|@LCQB@RKI|| MASSIV: Evolution and structural impact of alternative splicing
with Hugues Richard
MASSIV aims at systematically assessing the structural impact of alternative splicing (AS) and at identifying evolutionary conserved AS events at the scale of the human genome. Funding: ANR JCJC 2018-2021.
|@LCQB || Protein-protein interactions and mutational landscape prediction at the genome scale|
with Alessandra Carbone
We are developing methods to predict who interact with whom in the cell, and to assess the outcome of mutations. We rely on evolutionary information (conservation/coevolution), physico-chemical and geometrical descriptors.
|@LCQB|| RIBONETWORK: Exploring co-traductional networks during evolution
with Mathilde Garcia
This project aims at exploring the networks of interactions and control specific to genetic expression at play during translation, through system biology approaches.
|@Paris || Meet-U: educating through research immersion
with Anne Lopes
This project aims at bridging the gap between education and research, especially in computational biology. Sponsors: SFBI, GDR BIM, ED SDSV, IBPS, IUF.
|@France || Prediction of protein and protein complexes 3D structures
with Sergei Grudinin, NANO-D, INRIA Grenoble.
We are developing approaches that combine geometry (shape complementarity, voronoi contact areas) with evolutionary information (conservation and coevolution). We are also developing methods to predict protein functional transitions.
|@France || Evolution and alternative splicing of disordered regions|
with Juan Cortés, LAAS, CNRS, Toulouse.
We are studying the evolution of the local structural preferences of alternatively spliced intrinsically disordered regions.
with the universities of the 4EU+ alliance
We are implementing the Meet-U formula at the european level with the University of Heidelberg, Charles University (Prague) and the University of Warsaw.
|@Europe|| INDEPTH COST Action |
with 50 labs in 19 countries
This project aims at deciphering how nuclear architecture, chromatin organization and gene expression are connected and modified in response to internal and external cues in plants. Funding: COST-Action 2018-2021.
| New Directions of AI in Structural Biology Workshop
August 2-4, Marseille, France
This small in-person gathering brought together researchers from computational structural biology and several machine learning communities, including natural language processing, computer vision, and geometric learning, to discuss the current state of the protein structure prediction field and future challenges. Despite apparent dramatic progress, many challenges remain. They include the understanding of multiple functional states, protein flexibility and transitions, associations with other proteins, and protein design for a specific function.
| Integrative Structural Modeling Symposium
July 8, Online
This mini-symposium focused on recent developments and applications in integrative structural modeling, in a redefined landscape owing to the spectacular advances of cryo-EM and deep learning-powered protein structure prediction. Invited speakers: R. Pellarin (CNRS-Institut Pasteur, Paris); E. Karaca (Izmir Biomedicine and Genome Center); S. Grudinin (INRIA, Grenoble); S. Jonic (CNRS-Sorbonne Université, Paris).
| Meet-4EU+ 2021 Symposium
Jan. 25, Online
Meet-4EU+ is inspired from the Meet-U initiative and is implemented at the European level. Nine teams coming from the Universities of Heidelberg and Warsaw, Charles University and Sorbonne Université addressed the open questions of TAD and compartment calling from Hi-C data. Invited speakers: A. Pekowska (Nencki Institute, Warsaw); B. Moindrot (I2BC, U. Paris-Sud); N. Servant (Institut Curie, Paris); J. Mozziconacci (MNHN, Paris).
| Noncanonical amino acids Symposium
Oct. 21-22, Jussieu Campus, Sorbonne Université
The aim of this 2-day symposium was to gather chemists, biochemists, biologists and biophysicists involved in the development of new technologies using ncAAs and in their application to biological questions. 89 researchers attended the symposium, which covered a wide range of topics ranging from synthetic methodologies to applications in biology and biophysics. Invited speakers: H. Wennemers (ETH Zürich); D. Jones (Cardiff University); M. Gondry (I2BC, Saclay); I. Coin (Universität Leipzig); T. Sakmar (The Rockefeller University).
| Meet-U 2018 Colloquium
Jan. 10, Jussieu Campus, Sorbonne Université
Meet-U aims at bridging the gap between teaching and research. This meeting day gathered about 150 participants coming from different universities and research institutions around a common topic in structural bioinformatics, namely protein-protein docking. Invited speakers: A. Bonvin (Utrecht University); F. Cazals (INRIA, Sofia-Antipolis); F. Fraternali (King's College, London); S. Grudinin (INRIA, Grenoble); D. Ritchie (INRIA, Nancy).
| Young Researchers' Meeting: Modeling Complex Biological Systems
Dec. 13, Jussieu Campus, Sorbonne Université
This meeting gathered young researchers contributing to the development and/or application of computational methods to the modeling of complex biological systems. Topics included statistical analysis of (meta-)genomic sequences, molecular structures, dynamics and interactions, cell migration and geometry, infection dynamics, population dynamics and regulatory networks reconstruction. Invited speakers: V. Fromion (MaIAGE Unit, INRA); F. Major (IRIC, University of Montréal).
| ISCD Summer School 2017: Scientific Trends at the Interfaces Bioinformatics – Visual Data Analysis
July. 17 - Aug. 11, Roscoff Marine Station, Sorbonne Université
This summer school aimed at training motivated students in Bachelor’s and Master’s degrees from all over the world in bioinformatics and data visualization. I participated in the organization of the first two weeks, dealing with protein structures and protein-protein interactions, high-throughput sequence analysis, gene regulatory networks, evolutionary processes, phylogeny and co-evolution.
| Mini-symposium BIOMATH: Formal methods in the eyes of biological data
June 5, Ronce-les-Bains, France
This mini-symposium highlighted recent mathematical developments toward elucidating biological questions or modeling complex biological systems. It illustrated the way formal methods and models can be used to understand the functioning and emergent properties of biological systems, and are revised/improved based on their agreement with the empirical observations obtained on these systems. Invited speakers: S. Grudinin (Nano-D, INRIA); L. Jacob (LBBE, UCB Lyon 1); A. Lambert (LPSM, Sorbonne Université - SMILE Group, CIRB, Collège de France); A. Trouvé (CMLA, Ecole Normale Supérieure).
| Symposium on the Evolution of Alternative Splicing
July 12-16, Vienna, Austria
This symposium aimed at moving beyond simple comparisons of alternative splicing events across species to the study of the functional impact of new isoforms during evolution. It highlighted the latest advances in the field, notably related to the following questions: How did splicing evolve between species? What portion of AS might just represent “noise”? What is the functional impact of AS on the evolution of proteins? Invited speakers: C. Burge (Department of Biology, MIT, MA, USA); M. Tress (CNIO Bioinformatics Unit, Spain)
| ICS Summer School 2014: Scientific Trends at the Interfaces Bioinformatics – Visual Data Analysis
July. 15 - Aug. 8, Roscoff Marine Station, Sorbonne Université
This summer school aimed at training motivated students in Bachelor’s and Master’s degrees from all over the world in bioinformatics and data visualization. I participated in the organization of the first two weeks, dealing with protein structures, dynamics and interactions, high-throughput sequence analysis, gene regulatory networks, evolutionary processes, genomes organisation and dynamics.
| Signaling pathways: Interplay between microscopic changes and global behavior of biological systems|
Oct. 8-10, ENS de Cachan, France
The main focus of this workshop was the problem of how to deal with the different organizational levels of biological systems. It highlighted recent developments in multiscale representations/approaches, linking microscopic dynamical changes to macroscopic spatio-temporal dynamics.
with Jessica Andreani, Isaure Chauvot de Beauchêne, Anne Lopes, Matthieu Montes and Sjoerd de Vries
We organize regular meetings to exchange in a very open and informal way on diverse topics of structural bioinformatics and molecular modeling. Our goal is to foster new collaborations toward solving challenging problems.
|@GDR BIM|| MASIM: Méthodes Algorithmiques pour les Structures et Interactions Macromoléculaires |
animated by Frédéric Cazals and Yann Ponty
This working group is dedicated to structural bioinformatics and more specifically to methodological developments in the field. It aims at uniting a community characterized by a great diversity in methods, models and molecules.