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Research engineer Bioinformatician/Computational biologist - PSI plateform

The IGFL is seeking a Staff scientist/Research engineer Bioinformatician/Computational biologist (M/F) for support and training at the lab scale

 

Interested to apply?

Please fill the form here

Contact :

sandrine.hughes[arobase]ens-lyon.fr

General information

Place of work: IGFL UMR 5242 / ENS de Lyon – Lyon 07 France

Minimum educational qualifications: PhD/Engineer

Desired starting date: Asap

Contract duration: CDD 1 year, renewable 2 times

Salary: Remuneration based on experience (from 2400€/month to 2800€)

Missions

The engineer will be responsible for the development of bioinformatics tools and supporting the IGFL teams (user support and training). He/she will participate in the analysis of data obtained from new sequencing technologies within the NGS sequencing platform of the IGFL (PSI), and will interact with the Equipex+ Spatial-Cell-ID and the CAN of the UAR Biosciences. The support to the sequencing data analysis will be done specifically via training users. He/she will participate in multiple projects in genomics, transcriptomics and epigenomics on various subjects, in model or non-model organisms.

 

Activities

  • Define, in agreement with biologists, the most appropriate study design for the biological problem posed and advise users on the analysis and interpretation of data for projects on the PSI platform
  • Support, and if necessary ensure in part, the completion of biological data analysis projects of the unit, using current bioinformatics, biostatistics and bioanalysis tools
  • Identify, design and develop the bio-computing tools adapted to the questions asked, allowing the exploitation of the data obtained
  • Spread the use of analysis tools by making them accessible to the members of the unit, and more widely, on local servers and platforms (Galaxy, Nextflow,...). This activity will be carried out in connection with the bioinformatics network being structured between the laboratories of the ENS de Lyon, the PSMN, the UAR Biosciences and the Equipex+ Spatial-Cell-ID.
  • Develop and/or adapt tools to disseminate the data acquired by the teams to the local, national and international scientific community
  • Structure a network around bioinformatics within the unit to improve the interactions of the teams of the site concerning the analysis tools
  • Participate in the training activities of the PSI platform and to develop the axes concerning the principles and the implementation of biological data analysis techniques
  • Disseminate and valorize the results in the form of technical reports, publications or oral presentations
  • Organize and be up to date on technology and scientific developments

 

Expected Skills

  • General theoretical knowledge in the field of life sciences (physiology, evolution, development) and, if possible, in the field of functional genomics
  • Mastery and/or understanding of current analysis tools for omics data in all their diversity: high-throughput sequencing, especially single cell, for transcriptomics, epigenomics, genomics, metagenomics, spatial transcriptomics...
  • Theoretical and practical knowledge in programming and biostatistics (R, bash, python and/or equivalent languages)
  • Experience in working on computing clusters
  • Interest in modern visualization tools (e.g. shiny)
  • Experience in collaborative tools: workflow management systems (e.g. NextFlow, snakemake, Galaxy,…), versioning (e.g. GitHub)
  • Knowledge of the deontology, ethics, law and regulations concerning the research field (in particular on confidentiality, computer security, data backup and protection...)
  • Ability to work in collaboration with experimental biologists, bioinformaticians and biostatisticians
  • Ability to manage several projects in parallel on various subjects and in interaction with different partners
  • Proficiency in scientific English (oral and written)
  • Excellent interpersonal skills
  • Ability to work within a team

 

Context

The Institute of Functional Genomics of Lyon (IGFL) is a mixed unit (Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, INRAe) which includes more than 100 people and 12 research teams, all using data from new sequencing technologies in their research themes. It is located within the ENS of Lyon in the Gerland district.

The engineer will have a key organizational role within the institute and the site to support the scientific projects of the teams within the sequencing platform of the IGFL. The projects will be very diverse and may concern the quantitative and/or spatial analysis of transcriptomic (e.g. single cell) or genomic traits, or epigenetic problems, and will be applied to various model organisms (Drosophila, zebrafish, mice, human cell lines) and non-model organisms (semi-aquatic insects, crustaceans, ...)

The research engineer will be integrated into the sequencing platform of the IGFL (PSI) which has a transversal position within the institute and interacts with all the teams of the unit, the other units of the site, and is an integral part of the Equipex+ Spatial-Cell-ID project. PSI carries out an important part of the sequencing projects of the teams, in particular in the exploratory phases for the development of innovative and/or risky approaches requiring custom analyses. In addition to being a strong support to the platform activities, the engineer will allow to gather and unite the bioinformatics competences of the unit, both in terms of people and resources, to allow the development of new relevant tools and to make them accessible to the largest number. Thus, in addition to supporting the implementation of projects, one of the objectives of the engineer will be to help the teams of experimental biologists to acquire skills in the use of analytical tools through direct training events. Finally, the engineer will interface and promote exchanges between the institute and the local bioinformatics and numerical analysis network within the UAR Biosciences (CAN), the computing mesocenter of the ENS (PSMN) and the Equipex+ Spatial-Cell-ID project.

The 12 months CDD can be renewed twice while the direction of the unit works with the supervising bodies of the laboratory in the possibility of ensuring the sustainability of the position on a permanent basis.