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.

News

July 4, 2018

The article:
Raucci R, Laine E, Carbone A. Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity, Structure, 2018  [ Link to the article ]
has been recommended in F1000Prime as being of special significance in its field by F1000 Faculty Member Alexandre Bonvin. 

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.
Link to the article

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.

 

To the Article

March 19, 2018

In the framework of their cooperation, IFOM (Milan) and CQB (Paris) have set up a scientific rotation program specifically targeted to PhD students.
Students can spend three months in a host group on a scientific topic, with the goal of exploring new approaches and contexts,and acquiring new skills.

Here you can find general rules and how to apply.
Here you can find a list of currently posted projects ( you can also apply spontaneously outside of posted projects).

Contact: phd-rotation@ifom.eu

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.

To the Article
 

January 10, 2018

Elodie Laine of the Analytical Genomics team co-organized the Meet-U colloquium on the 10th of January 2018: http://meet-u.org/colloquium_2018.html. Meet-U aims at bridging the gap between teaching and research in computational and quantitative biology. It brings together Sorbonne Université, Univ. Paris-Sud and Univ. Paris-Diderot.
The theme of this year was protein-protein docking: http://meet-u.org/edition_2018.html. »

December 18-19, 2017

 Marco Cosentino Lagomarsino of the GenomicPhysics team organizes the conference Quantitative Methods in Gene Regulation IV ( here you may find the poster image).

December 13, 2017

Alessandra Carbone and Elodie Laine are organizing the "UPMC Young Researchers' Meeting: Modeling Complex Biological Systems"

The talks on current work in computational biology at UPMC will be given by PhD students and Postdocs working at UPMC labs. It will be an opportunity to listen at ongoing research and learn what is done in close by departments.

The up to date program is available here
 

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