriate pipelines to produce fully integrated figure panels for scientific publications. Experience with handling high throughput sequencing and single cell sequencing data is essential. Knowledge of the hematopoietic system would be appreciated but is not mandatory. We have acquired expertise in functional genomic characterization of human lymphoid malignancies (Roos-Weil et al. Cancer Discov. 2019, Blood 2020).

Recently generated whole genomes sequences, targeted sequences, RNA-seq and Illumina methylation array on 15-20 Waldenstrom macroglobulinemia patients will be analyzed and integrated together with clinical data to identify novel alterations. Mouse models have been analyzed with respect to the germinal center reaction in the context of Waldentrom macroglobulinemia somatic mutations, including mutation of the PU.1 transcription factor.

Votre profil :

This includes both bulk and single cell expression data. Studies on acute myeloid leukemia (AML) will aim at defining the cellular and molecular trajectory from a normal cell to a leukemic cell using single cell transcriptome data from human-cell based models in which fusion oncogenes are induced either through lentiviral delivery or through CRISPR-Cas9 editing (including using induced pluripotent stem cells & primary human cells at different stages of development). These data will be compared to single cell transcriptomes from human AML available from our involvement in national consortiums. Integration with ChIP-seq, ATAC-seq, mass spectrometry and CRISPR-based screening data will be performed to further define the molecular mechanism of transformation and AML maintenance and investigate treatment escape and resistance.

These analyses will inform functional validation that will be performed on an already available set of cellular and in vivo models (Thirant et al. Cancer cell 2017, Lopez et al. Cancer Discovery 2019).

Required qualities: - Bioinformatics Engineer (Master or PhD) with strong biological background and mathematical interest

- Mandatory technical skills : o > 2 years Omics data analysis experience (genomics, transcriptomics, epigenomics) o R and Python programming o High-Performance Computing usage (Bash and Slurm) o Workflow Manager (Snakemake or Nextflow) o Code versioning (Git) o Report generation (R markdown or Python notebook) - Multi-projects management experience - Multi-level heterogeneous omics data integration knowledges - Machine learning / IA knowledges will be a plus - Autonomous, proactive, dynamic and rigorous - Team spirit and good interpersonal/communication skills.

A propos de Gustave Roussy :

Gustave Roussy, premier centre de lutte contre le cancer en Europe, est un établissement de santé privé participant au service public hospitalier. Pôle d'expertise global contre le cancer entièrement dédié aux patients, il réunit sur deux sites près de 3 000 professionnels dont les missions sont le soin, la recherche et l'enseignement.

Dans le cadre de notre politique volontariste en faveur de l'insertion des personnes en situation de handicap, toutes les candidatures reçues sont étudiées à compétences égales.