Bioinformatic scientist (IE/IR)

Context and laboratory

In the frame of the Paris Kids Cancer consortium, a trans-IRPs project is funded that aims at constructing and characterizing a cellular atlas of pediatric cancers based on single-cell transcriptomics and exploring the relationships between development, immune cells and tumor cell phenotypes. To consider both intra-tumor heterogeneity (within tumors) and inter-tumor heterogeneity (between patients), the project will first integrate single-cell RNA-seq data of tumor cells from several pediatric cancer types to further investigate commonalities and relationship between transcriptional and signaling networks. Tumor cell data will be compared to single-cell atlas of normal cells during development that are already published and/or to data generated in the frame of PKC. All non-malignant populations will be integrated from available pediatric malignancies to explore the commonalities and differences of the various populations of the tumor microenvironment  with a strong focus on immune cells.

This project offers a unique opportunity to participate in the understanding of tumor initiation and progression of pediatric cancers. The collaborative aspect of the project and interactions with the various teams of the PKC consortium will create a highly synergistic environment. Two bioinformatic scientists will be recruited for the project, one being based at Institut Curie and one being based at Gustave Roussy.

Missions

The candidate will:

• Actively participate in the development of a common analysis pipeline to obtain robust count tables from single-cell transcriptomic raw data.

• Run the analysis pipeline on various single-cell RNA-seq datasets obtained in-house and other teams of the PKC consortium as well as published/external datasets.

• Use and/or develop methods and strategies to explore the data in close collaboration with biologists. One key aspect will be to perform various integrations of filtered data to address tumor cell phenotypes, links with normal cells of the development and characterize non-malignant populations of the tumor microenvironment.

• Actively participate in the preparation of a dedicated Web server to share the various atlases.

• Present in team meetings.

The candidate will be supervised by the researchers leading the PKC pan-pediatric atlas project at Institut Curie (Dr Isabelle Janoueix-Lerosey and Dr Joshua Waterfall). This project will be performed in close collaboration with researchers leading the project at Gustave Roussy (Dr Thomas Mercher and Dr Florent Ginhoux).

She/he will benefit from daily exchanges with people working on pediatric cancers and computational biologists with strong expertise. Additionally, the candidate will have the opportunity to interact with the broader bioinformatics community at Institut Curie through the Curie Bioinformatics Hub.