Single Cell RNAseq of innate immune cells and integration with metabolome and microbiome data

Type de poste
Niveau d'étude minimal
Durée du poste
Contrat renouvelable
Contrat renouvelable
Détails de renouvellement
Financement déjà acquis
Date de prise de fonction
Date de fin de validité de l'annonce

33076 Bordeaux

Maya Saleh
Macha Nikolski
Email du/des contacts

A post-doctoral position (18 months, extendable) is available to work jointly in the <ImmunoConcept (UMR 5164) and the Bordeaux Bioinformatics Center in Bordeaux (Bordeaux, France), under the supervision of Dr. Maya Saleh and Dr. Macha Nikolski. The research project consists in developing methods and analyzing human samples by single cell RNA sequencing for mapping of the innate immune cells associated with the response to immunotherapies and the functional microbiome linked to the control of cancers.


IMMUNOLOGY from CONCEPT and EXPERIMENTS to TRANSLATION (ImmunoConcept) CNRS UMR 5164 - University of Bordeaux, aims to dissect the role of the innate immune system and host-microbiome interactions in oncoimmunology, including the response of patients to immunotherapies (efficacy and toxicity manifested as inflammatory and / or autoimmune responses). ImmunoConcEpT brings together all of the Bordeaux forces in immunology and has 50 members including 6 CNRS or INSERM researchers, 4 University Professors, 10 University Professors-Hospital Practitioners, 4 engineers and 3 administrative assistants. The two main lines of research within my team will be the mapping of the innate immune cells associated with the response to immunotherapies and the functional microbiome linked to the control of cancers. In parallel, we study the metabolome, hence the need to in bioinformatics that allow analysis and integration of multi-omic data.
The Bordeaux Bioinformatics Center (CBiB, is a bioinformatics research team at the IBGC (UMR 5095) and a core facility that provides access to high-performance computing resources, develops bioinformatics methodologies and performs data analysis. We bring to researchers the best tools to manage and understand biological data. We focus mainly on the development of bioinformatics for analysing datasets acquired using high-throughtput omics technologies and offer state-of-the-art technologies for working with clinical, translational, and basic science data – from acquisition and storage to analysis and sharing. From a few samples to several tens of thousands, the Innovation Centre provides complete DNA, RNA, metabolomics and proteomics analysis.

Goals of the project

The candidate will work at the ImmunoConcEpT laboratory to design, develop and implement Single Cell RNAseq pipelines for the project. These pipelines will be designed jointly by the candidate and the CBiB team, its modules will be integrated into existing CBIB pipelines and made available to the ImmunoConcEpT team. To do so, the candidate will participate in their portability on academic computing servers. The candidate will be responsible for designing the experimental design of single-cell analysis studies by working routinely with biologists from the ImmunoConcEpT team. He / she will produce the bioinformatics analyzes, carried out jointly with the CBiB team. The candidate will work as a team member under the leadership of the Biology Team Leader (Dr. Maya Saleh, ImmunoConcEpT) and Bioinformatics (Dr. Macha Nikolski, CBiB). He / she will work for the adaptation of existing analysis modules and with the data integrators to link the analysis modules to the biological sample circuit management tools and the clinical and omics data repositories.

The candidate will develop a methodology for integrating scRNA-seq, metabolomics and microbiome datasets for deciphering molecular and metabolic pathways, used for stratifying cancer patients and predicting their response to immunotherapies. Indeed, the integration of scRNA-seq datasets with other omics data is challenging due to multiple aspects such as e.g. the dropouts. These bioinformatics developments will be applied to the newly acquired data, generated by the team of Maya Saleh (ImmunoConcEpT) for cohorts of patients with cancer or inflammatory diseases. Single-cell transcriptomics, metabolomics and microbiome sequencing will help to elucidate the innate immune mechanisms in play.

Candidate Profile :

  • PhD degree in bioinformatics, high level engineer or equivalent
  • Dedicated, pro-active and with a personal fit into the team
  • Good communication skills that allow productive interactions with biologists, clinicians and bioinformaticians (e.g. discussing models / analyses choices)
  • Programming skills (R, Python) in Unix environment are essential
  • Data analysis methodologies such as ACP, Clustering, t-SNE,…
  • Prior experience in NGS data analysis is essential, experience in sc-RNAseq data analysis would be a plus
  • Ability to communicate in both spoken and written English
  • Autonomous and rigorous with a critical mind

Job offer :

There are several unique features of this job opportunity :

  • Working with enthusiastic teams and an already-setup laboratories
  • CNRS and the University of Bordeaux offer access to state-of-the-art infrastructures and a competitive salary
  • Basic science approaches to address clinically relevant issues in collaboration with clinicians
  • Two international-friendly teams

Availability, type and duration of the contract :

Starting from January 2020

CDD, 18 months, renewable

How to apply :

Cover letter, CV and references contacts may be directed to Maya Saleh and Macha Nikolski, and

Equipe adhérente personne morale SFBI
Equipe Non adhérente