Quantification and modelling of embryonic lymph node organogenesis at the single cell scale

Position

Ph.D. Student

Published Date

14 janv. 2021

25 févr. 2021

Until filled

Application

poster

Application deadline

Keywords

Quantitative embryogenesis, whole-mount analysis, peripheral nervous system, immune system, image analysis, machine learning, big data analysis

The role

We are seeking a highly motivated candidate strongly interested in interdisciplinary science, to join our groups (van de Pavert and Guignard labs) and work on a project at the crossroad between Computer Science and Developmental Biology.

The project aims at studying lymph node (LN) formation during mouse embryonic development. LN formation requires hematopoietic lymphoid tissue inducer cells (LTi) to interact with mesenchymal cells at precise locations within the embryo, where they subsequently form aggregates. We have postulated that the peripheral nervous system outgrowth initiates the earliest events in LN formation. Indeed, preliminary data show that LTi aggregates morphology and cell density is affected in mouse embryos lacking neuronal subsets.

To understand the relationship between neuronal outgrowth and lymph node formation, the successful candidate will work between the van de Pavert lab and the Guignard lab to develop new computational methods to reconstruct and quantify LTi aggregates and peripheral nervous system morphology at the single cell scale. The reconstructions will then be used to develop a machine learning framework to systematically quantify phenotypes in perturbed mouse embryos. These quantifications will in turn allow to model the effects of neuronal outgrowth on LN formation.

The successful candidate will work towards:

  • building a library of whole-mount mouse embryo images

  • developing computational methods for the analysis of the generated library, including: reconstruction and mapping of the neuronal network and quantification of LTi aggregate morphologies and positions

  • developing computational methods to automatically stage mouse embryos

  • modelling LN formation in relation to neuronal network morphology

The role

We are seeking a highly motivated candidate strongly interested in interdisciplinary science, to join our groups (van de Pavert and Guignard labs) and work on a project at the crossroad between Computer Science and Developmental Biology.

The project aims at studying lymph node (LN) formation during mouse embryonic development. LN formation requires hematopoietic lymphoid tissue inducer cells (LTi) to interact with mesenchymal cells at precise locations within the embryo, where they subsequently form aggregates. We have postulated that the peripheral nervous system outgrowth initiates the earliest events in LN formation. Indeed, preliminary data show that LTi aggregates morphology and cell density is affected in mouse embryos lacking neuronal subsets.

To understand the relationship between neuronal outgrowth and lymph node formation, the successful candidate will work between the van de Pavert lab and the Guignard lab to develop new computational methods to reconstruct and quantify LTi aggregates and peripheral nervous system morphology at the single cell scale. The reconstructions will then be used to develop a machine learning framework to systematically quantify phenotypes in perturbed mouse embryos. These quantifications will in turn allow to model the effects of neuronal outgrowth on LN formation.

The successful candidate will work towards:

  • building a library of whole-mount mouse embryo images

  • developing computational methods for the analysis of the generated library, including: reconstruction and mapping of the neuronal network and quantification of LTi aggregate morphologies and positions

  • developing computational methods to automatically stage mouse embryos

  • modelling LN formation in relation to neuronal network morphology

Requirements

The student should be enthusiastic, creative and ambitious, have good communication skills and be eager to learn. A master degree with major or minor in computer science is required. Affection for developmental biology is preferred. Some experience in developmental biology is also preferred but not required. Note: exception can be made for students who have not studied computer science if the student can prove coding skills.

The offer

  • 3-year Ph.D. position in the van de Pavert lab and the Guignard lab

  • Target start date: from September 2021

Application procedure

All applications must be done through the CENTURI portal at this address: https://centuri-livingsystems.org/application-form-phd2021-26/


Questions can be addressed to Serge van de Pavert or to Léo Guignard by email with the mention [Job-2021] in the title.


Serge van de Pavert: vandepavert@ciml.univ-mrs.fr

Léo Guignard: leo.guignard+lab@gmail.com

Selection process and calendar

Call open for applications: January 15 - February 26


Interviews of shortlisted candidates by the evaluation committee: April 20 to April 22.

The pre-selection process will be based on qualifications and expertise reflected on the candidates CV and motivation letter. It will be merit-based. All candidates will be informed whether they have been pre-selected or not.


Final candidate selection: April 27


Expected decision from the candidate: May 4

Location

Léo Guignard and Serge van de Pavert labs