The Laboratory of Computational and Quantitative Biology (LCQB), headed by A. Carbone, is an interdisciplinary laboratory working at the interface between biology and quantitative sciences. It is built to promote a balanced interaction of theoretical and experimental approaches in biology and to foster the definition of new experimental questions, data analysis and modeling of biological phenomena. Our projects address questions on biological structures and processes through the gathering of experimental measures, the in silico generation of new biological data that remain inaccessible to experiments today (modeling of biological systems), the development of statistical methods for data analysis, and the conception of original algorithms aimed to predictions. The lab is supported by the CNRS and Sorbonne Université.


May 3, 2020

A.Carbone and F.Oteri work on the Spike protein of SARS2 in collaboration with the group of F.L.Cosset at CIRI in Lyon, expert in non-replicative retroviral pseudoparticles. Based on coevolution analysis of patient sequences and sequences from bats and other species, they aim at identifying key residues in the Spike protein involved in the entry mechanism of the virus in human cells. In the past, the two groups successfully combined their computational and experimental methods to unravel critical features of the original HCV fusion mechanism.

May 2, 2020

The team "Statistical Genomics and Biological Physics" has obtained financial support by the Faculty of Sciences and Engineering of Sorbonne Université, to develop sequence-data driven models of evolutionary landscapes and selective constraints acting in the Covid-19 causing virus SARS-CoV-2. The projects aims at finding signatures of selection in the rapidly increasing number of available 
genomes, and to interpret them in terms of protein structure, function and protein-protein interactions inside coronaviruses and with the host (e.g. the famous interaction of the viral spike protein with the human ACE2 receptor). 

December 2, 2019

The "Emergence program" promoted by the "Ville de Paris" is awarded to projects encouraging the creation and the development of new research teams in the Paris region.
Zhou Xu received one of these recognitions for 2019.

November 15, 2019

Nonribosomal peptide synthetases (NRPSs) are microbial megaenzymes that make a wide variety of small-molecule products, including many that are clinically used as antitumors, antibiotics, or immunosuppressants. Peptide synthesis proceeds with assembly-line logic, where each station on the NRPS assembly line is a multidomain unit called a module. While the function of single modules is well studied, much less is known how they work together. Researchers from the Schmeing lab at McGill University have resolved several dimodular NRPS structures, which show coordinated interactions between modules, and large conformational changes between catalytically relevant states. Martin Weigt from the “Statstical Genomics and Biological Physics” team has performed complementary coevolutionary analyses using the direct coupling analysis (DCA), which confirm the biological relevance and evolutionary conservation of the observed inter-modular interactions. DCA analysis has also allowed to suggest mutations in a module-swapped chimeric NRPS protein, which significantly increased the activity of the protein, a result of direct relevance toward the longstanding goal of NRPS bioengineering for production of new-to-nature bioactive small molecules.

Link to article in Science

November 14-15, 2019

The "6th Cross Disciplinary Genomics: from Single Cells to Omics" will be held on November 14-15, 2019, at Amphitheatre 25 - Campus PMC, Sorbonne Université.

There is no participation fee but registration is required. 

October 24, 2019

GEMME makes the cover of the MBE november issue.

September 23, 2019

GEMME is a fast, scalable and simple method to predict mutational landscapes from natural sequences. It demonstrates how deleterious effects of a protein mutation are identified by looking at the closest known sequence accepting the mutation in the evolutionary tree of sequences and at its epistatic changes.  The article just appeared in Molecular Biology and Evolution.

Link to the article
Link to the webserver 

July 24, 2019

We propose the concept of "interacting region" and the dynJET2 method toward deciphering the complexity underlying protein surface usage and deformability. Interacting regions account for the multiple usage of a protein's surface residues by several partners and for the variability of protein interfaces coming from molecular flexibility. dynJET2 predicts interacting patches by crossing evolutionary, physico‐chemical and geometrical properties of the protein surface with information coming from complete cross‐docking (CC‐D) simulations. 

Link to the Article


June 10, 2019

The Team of Diatom Functional Genomics (R. Annunziata, A. Ritter, A.E. Fortunato, A. Manzotti, S. Cheminant Navarro, J.P. Bouly and A. Falciatore), in collaboration with the team of Biology of Genomes (Nicolas Agier) and Marco Cosentino Lagomarsino at the LCQB characterized the circadian rhythms of the marine diatom Phaeodactylum tricornutum and identified the bHLH-PAS protein RITMO1 as the first known regulator of these rhythms in these algae. This study, published on Proceedings of the National Academy of Sciences (PNAS) adds new elements to our understanding of diatom biology and offers new perspectives to elucidate timekeeping mechanisms in marine algae.

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.

To the Article


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