Open positions at CBIB

Bioinformatics research scientist - Single Cell RNAseq of innate immune cells

Starting date: January 2020

Contract: CDD, 18 months, renewable
Location: Bordeaux, France
Laboratory: Bordeaux Bioinformatics Center (CBiB) 
Address: CBiB 146 Rue Léo Saignat 33076 Bordeaux Cedex

Description :

A post-doctoral position (18 months, extendable) is available to work jointly in the ImmunoConcept (UMR 5164) and the Bordeaux Bioinformatics Center in 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, https://www.immuconcept.org/team_member/maya-saleh/ 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, https://www.cbib.u-bordeaux.fr/en) 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.

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.


By using these data, the candidate will develop a methodology for integrating these already acquired datasets for deciphering molecular and metabolic pathways, used for increasing invasion. Indeed, due to differences in experimental platforms and biological sample batches, the integration of multiple scRNA-seq datasets remains challenging.


These bioinformatics analyses will be extended by integrating newly acquired data, generated by the team of Thomas Daubon (IBGC, UMR 5095 CNRS) for several glioblastoma models in co-culture with neurons or white matter tracts in acute brain slices. Bulk and single-cell transcriptomics will help to elucidate the invasive mechanisms in play.

Skills needed :

  • 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 :

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

CONTACTS:

Cover letter, CV and references contacts may be directed to Maya Saleh and Macha Nikolski, msaleh@immuconcept.org and macha.nikolski@u-bordeaux.fr.

 

Postdoc : Investigating White Matter Tract invasion by single-cell sequencing data analysis

Starting date: Jan 2020
Location: Bordeaux, France
Laboratory: Bordeaux Bioinformatics Center (CBiB) 
Address: CBiB 146 Rue Léo Saignat 33076 Bordeaux Cedex

Description :

A post-doctoral position (12 months, extendable) is available in the Bioinformatics team at the IBGC, UMR 5095 CNRS to work with Dr. Macha Nikolski and Dr. Thomas Daubon. The research project consists in developing methods and analyzing human and culture samples by single cell RNA sequencing for understanding invasion processes in glioblastoma.


Glioblastoma (GBM) is the most deadly type of human cancer. Most patients diagnosed with this grade IV malignant glioma survive for about 15 months. Even with optimal treatment, the estimated recurrence rate is more than 90%. Recurrence is mostly caused by the regrowth of highly invasive cells that spread from the tumor bulk and are therefore not removed by resection. A large number of GBM cells are invading around the tumor core. Invasion on blood vessels is a well-described phenomenon, but a majority of cells invade along white matter tracts. This latter mode, also known as perineuronal satellitosis, is not well described in the literature (observed by Scherrer in 1950). Furthermore, the molecular relationship between glioma and white matter tracts remains largely unknown. Recent publications described neurogliomal synapses in glioblastoma (Venkataramani et al, Nature), in pediatric glioma (Venkatesh et al, Nature), or in cerebral metastasis (Zeng et al, Nature), which interconnects the neuronal network to the cancer network. Glutamate influx via NMDAR induces calcium flux into the glioma network, and by consequence, tumor cells are invading the surrounding tissues. Single-cell transcriptomics was performed in the publications related to glioma, and massive amount of data was generated in Venkataramani et al.


By using these data, the candidate will develop a methodology for integrating these already acquired datasets for deciphering molecular and metabolic pathways, used for increasing invasion. Indeed, due to differences in experimental platforms and biological sample batches, the integration of multiple scRNA-seq datasets remains challenging.


These bioinformatics analyses will be extended by integrating newly acquired data, generated by the team of Thomas Daubon (IBGC, UMR 5095 CNRS) for several glioblastoma models in co-culture with neurons or white matter tracts in acute brain slices. Bulk and single-cell transcriptomics will help to elucidate the invasive mechanisms in play.

Skills needed :

  • 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 and clinicians (e.g. discussing models / analyses choices)
  • Programming skills (R, Python) in Unix environment are essential
  • 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

CONTACTS:

Macha Nikolski - macha.nikolski@u-bordeaux.fr 

Thomas Daubon - thomas.daubon@u-bordeaux.fr