A postdoctoral research fellow position is available for 1-year at CRCT (Toulouse Cancer Research Center) in Corinne Bousquet’s Research group « Microenvironment & Therapeutic Resistance in Pancreatic Neoplasms. »

The project aims at understanding pancreatic cancer heterogeneity in spatial cell positioning, focusing on the interplay between cancer cells, cancer-associated fibroblasts and immune cells, to understand immune cell exclusion within sub-tumor microenvironment areas. To do so, bioinformatic and image analyses shall be developed using public and personal transcriptomic (bulk, single-cell, spatial) databases, as well as multiplex RNA and protein immunohistofluorescence on pancreatic cancer tissue, respectively.

Toulouse is a dynamic research area located in south of France that comprises many internationally recognized laboratories (fundamental cell biology, pharmacology, cancerology, immunology, metabolism, agronomy…) and gives access to a network of high-level skills research platforms in life sciences (GENOTOUL – Un ensemble de ressources au service de la R&D, e.g. imaging, cytometry, bioinformatics, genomics & transcriptomics, biostatistics ; Metatoul - Home (inrae.fr), e.g. metabolomics & fluxomics; Toulouse Proteomics Infrastructure | IPBS, e.g. proteomics) making possible almost all research projects.

The Toulouse Cancer Research Center, accredited by INSERM, CNRS and Toulouse University, is internationally recognized and offers a productive scientific environment centered on basic, transdisciplinary (bioinformatics, mathematics & physics in close link with the Toulouse Laboratoire d’analyse et d’architecture des systèmes | LAAS-CNRS and Laboratoire de Physique et Chimie des Nano-objets (insa-toulouse.fr)), and clinical research (in close link with the IUCT Oncopole - Institut Universitaire du Cancer de Toulouse - Accueil (iuct-oncopole.fr)), to understand and treat cancers. CRCT brings together a total of >250 Researchers, MDs, University Professors, Technicians, Students and Post-docs of many nationalities. CRCT offers on-site state-of-the-art technological platforms with personalized project support, including single cell RNAseq (Le pôle technologique DU CRCT - Centre de Recherches en Cancérologie de Toulouse (crct-inserm.fr)).

·         Read & digest the literature in the pancreatic cancer field to sort, collect and clean the most important public transcriptomic databases accessible online

·         Interact with collaborators to also collect and clean personal transcriptomic databases

·         Compare, improve and adapt the most state-of-the-art bioinformatic analytic tools for transcriptomic analyses including spatial ones

·         Compare, improve and adapt the most state-of-the-art analytic tools for image analyses on pancreatic cancer tissue samples stained by multiplex RNA and protein immunohistofluorescence

·         Interact with team biologist members for developing in vitro and in vivo assays for the functional characterization of bioinformatic-selected hits

·         Experimental design & organization, Statistical analysis especially at patient-level, Result interpretation & reporting (oral in english during Labmeetings; written for grant reporting & application, and manuscript preparation)

·         Involvement in the tutoring of 1 to 2 Master/ PhD Students

·         Strong interaction with other Lab members (help with experiment design, interpretation,…)

Know-how / Methodology aptitude

·         Skills in computational workflows are essential: Expertise in raw-data processing tools; Proficiency in R/Bioconductor, Python and Linux, with demonstrated experience analyzing patient-derived tumour bulk RNA-seq, single-cell RNA-seq and spatial transcriptomics datasets, including 10x Genomics Visium and Xenium; Familiarity with relevant processing pipelines (Cell Ranger, Space Ranger and Xenium Ranger), differential-expression tools (DESeq2, edgeR or limma), and single-cell/spatial analysis frameworks (Seurat, Scanpy and/or Squidpy); Experience with spatial deconvolution, copy-number inference, cell-type annotation, tumor microenvironment characterization, spatial neighborhood analysis  and cell–cell communication analysis.

·         Experience with patient-level statistical analysis, and reproducible is essential.

·         Experience in quantitative image analysis of tumor tissue sections processed by RNAscope and multiplex immunofluorescence is desirable: knowledge in tools such as ImageJ/Fiji, HALO, Imaris and/or QuPath; Relevant expertise includes image quality control, cell and tissue segmentation, RNAscope puncta detection and quantification, fluorescence intensity measurement, marker co-expression analysis, cell phenotyping, and spatial analysis of tumor–immune interactions; Experience developing reproducible image-analysis workflows and integrating imaging results with transcriptomic data is desirable.

Skills

·         Autonomy

·         Original & critical thinking

·         Highly motivated

·         High spirit of initiative

·         Rigorous

·         Work in team

Requirements

Seeking a passionated Post-Doc who ambitions an (international) academic research career

His/her skills should be demonstrated by proven track record of research accomplishments including first author publication(s) in international peer-reviewed respected journal(s) in the field

Salary

2.909,90€ gross monthly (for experience of 0-2 years post-PhD)

Salary will follow INSERM guidelines commensurate with training and experience