Institut de Biologie de l'École Normale Supérieure ENS . CNRS UMR8197 . Inserm U1024 Directeur : Pierre Paoletti

Description
Scientific scope and projects
Activities
Teaching
Softwares developed within the CBC

Description
IBENS hosts interdisciplinary research combining high-throughput observations with quantitative and systems biology. This type of research relies on the production and computational analysis of large datasets, as well as on the development of mathematical models and methods, generally followed by validation in collaboration with experimental teams.

The Computational Biology Center of IBENS (CBC) aims at reinforcing the synergies between the teams and platforms that are active in computational biology at IBENS, as well as increasing the visibility of this transversal axis within the Institute and at the national level. Currently, the CBC federates three platforms and six research teams in bioinformatics, systems biology modelling and bio-imagery.

Scientific scope and projects

Systems Biology

dynamical modelling of genetic/regulatory/signalling networks
The Computational Systems Biology team is involved in the development of a qualitative mathematical framework suitable for the modelling of cellular networks and the implementation of the framework and algorithms in the software GINsim. The biological applications encompasses development, in particular haematopoiesis.

Bioinformatics applied to genomics

Computational analysis of functional genomic data
The Computational Systems Biology team contributes to the development of the Regulatory Sequence Analysis Tools (RSAT) and specialised in genome-wide data obtained with ChIP-seq, ATAC-seq and single-cell RNA-seq, single-cell ATAC-seq

Pipelines to process functional genomics data
The Genomics facility and CSB team collaborate around the development of pipelines to process raw datasets of RNA-seq, ChIP-seq/ATAC-seq and more recently single-cell RNA-seq. These freely available pipelines combine state-of-the art tools, and take advantage of the workflow engine Eoulsan, which enables transparency, reusability, and parallel processing.

Comparative Genomics and evolution
DyoGen team

Bio-mathematic modelling

Modeling of biodiversity
The Modeling Biodiversity team uses mathematics and computation to address questions in ecology and evolution. We are particularly interested in understanding the processes that generate and maintain biodiversity. We use stochastic processes, Monte Carlo simulations, Bayesian statistics and phylogenetics, in combination with large scale empirical datasets, to study the diversification of species, the evolution of their phenotypes, and their assembly into ecological communities.

population dynamics, community diversity, and ecosystem function
Eco-Evolutionary Mathematics

Bio-imaging

Computational Bioimaging and Bioinformatics

Infrastructure for Computational Biology

Computing service + Bioinformatics platform

Activities
In addition to the scientific collaborations between members of the CBC, we are engaged in various activities:

– Bioinformatics Club
– Scientific seminars
– Mailing lists
– Organisation of symposia
– Workshop for researchers

Teaching
The CBC also aims at contributing to teaching computational biology, through the involvement of its members in the undergraduate program at ENS, supervision of intern trainees and apprentice, graduate school, and active participation to workshop for researchers at IBENS and in France.

Softwares developed within the CBC
The Computational Biology Center of IBENS develops many bioinformatics tools: