ENGINEER IN BIOINFORMATICS CONTRACT – Ican Team 1 and Imagine
Research Engineer in Bioinformatics
Job Description
Research Engineer in Bioinformatics
Teams’ description
Team 1 of UMRS 1166 (https:/:recherche-cardiovasculaire-metabolique.fr/) is involved in the research of the genetic and cellular causes of cardiovascular diseases both in animal and human models (cardiac tissues, induced pluripotent cells (iPSC) or mouse model) and in human genomic data, notably through bioinformatic analyses.
These studies focus on cardiomyopathies, one of the leading causes of heart failure and sudden death of the young person.
Until now, the bioinformatic approaches have mainly consisted on whole genome association analyses (GWAS) on sporadic cases cohorts and controls, or on exome sequencing to search for pathogenic variants involved in familial forms. However, these approaches are not sufficient to identify all the genetic factors involved.
Recently, the team obtained a new funding « maladie rare_résoudre les impasses diagnostiques » (“rare disease _ solving diagnostic impasses”) through the Aviesan ITMO Genetics, Genomics and Bioinformatics (ITMO GGB) call for Rare Disease Research Projects funded under the Priority Programme for Rare Disease Research. This call for funds was requested in collaboration with other teams, including Antonio Rausell’s (Clinical Bioinformatics Laboratory, Imagine Institute, https://www.institutimagine.org/en/RausellLab), to develop new approaches to address these diagnostic impasses.
Objectives and missions
The position is destinated to a candidate motivated for a research activity. He/She will be responsible for conducting the innovative bioinformatics analyses, based on the genomic data already compiled, thanks to recently developed detection tools but also through innovative approaches based on artificial intelligence (AI), in order to identify new genetic factors in coding and non-coding regions of the genome such as variations in the number of copies (CNV) or loss of function mutations (LoF).
The position have a double location : Sorbonne University School of Medicine, within the UMR_S 1166 (91 boulevard de l’Hôpital, 75013 Paris) and Imagine Institute (24 Boulevard du Montparnasse, Necker Hospital, 75015 Paris).
Key Activities
– Perform quality controls on genomic and clinical data related to the different projects of the teams
– Analyze genomic data from high-throughput sequencing, DNA chips, CNV and LoF detection tools produced in both teams
– Participate in the development and implementation of AI approaches developed by the Clinical Bioinformatics Laboratory of the Imagine Institute
– Design or develop new bioinformatics tools to meet the needs of units’ researchers
– Close interaction with the biologists of the units responsible for the various genomic projects carried out, in order to optimize the process of interpretation of the molecular and cellular impact of the identified variants, its coherence with the patients’ clinical signs, and its relationship with the pathophysiology of the studied diseases
Knowledge
– Bioinformatic analyses and statistics of DNA chip
– Bioinformatics analysis of sequencing data (including exome/genome and messenger RNA) in clinical research
– Machine learning knowledge
– Experience in statistical data analyses
– General knowledge in molecular biology (genetics) in order to understand and analyze the scientific problem in question and to be able to interact with the researchers of the units
– English language: B2 to C1
Skills
– Master Unix/Linux programming techniques as well as Python and R programming languages
– Proficiency in DNA chip data analysis software (Plink, etc.) and GWAS or imputation type analyses
– Mastering analysis of exomes / genomes including annotation of effects of variants and prioritization using pathogenicity scores
– Mastering the use of clusters/grids for high-performance scientific computing and parallel computing
– Mastering public databases in genomics (NCBI, GenCode, Biomart, etc.)
– Ability to manage large data storage and handling
– Write synthesis reports and present them orally (English and French) during lab meeting
Behavioral skills
– Scientific and experimental rigor
– Ability to work among a team environment
Desired experience
– Beginner accepted
Training desired
– Engineering degree or thesis
Recruitment level according to Sorbonne University remuneration grid
2-year fixed-term contract with a double assignment in Team 1 of UMR_S 1166 ICAN and in the Laboratory of Clinical Bioinformatics of the Imagine Institute (UMR 1163)
Position opening date: September 2021
Contact: send CV and cover letter by email to Sophie Garnier,