PostDoc en bioinformatique - H/F

Inserm France; Toulouse; Hybride; EUR 30 000 - 35 000; Plein temps

Résumé du poste

Inserm France invites applications for a 1-year postdoctoral research fellowship at CRCT, Toulouse, in the group of Corinne Bousquet. The project investigates pancreatic cancer heterogeneity, focusing on cancer cells, fibroblasts, and immune interactions using transcriptomics and multiplex imaging.

The candidate will curate public and in-house transcriptomic databases, develop bioinformatic and image-analysis pipelines, and collaborate on in vitro/in vivo assays.

Qualifications

• Proven track record in bioinformatics and tumor biology.
• Experience with transcriptomic datasets (bulk, single-cell, spatial).
• Experience with imaging analyses on multiplex RNA/IF stained tissues.

Responsabilités

• Read and digest literature to curate public transcriptomic databases.
• Interact with collaborators to collect and curate personal datasets.
• Adapt and optimize bioinformatic tools for transcriptomics, including spatial data.
• Adapt image-analysis tools for multiplex imaging and tissue samples.
• Collaborate with biologists for in vitro/in vivo validation of bioinformatic hits.
• Design experiments, perform statistical analyses, interpret results, and report findings.
• Mentor 1–2 Master/PhD students and collaborate within the lab.

Connaissances

R/Bioconductor

Python

Linux

Single-cell RNA-seq

Spatial transcriptomics

Image analysis

Statistics

Team collaboration

Formation

PhD in relevant field

Outils

Cell Ranger

Space Ranger

Xenium Ranger

QuPath

ImageJ/Fiji

HALO

Imaris

Description du poste

About the position

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.

• 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,…)

• 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,…)

• 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

• Original & critical thinking
• Highly motivated
• High spirit of initiative
• 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

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

Salary will follow INSERM guidelines commensurate with training and experience

Position characteristics

Offer info

Published on 10/02/2026 Contractuel Catégorie A Fixed-term contract - 12 months Full time Experience preferred License not required > Master degree level

01/12/2026