Two Postdoc positions in machine learning for single-cell genomics

Two Postdoc positions in machine learning for single-cell genomics

Keywords: single-cell genomics, multi-omics, machine learning, graph neural networks, optimal transport

We are looking for two highly motivated postdoctoral scientist (f/m/x) to join the Cantini lab, affiliated
to the PaRis Artificial Intelligence Research InstitutE (PRAIRIE), currently at École Normale Supérieure (ENS) and soon (Jan 2023) joining Institut Pasteur.
The recruited postdocs will work in Machine Learning for Single Cell Genomics. In particular, they
will be developing machine learning methods for multi-omics single-cell data integration, both aimed
at studying cellular heterogeneity and its underlying regulatory mechanisms.

Required skills

  • PhD in Data science, Computer Science, Computational Biology, or related fields
  • Previous experience in the design and implementation of machine learning tools/algorithms
  • Strong analytical and programming (R, Python…) skills
  • Previous experience with applications to biology, single-cell data analysis, graph neural
    networks, or optimal transport will be a plus

Team and location

The Cantini lab is an interdisciplinary team composed of researchers in data science, computational
biology and bioinformatics. The project will be developed in close collaboration with Gabriel Peyré
The recruited researchers will be based with all the team at Institut Pasteur, a world-renowned center of
excellence for research in infectious diseases, assuring tight collaboration with computational biology
and wet-lab biology experts. In addition, the affiliation to the PRAIRIE institute, one of the 4
Interdisciplinary Institutes for Artificial Intelligence research set up as part of the national strategy for
Artificial Intelligence, providing interaction at AI and machine learning level.


The Postdoc positions will be for 2 years, with possibilities for renewal. To apply, please submit: a cover
letter summarizing research interests and expertise and a Curriculum Vitae (including contact
information for at least two references) to Laura Cantini.

Postdoctoral / Engineer Research Fellow

Postdoctoral / Engineer Research Fellow

The Decision and Bayesian Computation (DBC) and Bayesian Computation (DBC), the Perception and Memory (PM) labs and the Image Analysis Hub (IAH) at the Institut Pasteur of Paris are seeking either a talented postdoctoral researcher or an engineer for a project at the frontier of neuroscience, modeling and computer vision. The recruited researcher will work on an muli-laboratory project which aims to explore how a depressive-like state alters neuronal circuits in the olfactory system by implementing an innovative technological approach to quantify brain connectivity in 3D. She/He will be in charge of modeling and analyzing the light-sheet microscope images generated during the project. The project involves the Perception and Memory lab, the decision and Bayesian computation lab and the Imaging Analysis Hub.

The proposed 2-year position (that could be extended) will mainly consist of the following tasks:
● Development within a new framework mixing Virtual reality tablet app and big data processing pipeline one shot learning procedure from minimal user input.
● Design a set of physics & geometry-informed self-supervised pretext tasks to improve segmentation learning.
● Develop within the Graph Neural Network (GNN) pipeline of the DBC lab a new approach to biological
neural circuit characterization.

The candidate should have, or expect to have, a PhD degree or equivalent degree (Engineer) in a related field with prior research experience stated in the above. The successful candidate could be
– an applied mathematician willing to work at the frontier of neurosciences
– a physicist willing to work at the frontier of neurosciences
– a machine learning engineer
– a neuroscientist with coding knowledge

Postdoctoral Researcher in AI

Postdoctoral Researcher in AI

Anita Burgun, PR[AI]RIE Chair is recruiting a postdoc

Université de Paris Cité is seeking a Postdoctoral Researcher in AI, to join a multidisciplinary group that develops research on AI application to health. The multidisciplinary group focuses on making fundamental progress in AI with application to rare genetic diseases and is affiliated with PR[AI]RIE Institute.

The job position is in Paris, France, at Imagine Institute, which will allow the researcher to benefit from a multidisciplinary environment, with access to data and expertise in genetics. The Postdoctoral Researcher will collaborate with PR[AI]RIE fellows that develop research on AI, researchers in genetics at the Imagine Institute/ UPC/ Necker Hospital, and researchers specialized in health informatics, health data science, and clinical decision systems from the UPC. The group is seeking a researcher that applies high standards to the research and is able to develop highly impactful AI in a complex and almost unexplored domain. Contrasting with other medical domains, most genetic diseases explored at Imagine Institute are very rare and pleiotropic. Therefore, dedicated AI approaches need to be designed.

The objective is twofold:

  • to generate new knowledge from real world and research data for better understanding of rare disease. Real world data should include time-stamped clinical data from Electronic Health Records.
  • to provide novel methods that generate knowledge networks from such high dimensional data. The data include complex histories of rare disease patients (clinal signs and symptoms) and omic data (genomic, transcriptomic, etc).

The network should be reusable to conceive new diagnosis tools and even to suggest new drug development.

The chosen candidate will be able to gain valuable experience in a well-recognized research institute in AI, acquire knowledge in medical domain, and publish academic papers. Postdoc research areas may include Machine Learning, Natural Language Processing, Reinforcement Learning, Active Learning, or other similar fields. The postdoc will be offered a 18 months contract that can be extended to 2 years. He/she will be located at Imagine institute (boulevard Montparnasse, Paris 14e). Candidates are welcome to send their applications to anita.burgun [at] (Anita Burgun, MD, PhD, PR[AI]RIE fellow), before the end of February.