Séminaire virtuel: vendredi 4 juin 2021
Sabine Peres (LISN / Paris Saclay) et Léonard Hérault (Aix Marseille Université)

13h00 - 13h30 – Sabine Peres (LISN / Paris Saclay)

Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism

Elementary Flux Modes (EFMs) provide a rigorous basis to systematically characterize the steady state, cellular phenotypes, as well as metabolic network robustness and fragility. However, the number of EFMs typically grows exponentially with the size of the metabolic network, leading to excessive computational demands, and unfortunately, a large fraction of these EFMs are not biologically feasible due to system constraints. However, only a few constraints can be integrated in the traditional computation; most of them must be treated in post-processing and thus do not save computational time. In this talk, we will present the biological constraints that we integrate into the EFMs calculation. We rely on a hybrid computational tool based on Answer Set Programming (ASP) and Linear Programming (LP) that permits the computation of EFMs while implementing many different types of constraints. We will illustrate this approach to the Escherichia coli core model in considering transcriptional and environmental regulations, thermodynamic constraints, and resource usage considerations.

13h30 - 14h00 – Léonard Hérault (Aix Marseille Université)

Single cell RNA seq assisted synthesis of a boolean transcription factors network to model early hematopoiesis and its alteration with aging.

We previously characterized early hematopoieisis in young and aged mice through hematopoietic stem cell (HSC) sc-RNA-seq analysis. Thanks to HSC clustering and pseudotime ordering as well as regulon analysis we showed differentiation paths of HSC toward three primed states and an accumulation of quiescent HSCs upon aging. Starting from these results coupled to current knowledge of transcriptionnal regulation of early hematopoiesis we built a boolean network using answer set programming in order to model HSC priming and its alteration with aging.

Dernière modification le 04/06/2021