Mots-Clés

Analysis of RNAseq ExomeSeq TCRseq scRNAseq spatial multiplex datasets calculate cell-cell proximity metrics spatial transcriptomics analysis Bioinformatics, systems Biology.

Description

Computational biologist, Bioinformatics Engineer position

 

Laboratory of Integrative Cancer Immunology

INSERM, Cordeliers Research Center, Paris, France 

Head: Dr Jérôme Galon

 

Position Summary

We are seeking a highly motivated and scientifically driven computational biologist/bioinformatician with projects focusing in immune-oncology. The candidate will bring his/her expertise to contribute to the team objective in identifying key immune surveillance pathways operating metastasis, primary tumors and pre-cancer lesions.

 

Contract:

1-year contract (renewable for 2 years) with salary based on experience and INSERM salary grids.

 

Responsibilities - Activities

- Use and adapt existing pipelines and develop novel computational methods and tools to analyze complex RNAseq, ExomeSeq, TCRseq, scRNAseq and spatial multiplex datasets.

- Implement computational methods to calculate cell-cell proximity metrics and infer cell neighborhoods from raw data of multiplex-immunofluorescence tumor tissue staining as well as spatial transcriptomics data.

 

The duties also include:

- Keep abreast of emerging methods in computational biology/bioinformatics, including non-supervised analysis of high-plex immunohistochemistry (IHC).

- Interact with the immunologists of the team to optimize the design of dry experiments and best adapt the analysis pipelines

- Drive the bioinformatics expertise in the team and provide mentorship for students and technicians

- Contribute to data synthesis and to the writing of papers

These responsibilities will be adapted to the candidate’ background and experience

 

Skills and qualifications

- Master 2 or PhD with a solid background in Bioinformatics, Computational Biology or Systems Biology (>2 years experience would be a plus)

- Experience in utilizing JAVA, Python and R programming languages as well as bioinformatics pipeline development (prior experience in working with high dimensional omics datasets is a real plus)

- Ability to be inventive, to solve problems and present novel ideas in method development and data analysis

- Ability to work independently while being able to communicate effectively and evolve in a multidisciplinary research environment

- Knowledge of tumor immunology will be considered as a plus.

- Broad knowledge of biostatistics (from signal analysis to survival analyses)

- Fluency in written and spoken English.

 

Example of publications from the lab related to the field

• Locke FL, et al. Nature Med. 2024 Jan 17. (IF: 53.4)
• Scholler N, et al. Nature Med. 2022 Sep;28(9):1872-1882.  (IF: 53.4)
• Angelova M, et al. Oncoimmunology. 2021 Apr 25;10(1):1912250. (IF: 7.7
• Galon J, Bruni D. Immunity, 2020 Jan 14, 52 (1), 55-81 (IF: 43.5)
• Mascaux C, et al. Nature. 2019 Jul;571(7766):570-575   (IF: 69.5)
• Galon J & Bruni D. Nature Reviews Drug Discovery. 2019 Mar;18(3):197-218. (IF: 112.3)
• Mlecnik B, et  al.  Bioinformatics. 2019 Oct 1;35(19):3864-3866. (IF: 6.9)
• Bindea G, et  al.  Bioinformatics. 2013 Mar 1;29(5):661-3. (IF: 6.9)
• Bindea G, et al. Bioinformatics. 2009 Apr 15;25(8):1091-3. (IF: 6.9)
• Angelova M, et al. Cell. 2018 Oct 18;175(3):751-765   (IF: 66.9)
• Pagès F, et al. Lancet. 2018 May 26;391(10135):2128-2139. (IF: 202.7)
• Van den Eynde M, et al. Cancer Cell 2018 Dec 10;34(6):1012-1026.  (IF: 50.3)
• Galon J, et al. Science 2006  313:1960-4 (IF: 63.7)
• Pagès F, et al. N Engl J Med. 2005 Dec 22;353(25):2654-66. (IF: 176.1)

 

About Host Lab

The Laboratory of Integrative Cancer Immunology, based at the Cordeliers Research Center in Paris, France, is headed by Jérôme Galon. Comprising a diverse team of researchers, clinicians, technicians, post-doctoral fellows, PhD candidates, and students, our collective mission is to uncover new mechanisms of tumor immune surveillance and evasion, ultimately advancing cancer treatment approaches.

 

We aim to understand tumor progression and immune reaction against cancer from pre-cancerous lesion to metastasis by using integrative biology and bioinformatics, to improve the immunotherapeutic management of cancer patients. Our research projects are focusing on the analysis of the pre-existing immunity and its modulation.

 

The Centre de Recherche des Cordeliers (CRC) is a public research center of excellence located in the heart of Paris. CRC develops fundamental, translational and clinical research in the field of biology and health. CRC’s research projects are multidisciplinary, mainly in the fields of oncology, immunology, the study of metabolism and the major physiological functions of the body. The CRC has more than 500 people working in 16 teams in three departments with 3 ISO9001-certified technology platforms. The CRC is a renowned and dynamic research center which benefits from state-of-the-art technological facilities. CRC is headed by Professor Jessica Zucman-Rossi, a specialist in oncology and tumor genomics. The Centre de Recherche des Cordeliers is administrated by Inserm, Sorbonne Université, and Université Paris Cité, with the participation of the CNRS and Université Sorbonne Paris Nord.

 

Application

Interested candidates are invited to submit a motivation letter, CV and the contact details of 2 references to Jérôme Galon (jerome.galon@crc.jussieu.fr), the lab director, and Assia Hijazi (assia.hijazi@sorbonne-universite.fr), the lab manager.

The position is to be filled as soon as possible.

 

 

Laboratory of Integrative Cancer Immunology

INSERM, Cordeliers Research Center

15 rue de l’Ecole de Medecine, 75006, Paris, France 

 

Affiliation

INSERM,  Paris, France.

Equipe Labellisée Ligue Contre le Cancer

Université Paris Cité, Paris, France

Sorbonne Université, Paris, France

 

Email: jerome.galon@crc.jussieu.fr

URL1 : http://www.ici.upmc.fr

URL2 : https://www.crcordeliers.fr/

Tel  : +33 1 44 27 9085