Bio-Computing expert! Bio-computing engineer / single cell analyses of direct reprogramming in vivo

About

We are looking for a bioinformatics engineer to join our CellPath consortium. An 18-month funding opportunity is available within the Jarriault team (IGBMC, Strasbourg); this work will be carried out in collaboration with the Heinrich team (SBRI, Lyon).

Our consortium is working on cellular plasticity and the ability of differentiated cells to change their identity, a phenomenon known as direct reprogramming or transdifferentiation. We are studying the transdifferentiation path (rectal-to-neuron) observed naturally in C. elegans. We will then compare this to a glial-to-neuron path in a mouse model to identify common mechanisms.

Jarriault team:

We have identified natural events of direct reprogramming in C. elegans, a small microscopic worm (http://hobertlab.org/c-elegans-nobel-prizes/), which we study at the single-cell level. We have developed a method to purify a single reprogramming cell over time, and have obtained extensive bulk and single-cell RNA-Seq and Dam ID data. Using these tools, we aim to track not only transcriptional dynamics but also intermediate cellular states (‘transition states’) during reprogramming to identify key regulatory nodes, and to do so in vivo within an integrated and physiological model. Our international team (http://igbmc.fr/research/department/1/team/8/), is based at the IGBMC (http://igbmc.fr/), a multidisciplinary institute in Strasbourg.

In addition to working with the bioinformaticians in our teams, you will be able to interact directly with other teams interested in similar topics and approaches (e.g. http://igbmc.fr/research/department/1/team/131/, http://igbmc.fr/research/department/1/team/6/, https://www.igbmc.fr/equipes/regulation-genomique-computationnelle, for example), as well as bioinformaticians associated with the institute’s sequencing platform.

Responsibilities

• Managing the transfer and storage of raw data on the teams’ servers
• Setting up a standardised archiving system for analyses (protocols, codes, etc., and key parameters for each) within the teams
• Implementing (and potentially developing) analysis tools and interfaces within the teams for use by researchers: omics, RNA-Seq
• Participating in the bioanalysis of omics data (primarily RNA-Seq) generated in the laboratory (quality control and analysis) and its interpretation – cross-comparison between models.
• Participation in the drafting of specialised sections of articles

Required knowledge and skills

• Knowledge of genomic data and bioanalytics
• Knowledge of tools for analysing and visualising RNA-Seq data and, ideally, DAM ID and ATAC Seq
• Knowledge of methods for analysing single-cell genomic data and the classification methods used (ACP, K-means, t-SNE, PLS, etc.)
• Proficiency in the Unix environment
• Bash, R, Python or Perl
• advanced knowledge of biology

Plus:

• Experience in developing data analysis pipelines

Required qualities

• Self-motivated and meticulous, good interpersonal skills, a passion for teamwork and knowledge-sharing. Initiative, curiosity, technical creativity.
• Proficiency in scientific English

Qualifications:

Master’s degree or engineering degree in bioinformatics or biostatistics with research experience, or PhD

To apply, please send a detailed CV (including research experience and a list of publications), a cover letter and the contact details of 2–3 referees to Sophie Jarriault: sophie@igbmc.fr