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December 18, 2018

Phenotypic diversity can arise from changes in the gene content of the genomes but also from modifications in the regulation of gene expression. The "genetic networks" team compared gene expression in 8 yeast species to find "regulatory outliers", i.e. conserved genes with special expression profiles compared to their orthologues. The combination of this approach with other functional genomics data (transcriptomics analyses and chromatine immunoprecipitation followed by deep sequencing) led us to identify two genes which are involved in the survival of the human pathogen Candida glabrata upon iron starvation conditions. Iron starvation being a key challenge for C. glabrata survival in blood, this discovery may help us to better understand the invasive strategy of this emerging pathogen.

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December 6, 2018

The latest publication of the new LCQB team "Telomere and Genome Stability" (Héloïse Coutelier and Zhou Xu) makes the cover of the December issue of Genes & Development!    The article (Coutelier et al. 2018 Genes Dev.) shows that telomere-induced senescent cells can adapt to the DNA damage checkpoint safeguard mechanism to force cell division, leading to increased genome instability, with important ramifications for aging and cancer. The cover displays cells bearing a fluorescent reporter construct monitoring of the checkpoint status in single cells.

September 10, 2018

The group Evolution and immunology of pathogens ( Rouzine, Pedruzzi, Barlukova) published the article "Evolutionary Footprint of Epistasis" on PLOS Computational Biology.

June 22, 2018

Pierre Louis Blaiseau of the Genetic Networks team recently published « Monod and the phenomenon of diauxie » in the Bulletin d’Histoire et d’Epistémologie des Sciences de la vie. This article described a part of the scientific activity of the Jacques Monod until then neglected by the historians: its interest during all its career for the mechanisms of enzymatic inhibition. Besides, it showed that, contrary to the standard narratives, the phenomenon of « diauxie » (double growth) was discovered by Monod during his thesis and not by the previous Frederic Diénert’s work

June 6, 2018

The Diatom Functional Genomics Team (L Taddei, GR Stella, JP Bouly, M. Jaubert and A. Falciatore) reported novel strategies to deal with environmental light stress in marine diatoms.  Their results recently published on Plant Physiology reveal that diatoms modulate non-photochemical quenching of excess excitation by activating different members of the LHCX protein family, with different light intensity activation thresholds and different patterns of association with photosystem II. This leads to mechanistically different and physically segregated excess energy quenching processes, as required for proper light-stress acclimation in the extremely variable conditions of the oceans.

June 5, 2018

Local Interaction Signal Analysis (LISA) is an empirical function designed to estimate protein-protein binding affinities. It explores the geometry of contact distributions at protein-protein interfaces and enables to identify hot-sites of favorable contacts playing a major contribution in binding affinity. LISA applies to a large variety of complexes resulting in a very stable behavior. It outperforms all existing comparable predictor methods predicting binding affinity.

The Analytical Genomics team.
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March 19, 2018

Several members of LCQB co-authored « Meet-U: educating through research immersion », which appeared in PLOS Computational Biology on 03/15/2018. Meet-U is a new educational initiative that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. In this paper, we report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, and with protein–protein docking as the subject of the course.

 

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March 6, 2018

"A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism" appeared in PLoS Pathogens, from A.Carbone team. This work sheds light on important structural features of the HCV fusion mechanism and contributes to advance our functional understanding of this process. This study also provides an important proof of concept that coevolution can be employed to explore viral protein mediated-processes, and can guide the development of innovative translational strategies against challenging human-tropic viruses.

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October 12, 2017

F.Nadalin and A.Carbone published CIPS, a new computational method for scoring protein docking decoys based on a combination of residue-residue contact preferences and interface compositional bias. CIPS outperforms state-of-the-art methods on screening protein-protein docking models and improves the ranking on 28 CAPRI targets. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis.

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June 28, 2017

Eleonora De Lazzari* published her findings on scaling laws for gene families. A striking quantitative invariant in evolutionary genomics is the scaling with genome size of the number of proteins sharing a specific function. E.D.L. showed that such scaling laws exist systematically at the level of single evolutionary families. This provides a novel view of the links between evolutionary expansion of protein families and gene functions.This work was performed in collaboration with J Grilli (U. Chicago) and S Maslov (U. Illinois).

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