Computational biologist in single cell OMICS applied to immune-oncologyCancer Research Center of Lyon - CDD 2 years with possible extension to 3 years
Poste et missions
We are seeking a highly motivated and scientifically driven computational biologist/bioinformatician who will bring his/her expertise to contribute to the efforts of the team in identifying key immune surveillance pathways and immune escape mechanisms operating in tumors. The successful candidate will take the lead of a project that aims to identify novel immunosurveillance pathways by performing a comprehensive comparison of tumors from patients with a paraneoplastic neurological syndrome (PNS) and conventional non-PNS tumors through computational analysis of single cell RNA-sequencing data of immune cells, tumor cells and stromal cells, antigen receptor sequencing data and of spatial data of the tumor immune contexture based on multispectral immunofluorescence tissue imaging. It follows our recent observations with the team of J. Honnorat (INMG Lyon) that ovarian and breast carcinomas from PNS patients differed from their non-PNS counterpart by a massive infiltration by CD8 T cells and antibody producing plasma cells, as well as signs of tumor immune attack, indicating efficient and concomitant in situ anti-tumor cellular and humoral immunity. This project is part of a large effort of the team to discover novel tumor immune surveillance pathways using single cell OMICS in early versus advanced tumors, for which the candidate is also expected to participate according to his/her skills.
Recent publications from the lab related to the field
– Small M et al. (2018) Acta Neuropathol. 135(4):569-579.
– Chefdeville et al. (2019) Acta Neuropathol. Com. 7(1):38.
– Hubert et al. (2020) Science Immunology 5(46).
– Use and adapt existing pipelines and develop novel computational methods to analyze complex scRNAseq datasets to identify features/pathways in immune cells, tumor cells and/or stromal cells associated with the higher immunogenicity of PNS tumors
– Exploit TCR-seq and BCR-seq data to provide a comprehensive picture of B and T cell clonotype diversity and cell trajectories in relation to their transcriptomic features
– Implement computational methods to calculate cell-cell proximity metrics and infer cell neighborhoods from raw data of multiplex-immunofluorescence tumor tissue staining
– Interact with the immunologists of the team to optimize the design of dry experiments and best adapt the analysis pipelines to the complexity of the tumor immune ecosystem and to the project objectives
– Contribute to data integration/synthesis and to the writing of papers
– Keep abreast of emerging methods in computational biology/bioinformatics
Skills and qualifications
– PhD in Bioinformatics, Computational Biology, Systems Biology/Immunology or related field with at least 1 first author paper or Master/Engineer degree in the same fields with > 1 year experience.
– Experience in utilizing Python and R programming languages as well as bioinformatics pipeline development
– Prior experience in working with high dimensional single cell omics datasets is a plus
– Ability to be inventive and to present novel ideas in method development, data analysis and interpretation
– Knowledge of tumor immunobiology will be considered as an advantage. At least, curiosity for immunology and willingness to learn its basic aspects applied to oncology is required
– Strong problem-solving skills and ability to work independently
– Strong collaboration skills and ability to evolve in a multidisciplinary research environment
– Excellent organizational and time management skills
– Strong oral and written communication skills
Interested candidates should submit a motivation letter, CV and contact details of 2 references to Bertrand Dubois (Bertrand.firstname.lastname@example.org). The position is to be filled as soon as possible. The closing date for applications is June 1st 2022.