Experience

2021-... PhD Student
ComBi group @ Laboratory of Digital Sciences in Nantes (LS2N) & Nantes University, Nantes, France
Logic programs to infer computational models of human embryonic development

Under the supervision of Jérémie Bourdon (LS2N), Carito Guziowloski (LS2N) and Laurent David (CR2TI).

The advent of new single-cell sequencing technologies now allows for a detailed and in-depth analysis of the gene regulatory mechanisms involved in human embryonic development. This advancement opens new perspectives in the complex and limited study of embryonic development. This thesis focuses on the computational modeling of development to better understand the gene regulatory mechanisms involved. To this end, we present SCIBORG, a method that infers Boolean networks modeling the stages of development of interest. By combining gene interactions from prior knowledge with observed gene expression in embryonic cells, Boolean models are learned, indicating the mechanisms involved in the studied developmental stages. We applied our method to two developmental stages of the trophectoderm and discovered distinct regulatory mechanisms in our models. Overall, this thesis proposes a method for modeling the regulatory mechanisms involved in a cell differentiation process, providing a valuable tool for studying human embryonic development.

2021 (6 months) Research intern
Pleiade group @ Inria, Bordeaux, France
Seed detection in metabolic networks

Under the supervision of Clémence Frioux.
2020 (4 months) Bioinformatics technician
University Hospital of Bordeaux, Bordeaux, France
Technician in the Bioinformatics unit of the Biology and Pathology Pole of the Bordeaux University Hospital.
2020 (4 months) Research intern
Translational Research in Gene Therapy (TaRGet), Nantes, France
Implementation of an NGS library preparation protocol without DNA amplification step (PCR-free protocol)

Under the supervision of Émilie Lecomte.

Implementation of a PCR-free protocol to prepare DNAs for Illumina sequencing.
Development of SSV-Coverage, a program in Python 3 allowing the creation of a coverage graph.


Education

2021-present PhD in Computer Science
Nantes University, France
Specialization Computational Biology
2019-2021 Master in Computational Biology
University of Bordeaux, France
Specialization Computational Biology
2018-2019 Bachelor in Computational Biology
University of Évry, France
Third year of Life Sciences Bachelor specialization Biology and Computer Science
2016-2018 DUT Biological Engineering option Computational Biology
University of Clermont Auvergne, Aurillac, France
Equivalent of 2 first years of a Bachelor