Post doctoral - M/F

CNRS - National Center for Scientific Research; France; On-site; EUR 32,000 - 42,000; Full time

Job summary

CNRS – Institut Necker Enfants Malades - Centre de Recherche invites a First Stage Researcher (R1) to design and conduct research on retrotransposons in gene regulation, using transcriptomic and epigenomic data. You will work with the RETROGEN team to apply sc/snRNA-seq and sc/snATAC-seq analyses, develop methods and contribute to publications.

Applicants should have a PhD in bioinformatics or related field and strong skills in R or Python, Linux, and reproducible pipelines.

Qualifications

• PhD in bioinformatics, genomics, computational biology, or a related field.
• Experience with single-cell and multi-omics analyses and statistical methods.
• Strong programming and data analysis skills in R and Python; ability to design reproducible workflows.

Responsibilities

• Design and conduct research on retrotransposons in gene regulation using transcriptomic and epigenomic data.
• Analyze sc/snRNA-seq, sc/snATAC-seq, and multiome data and integrate public and internal datasets.
• Develop statistical analyses and reproducible workflows; document methods, data, and code.
• Collaborate with experimental biologists for validation and contribute to manuscript preparation and grants.

Skills

R

Python

Linux

HPC

RNA-seq

ATAC-seq

Git

English

Education

PhD in bioinformatics, genomics, computational biology, or related field

Tools

Nextflow

Snakemake

Job description

Organisation/Company CNRS Department Institut Necker Enfants Malades - Centre de Recherche Research Field Neurosciences Biological sciences Researcher Profile First Stage Researcher (R1) Application Deadline 18 Nov 2026 - 23:59 (UTC) Country France Type of Contract Temporary Job Status Full-time Hours Per Week 35 Offer Starting Date 1 Dec 2026 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

-Design and conduct, with scientific autonomy and in consultation with the team leader, research projects on the role of retrotransposons in gene regulation and changes in cellular state, incorporating transcriptomic and epigenomic data

Formulate scientific hypotheses, define analytical strategies, and interpret results within their biological context.

• Analyze transcriptomic and chromatin accessibility data at the single-cell or single-nucleus level (sc/snRNA-seq, sc/snATAC-seq, multiome).
• Identify retrotransposons associated with cellular programs and characterize their links to genes and regulatory networks.
• Study responses to changes in the cellular environment, particularly hypoxia and immune activation, as well as differentiation and neurogenesis programs.
• Contribute to the development and validation of methods for quantifying retroelements, notably RETROSCAPE, and integrate public and internal data.
• Develop statistical analyses and reproducible workflows; document methods, data, and code.
• Work with experimental biologists to define relevant validations and incorporate their results into the analyses.
• Draft manuscripts, present results, and contribute to grant proposals related to their projects.

The RETROGEN team, led by Manvendra Singh at INEM, studies the role of retrotransposons in genome regulation, development, and human diseases. It combines functional genomics, single-cell and multi-omic analyses, and computational approaches, particularly in the immune and nervous systems.

Qualifications

• Ph.D. in bioinformatics, genomics, computational biology, or a related field.
• Functional genomics, transcriptional regulation, and epigenetics; knowledge of transposable elements.
• Single-cell and multi-omics analyses, statistics, and analysis plans tailored to biological data.

Skills

• Proficiency in R and/or Python and the Linux environment; use of high-performance computing resources.
• Analysis and integration of RNA-seq and ATAC-seq data; consideration of technical biases, biological variability, and repetitive sequences.
• Development of well-documented code, version control (Git), and reproducible workflows (Nextflow, Snakemake, or equivalent).
• Critical interpretation of results, writing of articles, and scientific communication in English.

Skills

• Scientific independence, rigor, and the ability to propose new research avenues.
• Organization, prioritization, and the ability to see a project through to its completion.
• Teamwork, collaboration with experimental biologists, and knowledge transfer