Mots-Clés

transcriptomics, genomics, graphs, protein isoforms

Description

The Computational and Quantitative Biology Lab at Sorbonne University in Paris has an opening for a Post-doctoral researcher to join E. Laine's team in an ERC-funded project to explore proteome diversification in evolution.

Our team focuses on the fascinating diversity of proteins. More specifically, the different protein versions or isoforms that can be produced from a single gene. How this diversity emerged and expanded in evolution, how it impacted complex behavioural traits such as vocal learning in humans and songbirds.

You will join an interdisciplinary and highly collaborative team. You will work alongside highly motivated scientists passionate about developing innovative computational and AI methods for understanding the fundamental mechanisms of life's machinery toward optimally guiding biological intervention.

Job description

Our ERC-funded project, PROMISE, aims at leveraging the landscape of protein isoforms across hundreds of millions of years of evolution with cutting-edge AI techniques to determine how proteins function and interact with one another in vivo. 

You will contribute to the integration of high-throughput sequencing data, e.g. short- and long-read RNA-seq data as well as peptides detected in proteomic experiments, onto graph-based objects. You will expand on a data structure we have introduced for describing transcript diversity across species and on a prototype we have developed for mapping splice junctions. You will address the open question of the functional relevance of the transcripts inferred from annotations or detected in raw genomes. You will have the flexibility to explore different strategies and build upon innovative methodologies.

You will work in close collaboration with E. Laine (http://www.lcqb.upmc.fr/laine/), Associate Professor at Sorbonne University, and H. Richard, researcher at the Robert Koch Institute (Berlin, Germany).

Skills/Qualifications

We are seeking an enthusiastic and highly motivated scientist with bioinformatics or computer science background. The position requires strong algorithmic and programming skills as well as some knowledge about biological sequences and evolution. The following skills will be an advantage:

• Expertise in manipulating and integrating high-throughput sequencing data
• Prior experience with long-read RNA-Seq and/or mass spectrometry data
• Proficient coding in Python (and/or Julia, R, C++) and experience with good coding practices 
• Excellent organisation and interpersonal skills
• First-rate oral and written English communication capabilities.

Funding 

The position is fully funded for 2 years. The team benefits from excellent support thanks to an ERC Consolidator Grant. Salary will be commensurate to experience following Sorbonne University's pay scale. Start date is flexible but no longer than March 2024.

Environment

The multidisciplinary Laboratory of Computational and Quantitative Biology is located on the Jussieu Campus, in the center of Paris, France. We are part of the Institute of Biology Paris-Seine. We have connections with the Center for Artificial Intelligence and the Initiative for Interdisciplinary Research in Biology at Sorbonne University. We offer an outstanding scientific environment and we are committed to the advancement of a responsible science through an inclusive policy.

The team provides its members with many opportunities to collaborate with and receive feedback from an inter-disciplinary collaborative network of international researchers from complementary backgrounds and to take part in international community efforts.