Computational Biologist - Single cell & Long read analyses (M / F)

INSTITUT IMAGINE; Paris; Sur place; EUR 40 000 - 60 000; Plein temps

Résumé du poste

Un pôle de recherche sur les maladies génétiques à Paris recherche un biologiste computationnel pour travailler sur des projets de recherche sur l'auto-immunité et les mutations somatiques. Le candidat idéal aura un Master ou un PhD, et une expérience solide dans l'analyse de données unicellulaires. Ce poste offre une opportunité unique de contribuer à des recherches de pointe dans un environnement collaboratif.

Qualifications

• Solide expérience en analyse de données unicellulaires.
• Compétences en NGS et pipelines de données bulk.
• Connaissance des environnements Unix/Linux.

Responsabilités

• Analyser et intégrer les ensembles de données multi-omiques.
• Développer des pipelines bioinformatiques pour l’analyse des données.
• Collaborer avec les biologistes expérimentaux pour l'analyse des données.

Connaissances

Analyse de données unicellulaires

Programmation en R

Programmation en Python

Utilisation de Seurat

Formation

Master ou PhD en bioinformatique, génomique ou biologie computationnelle

Outils

Seurat

Scanpy

Bash

Nanopore

Description du poste

About us

Premier pôle européen de recherche, de soins et d’enseignement sur les maladies génétiques créé en 2007 au cœur du campus de l’Hôpital Necker-Enfants malades. Sa mission ? Mieux comprendre les maladies génétiques pour mieux les guérir.

L’Institut Imagine est un endroit unique au monde qui rassemble chercheurs, patients, médecins et personnels de santé dans une architecture créatrice de synergies au service d’une même ambition : changer la vie des familles touchées par les maladies génétiques.

Mission

We are seeking a highly motivated and skilled computational biologist to join our translational research team working at the interface of immunology, genomics, and intestinal pathology. The successful candidate will investigate the molecular continuum linking between Mendelian, non-Mendelian forms of autoimmune enteropathies and intestinal lymphomas. A particular focus will be on understanding why some patients with celiac disease fail to respond to a gluten-free diet, including those with refractory celiac disease types 1 and 2 (RCD1 and RCD2) and non-responsive celiac disease (NRCD). To achieve this, we use cutting-edge technologies such as single-cell sequencing and long-read RNA sequencing to study individual cells and identify genetic changes that may drive disease progression and treatment resistance.

The recruited scientist will analyze and integrate single-cell multi-omics datasets (including scRNA-seq, CITE-seq, scTCR-seq / VDJ-seq), whole-exome sequencing (WES) , and will help develop novel bioinformatic pipelines for long-read RNA sequencing (e.g., Nanopore) generated from 10x Genomics libraries, with a focus on identifying somatic mutations and clonal structures .

She / he will work in close collaboration with the bioinformatics core facility and experimental biologists to perform quality control, multi-modal integration, lineage and trajectory analysis, and mutational mapping in T cells, in the context of disease evolution from inflammation to lymphomagenesis.

This position provides a unique opportunity to contribute to high-impact research at the frontier of autoimmunity and cancer genomics.

Profile

Qualifications :

Master’s or PhD degree in Bioinformatics , Genomics , or Computational Biology ;

Solid experience in single-cell data analysis using tools such as Seurat, Scanpy, Monocle, Signac, Velocyto , etc.;

Proficiency in NGS workflows and bulk data pipelines ( STAR, Picard, samtools, DESeq2, EdgeR , etc.);

Experience with or strong interest in long-read transcriptomic analysis (Nanopore or PacBio), and familiarity with 10x Genomics-based single-cell library preparation;

Strong programming skills in R , Python , and Bash ;

Familiarity with Unix / Linux environments;

Understanding of immune repertoire analysis and somatic variant calling would be a strong asset;

Prior knowledge in mucosal immunology or lymphocyte biology is a plus;

Excellent communication skills and fluency in written and spoken English .

Conditions :

Start date : As soon as possible;

Contract : 12 months renewable;

Location : Paris, France (Institut Imagine).

Salary :

Salary will be established based on experience.

Application :

Please send your application in English (including CV, motivation letter, and references)