Bioinformatician engineer in spatial transcriptomics data analysis

European Commission; France; Hybride; EUR 40 000 - 55 000; Plein temps

Résumé du poste

L'Institut Curie recherche un chercheur en biologie computationnelle pour développer des pipelines d'analyse transcriptomique spatiale. Ce poste implique une collaboration avec des équipes multidisciplinaires pour explorer l'architecture tumorale et la réponse au traitement dans un environnement dynamique. Les candidats doivent avoir un Ph.D. dans un domaine pertinent et des compétences fortes en programmation et en analyse de données.

Prestations

Restauration collective

Remise des frais de transport jusqu'à 70%

Assurance santé complémentaire

Qualifications

• Ph.D. en biologie computationnelle ou bioinformatique souhaité.
• Compétences en Python et R requis.
• Connaissances en statistiques et apprentissage machine valorisées.

Responsabilités

• Développer des outils pour l'analyse transcriptomique spatiale.
• Analyser des données multidimensionnelles et spatiales.
• Fournir des formations et des tutoriels sur les outils développés.

Connaissances

Programmation en Python

Programmation en R

Analyse statistique

Machine Learning

Communication scientifique

Formation

Master ou Ph.D. en Biologie computationnelle, Bioinformatique

Outils

Environnements HPC

Description du poste

Organisation/Company Institut Curie - Research Center Department Administration Research Field Medical sciences » Cancer research Researcher Profile Recognised Researcher (R2) Positions PhD Positions Country France Application Deadline 31 Jul 2025 - 00:00 (Europe/Paris) Type of Contract Temporary Job Status Full-time Hours Per Week 39 Offer Starting Date 26 May 2025 Is the job funded through the EU Research Framework Programme? Horizon 2020 Is the Job related to staff position within a Research Infrastructure? No

The Institut Curie, a key player in the fight against cancer, combines a hospital and a research center with over 1,000 staff members. Its goal is to improve diagnosis, prognosis, and treatments through a continuum between basic research and innovation. The position is funded by the Institute of Women’s Cancers , an interdisciplinary initiative aiming for comprehensive care of breast and gynecological cancers, recognized as a University Hospital Institute (IHU) under the France 2030 program.

Description of the position

Scientific context

The biological and clinical heterogeneity of breast and lung tumors has a major impact on patient prognosis, diagnostic accuracy, and therapeutic strategies. Previous research conducted by several teams at Institut Curie has uncovered novel mechanisms linking aging and sex-related factors to cancer development and progression. Within the IHU framework, the laboratories of Fatima Mechta-Grigoriou and Hélène Salmon are leading a collaborative working group involving multiple research teams. Their joint objective is to investigate tumor architecture and cell–cell interactions between cancer, immune, and stromal cells, to gain deeper insights into the biology of women’s cancers.

• Costa A, Kieffer Y, Scholer-Dahirel A, Pelon F, Bourachot B, Cardon M, et al. Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer. Cancer Cell. 12 mars 2018;33(3):463-479.e10.
• Croizer H, Mhaidly R, Kieffer Y, Gentric G, Djerroudi L, Leclere R, et al. Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancer. Nat Commun. 1 avr 2024;15(1):2806.
• Kieffer Y, Hocine HR, Gentric G, Pelon F, Bernard C, Bourachot B, et al. Single-Cell Analysis Reveals Fibroblast Clusters Linked to Immunotherapy Resistance in Cancer. Cancer Discov. sept 2020;10(9):1330‑51.
• Grout JA, Sirven P, Leader AM, Maskey S, Hector E, Puisieux I, et al. Spatial positioning and matrix programs of cancer-associated fibroblasts promote T cell exclusion in human lung tumors. Cancer Discov. 2 nov 2022;12(11):2606‑25.

Goal of the position

The goal of the position is to develop computational pipelines for spatial transcriptomics analysis using Visium HD. These pipelines will be designed to characterize the composition and evolution of the tumor microenvironment in relation to age, treatment response, and cancer progression. A particular emphasis will be placed on CAF subpopulations and their interactions with cancer, immune, and endothelial cells.

As part of your responsibilities, you will:

• Develop, test, and implement computational tools for spatial transcriptomics analysis.
• Process and analyze multidimensional imaging and spatial data (stitching, segmentation, quantification, cell clustering).
• Work with researchers to design and apply image-processing algorithms for high-resolution microscopy datasets.
• Validate and optimize computational pipelines for large-scale data integration.
• Provide training and tutorials to facilitate the use of developed tools.
• Deliver publication-grade results, reports, and material.
• Follow the Good Practices of the Institut Curie Bioinformatic Cluster

All our opportunities are open to individuals with disabilities.

Organization of position

The position is embedded in a highly dynamic and multidisciplinary environment. It will initially be based in the laboratories of Fatima Mechta-Grigoriou and Hélène Salmon as a part of the IHU program. He/She will also join (or be part of) the bioinfo-HUB, a structure attached to the Institut Curie Bioinformatics Core Facility promoting exchanges and interactions between bioinformaticians and analysis good practices.

Candidate Profile

Qualifications & Experience

• Master or Ph.D. in Computational Biology, Bioinformatics, or a related field.
• Proficiency in programming languages such as Python and R
• Good knowledge in statistics and machine learning (IA/Deep learning is a plus)
• Great interest in biology, oncology and/or immunology
• Previous experience with single cell RNA-seq and/or spatial transcriptomics data analyses is a plus
• Ability to communicate scientific results in a clear and didactic manner
• Familiarity with high-performance computing (HPC) environments.
• Excellent interpersonal communication, teamwork and organizational skills
• Ability to self-learn and a problem-solving approach to work
• Flexibility and organizational skills to advance several projects in parallel.
• Fluency in English (written and spoken).

Additional Information

• Location: flexible work location at Institut Curie, rue d’Ulm, 75005 Paris and remotely.
• Contract: 18-month fixed-term position, with the possibility of a 18-month extension based on performance(CDD).
• Start date: As soon as possible.
• Working time: full time.
• Remuneration: according to the current grids
• Benefits: collective catering, reimbursement of transportation fees up to 70%, supplementary health insurance

The Institut Curie is an inclusive and equal opportunity employer and upholds strict standards in research integrity.

• Master or Ph.D. in Computational Biology, Bioinformatics, or a related field.
• Proficiency in programming languages such as Python and R
• Good knowledge in statistics and machine learning (IA/Deep learning is a plus)
• Great interest in biology, oncology and/or immunology
• Previous experience with single cell RNA-seq and/or spatial transcriptomics data analyses is a plus
• Ability to communicate scientific results in a clear and didactic manner
• Familiarity with high-performance computing (HPC) environments.
• Excellent interpersonal communication, teamwork and organizational skills
• Ability to self-learn and a problem-solving approach to work
• Flexibility and organizational skills to advance several projects in parallel.
• Fluency in English (written and spoken).