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Analytical Genomics

June 27-July 1, 2016

Alessandra Carbone organises with Ion Petre (Turku Centre for Computer Science) the special session "Computation in biological systems" at the international conference "Computability in Europe 2016", Université Paris 7, June 27th 2016 - July 1st 2016

June 21, 2016

On June 21, 2016, LCQB was the Paris Hub for the Global City Sampling Day, an international study of antimicrobial resistance spanning six continents, 32 countries and 54 cities. This event brings together more than 400 people, expected to collect about 12.000 samples of DNA, RNA and microbes from surfaces in well-traveled public meeting spaces. The data will help scientists of the MetaSub Global consortium better understand antimicrobial resistance in urban centers, and also identify new, naturally occurring drugs made by microbes, known as biosynthetic gene clusters. UPMC students in Computer Science and Molecular Biology, together with researchers collected more 80 samples at the entrance of parisian subway stations. The Paris event was organised by Hugues Richard (Analytical Genomics) and Ingrid Lafontaine (Biology of Genomes).

More information on the project: www.metasub.org

June 10, 2016

World Community Grid posts a news on Joint Evolutionary Trees 2 (JET2), a new large-scale method to predict protein-protein interfaces based on sequence and structure information.

To the Article and Software.

May 9, 2016

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized. Champeimont R, Laine E, Hu S-W, Penin F, Carbone A. Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins. Scientific Reports.

April 13, 2016

We achieved the complete reconstruction of genome history in a model yeast genus, providing a granular view of genome evolution linking gene content, chromosome rearrangements and protein divergence into a single evolutionary framework.

N Vakirlis, Sarilar V, G Drillon, A Fleiss, N Agier, J-P Meyniel, L Blanpain, A Carbone, H Devillers, K Dubois, A Gillet-Markowska, S Graziani, Nguyen H-V, M Poirel, C Reisser, J Schott, J Schacherer, I Lafontaine, B Llorente, C Neuvéglise and Fischer G. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Research (2016).

March 1, 2016

A.E. Fortunato, M. Jaubert, J.P. Bouly, M. Thaler and A. Falciatore from the Diatom Functional Genomics team in collaboration with J.S. Bernardes (Statistical Genomics and Biological Physics), A. Carbone (Analytical Genomics) and other international collaborators published on The Plant Cell the paperDiatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean.”  Full text paper.

Plant Cell Editor’s comment on this work.

January 1, 2016

E.Laine and A.Carbone just published a new large-scale method to predict protein-protein interfaces based on sequence and structure information - Joint Evolutionary Trees 2 (JET2). It is the first time that a method highlights, with such a precision, information on distinguished binding sites, possibly overlapping each other.

To the Article and Software.

December 21, 2015

Interview of the German National Radio to A.Carbone, where she gives some highlights on protein-protein interactions.
 

July 12-16, 2015

The symposium The evolution of alternative splicing  is co-organized within the framework of the 2015 meeting of the Society for Molecular Biology and Evolution by E. Laine (LCQB), H. Richard (LCQB), and J. Roux (UNIL). The event will take place in Vienna, Austria.
Registration is now open.  Abstract submission for oral presentation closes on February 8th.

June 5, 2015

Kenneth Wolfe from University College Dublin (http://wolfe.ucd.ie ) will give a seminar on:
"Origin and evolution of a reversible DNA rearrangement mechanism: yeast mating-type switching”

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