Mots-Clés

single-cell multiomics biostatistics machine learning

Description

Postdoctoral Fellow – S. Merkling Lab

Reporting to: Sarah Merkling, Principal Group leader                  

Contract term: This is a full-time, fixed term 3-year position on Institut Pasteur and CNRS (Centre National de la Recherche Scientifique) terms and conditions of employment. Expected start date is in January-March 2024. 

Please note that we will screen CVs and interview candidates from the start of the recruitment campaign. We encourage you to apply as soon as possible if you are interested in the role.

The research Group

The Insect Immunity & Infection Laboratory, headed by Dr Sarah Merkling is embedded within a CNRS Unit (UMR 2000 – Evolutionary Genomics, Modeling & Health) and the Insect-Virus Interactions Unit at the Virology department at Institut Pasteur. The lab’s primary focus is to understand interactions between Aedes aegypti mosquitoes and the arboviruses they transmit to humans (i.e. dengue viruses, Zika virus, Chikungunya virus). In particular, we aim to understand the molecular mechanisms underlying natural resistance or susceptibility of field-derived mosquito colonies to dengue viruses. To do so, we are developing cutting-edge methods (single-cell genomics, metabolomics, …) and aim to integrate them within a multi-omics framework. We also developed a CRISPR-Cas9 mediated genetic engineering pipeline for generating mutant mosquitoes and analyze the role of specific host factors in functional studies. Founded in 2021, the lab is composed by a PhD student, a post-doc, a bioinformatician and welcomes international students on a regular basis. It will grow further over the next years with the launch of the ERC Starting grant. We value teamwork, creative thinking, open-mindedness, kindness, and offer excellent training and mentorship at all levels. 

The project

The project is linked to the ERC Starting grant “ITSaMATCH”. The project’s goal is to study, at an unprecedented resolution, the trajectory of a virus through a mosquito’s body, with the aim to discover the tissular, cellular and molecular factors that mediate mosquito’s permissiveness to virus infection. The project will rely on hundreds of scRNA-seq and scATAC-seq datasets that will become a key resource for the lab and the wider research community.

Candidate’s Job description

The successful candidate will : 

1. Work closely with wet-bench biologists to develop Ad hoc pipelines to analyze next-generation sequencing data obtained by scRNA-seq and scATAC-seq.
2. Be responsible for developing new analysis pipelines using methods of mathematical modelling, biostatics and machine learning to gain insights into the biological system at hand. 
3. Be responsible for running, updating, and improving existing scripts (in R and Python) for analysis of genomic data derived from high-throughput techniques.
4. Be responsible for identifying and developing novel tools to improve the analysis’s efficiency, sensitivity, and functionality. 
5. Be responsible for creating, in collaboration with the C3BI-Hub, a website that will make the data accessible and explorable by the wider scientific community (Similar to http://aegyptiatlas.buchonlab.com or https://www.malariacellatlas.org).

The successful candidate will also have the opportunity to develop further projects and research questions that fit within the lab’s broad interests.

More generally, post-doctoral fellows are expected to: (1) lead their project and initiate or contribute to collaborative projects (within the lab and externally), (2) apply for grants, present their work at international conferences, and prepare publications and (3) share their experience to support more junior lab members. Support from the PI and training opportunities will be available for every key skill (e.g, grant writing, management, communication). 

Key experiences and competencies

Essential

• Doctoral degree in Computational Biology, Bioinformatics, Biostatistics, Artificial Intelligence, Computer Science or degree in another relevant discipline.
• Motivation to leverage methods in computational biology, biostatistics and mathematical modelling to understand a biological system (mosquito-virus interactions).
• Experience in scientific programming in the areas of DNA and/or RNA next-generation sequence analyses.
• Working proficiency in UNIX/Linux.
• Proficiency in R and Python, or other script programming languages (Bash, Perl,…)
• Familiarity with tools and processes for reproducibility and maintainability in software development and data analysis (Git, Docker, …)
• Experience using classical and/or deep machine learning methods (using TensorFlow/Keras).
• Experience in statistical modelling, particularly Bayesian modelling (e.g. using STAN and/or PyMC).
• Experience with large-scale computational analysis; running software on a high-performance computing cluster or cloud environment.
• Excellent communication skills in English
• Self-driven and able to work independently in an organized manner while being part of a team.

Desirable

• Background (e.g. BSc or work experience) in biology. 
• Experience with single-cell and/or spatial multi-omics analytics and computational method development in the area.
• Demonstrable publication record in peer-reviewed journals.

Working at Institut Pasteur

Institut Pasteur provides an international and dynamic research environment that supports postdoctoral training. Specific opportunities include access to the Pasteur alumni network and individual career coaching programs that help preparing for the post-doc to PI transition, industry transition, entrepreneurship, or any other exciting career in science. Access to a wide range of state-of-the-art equipment and technology platforms is provided, and multiple opportunities to supervise students, organize scientific meetings, participate to institutional life will be available.

Institut Pasteur and CNRS are committed to foster an inclusive and diverse work environment. Candidates will be evaluated solely on qualifications using open, transparent and merit-based recruitment process based on the European HRS4R standards. 

Contact us! 

Please send your CV, the names and contact information of three references, and a cover letter to sarah.merkling@pasteur.fr.