Biologie Computationnelle et Quantitative - Laboratory of Computational and Quantitative Biology (LCQB)

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 the University Pierre and Marie Curie (UPMC).


December 2014

A. Gillet-Markowska, H. Richard, G. Fischer & I. Lafontaine just published a new tool - Ulysses - providing an accurate detection of low-frequency structural variations in large insert-size sequencing libraries. Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes.
Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries
Bioinformatics 2014; doi: 10.1093/bioinformatics/btu730

November 13-14, 2014
The 4th Cross Disciplinary Genomics meeting "Up-and-Coming Advances in Genome Sciences" will be held at UPMC, in the Jussieu Campus. There is no participation fee but registration is required.
November 10, 2014
The "Biology of Genomes" team and the "Intraspecific Variation and Genome Evolution" team from the Université de Strasbourg have published the first population genomics survey in a yeast different form a Saccharomyces species. This study reveals that consequently to a large-scale introgression event, two different mutational regimes can coexist within the same genome.
November 7, 2014
Alice Coucke, Eleonora De Leonardis and Matteo Figliuzzi (Statistical Genomics Group) and Vittore Scolari (Genomic Physics Group) co-organize the 2nd edition of the conference:
Paris Biological Physics Community Day 2014
The conference will be held at Centre Culturel Irlandais in Paris
October 8-10, 2014
From the Analytical Genomics team:

The international meeting "Protein-Protein Interactions on the Genome Scale" is organized within the framework of the MAPPING project (Investissement d'Avenir en Bioinformatique) by A.Carbone.
The event will take place at UPMC, Jussieu Campus.
Registrations are open.
July 2014
Now open: 2 postdoc positions are available in the "Analytical Genomics" team.
One position deals with protein conformational dynamics and co-evolution analysis (description here). The other one deals with protein annotation at large scale using probabilistic models (description here).
Please contact: Alessandra Carbone.
July 15 - August 8, 2014
A.Carbone and E.Laine, from the Analytical Genomics Team, organize the ICS Summer School 2014 "Scientific Trends at the Interfaces - Bioinformatics and Scientific Visualization". Information on the school can be downloaded here.
March 28, 2014
The Biology of Genomes team participated to the complete design and synthesis of the first eukaryotic synthetic chromosome. We compared replication dynamics of synthetic and native chromosome III and saw few dramatic changes in spite of several autonomously replicating sequences having been deleted.

Total Synthesis of a Functional Designer Eukaryotic Chromosome. Annaluru, Muller et al., Science (2014) DOI:10.1126/science.1249252

February 8, 2014
From the "Analytical Genomics" team:
A World Community Grid Lecture Series webcast describing the work done by the team and its collaborators on protein-protein interactions, within the framework of the "Help Cure Muscular Dystrophy" project.
January 23 -24, 2014
Hugues Richard, from the Analytical Genomics team, co-organizes the 10th edition of the workshop: Statistical Methods for (Post-) Genomics Data (SMPGD). The Laboratory Genomics of Microorganisms will hosts the meeting at the UPMC main campus, Paris, France.
December 24, 2013
From the "Genomic Physics" group:
Gherardi M, Mandrà S, Bassetti B, Cosentino Lagomarsino M, "Evidence for soft bounds in Ubuntu package sizes and mammalian body masses" Proc Natl Acad Sci USA. 2013 Dec 24;110(52):21054-8.
link to UPMC web site (in French)
link to highlight on PNAS web site
December 19, 2013
From the "Statistical Genomics and Biological Physics" team:

EJ Molinelli, A Korkut, W Wang, ML Miller, NP Gauthier, X Jing, P Kaushik, Q He, G Mills, DB Solit, CA Pratilas, M Weigt, A Braunstein, A Pagnani, R Zecchina, C Sander, "Perturbation Biology: Inferring Signaling Networks in Cellular Systems", PLoS Comp. Biol. 9(12): e1003290 (2013).
December 3, 2013

Vittore Scolari (Genomic Physics group) and Alice Coucke (Statistical Genomics team) co-organize the 1th edition of the conference:
Paris Biological Physics Community Day 2013
The conference will be hosted at Centre Culturel Irlandais in Paris.
October 28, 2013
The Analytical Genomics team releases the complete cross docking data of Mintseris Benchmark 2.0. The analysis will be available in a few weeks with the article appearing in PLoS Computational Biology. The dataset of protein-protein interactions was produced with over 7 months of computations on World Community Grid and with the help of thousands of internautes providing their computer time to dock about 300000 conformations per protein pair in the set of 28224 possible pairs in the Mintseris dataset.
October 10-11, 2013
Cross Disciplinary Genomics. Biological networks: current and future challenges.3rd Symposium, October 10-11 2013, Jussieu Campus, UPMC, Paris, France.
August 22, 2013
From the "Statistical Genomics and Biological Physics" team:

S. Cocco, R. Monasson, M. Weigt, "From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction", PLoS Comp. Biol. 9(8): e1003176 (2013).
July, 2013
Alessandra Carbone has been elected Senior Member at the Institut Universitaire de France.
July 1-5, 2013

Alessandra Carbone organizes the special session in "Computational Molecular Biology" at Computability in Europe 2013 - The Nature of Computation: Logic, Algorithms, Applications. July, 1st-5th, 2013, Univ Milano-Bicocca, Milano, Italy.
June 27 - July 5, 2013

Marco Cosentino-Lagomarsino organizes the workshop on statistical physics/biology 'Quantitative Laws of Genome Evolution', 27 June – 5 July 2013 Lake Como School of Advanced Studies in Complex Systems, Villa del Grumello, Como, Italy.
June 2013

The project COEVSTAT (co-PI Martin Weigt, Statistical Genomics and Biological Physics team) has been selected for funding by the Agence Nationale de la Recherche (ANR).
June 25-28, 2013

Angela Falciatore organizes the EMBO Workshop "The molecular life of Diatoms", 25-28 June 2013, Collège de France, Paris, France
April 2013

A PhD scholarship has been allocated by the Institut des Systèmes Complexes to the Statistical Genomics and Biological Physics team (co-direction with R. Monasson, LPTENS).
April 12, 2013

Marco Cosentino-Lagomarsino organizes the upcoming "Fourth Journée Darwin", at Institut Henri Poincaré, April 12, 2013, 10h - Amphithéâtre Hermite, Paris, France.
February 25, 2013

Guénola Drillon (from the teams 'Analytical Genomics' and 'Biology of Genomes') will defend her thesis entitled "Combinatorics of chromosomal rearrangement and ancestral genome reconstruction in eukaryotes" on Monday, February 25, 2013 at 2pm - Campus des Cordeliers (15 rue de l'école de médecine, 75006 Paris), Auditorium Bilski-Pasquier.
February 3, 2013

The Analytical Genomics team published: A.Mathelier and A.Carbone, Large scale chromosomal mapping of human microRNA structural clusters, Nucleic Acids Research, in press.
January 30, 2013

The Direct Coupling Analysis - - website is online now! It offers information on DCA and downloadable software. A DCA webservice will follow soon.
January 9, 2013

The Analytical Genomics team has a feature article in International Science Grid This Week: Desktop power helps map protein dance
January, 2013

The Diatom Genomics team (M.Huysman, A.Fortunato, A.Falciatore) and collaborators at the University of Ghent: M.J.J. Huysman, A.E. Fortunato, M.Matthijs, B.Schellenberger Costa, R.Vanderhaeghen, H.Van den Daele, M.Sachse, D.Inzé, C.Bowler, P.G. Kroth, C.Wilhelm, A.Falciatore, W.Vyverman and L.De Veylder (2013) AUREOCHROME1a-Mediated Induction of the Diatom-Specific Cyclin dsCYC2 Controls the Onset of Cell Division in Diatoms (Phaeodactylum tricornutum), Plant Cell, in press, 2013.
January 2013

The Biology of Genomes and the Genomic Physics teams just published a joint work: Nicolas Agier, Orso Maria Romano, Fabrice Touzain, Marco Cosentino Lagomarsino and Gilles Fischer, The spatio-temporal program of replication in the genome of Lachancea kluyveri" Genome Biology and Evolution, in press, 2013.
January 2013

Marco Cosentino Lagomarsino has a new paper on his HSFP project: Zhicheng Long, Eileen Nugent, Avelino Javer, Pietro Cicuta, Bianca Sclavi, Marco Cosentino Lagomarsino and Kevin Dorfman. Microfluidic chemostat for measuring single cell dynamics in bacteria, Lab Chip, 2013, in press.
January 2013

A new application of Direct Coupling Analysis by Martin Weigt just appeared: M. Ekeberg, C. Lövkvist, Y. Lan, M. Weigt, E. Aurell, Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models, Phys. Rev. E 87, 012707 (2013).
November 30, 2012

An ATIP-Avenir Plus 2013-2014 was awarded to Gilles Fischer and his team Biology of Genomes
November 30, 2012

An ATIP-Avenir Plus 2013-2014 was awarded to Angela Falciatore and her team Diatom Genomics
November 27, 2012

Alessandra Carbone received the Grammaticakis-Neuman Prize of the Académie des Sciences for her applications of Mathematics to Biology.
October 25-26, 2012

Cross Disciplinary Genomics 2012 : From Genome to Ecosystem, October 25-26 2012, Jussieu Campus, UPMC, Paris, France.