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June 2, 2017

Plasmobase is a unique database designed for the comparative study of 11 Plasmodium genomes. Plasmobase proposes new domain architectures as well as new domain families that have never been reported before for these genomes. It allows for an easy comparison among architectures within Plasmodium species and with other species, described in UniProt. Joint work of J.Bernardes and A.Carbone.

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April 18, 2017

Marco Cosentino-Lagomarsino and Gilles Fischer collaborated with Gianni Liti’s team to generatate end-to-end genome assemblies for 12 yeast genomes based on long-read sequencing. These population-level high-quality genomes with comprehensive annotation enable the first explicit definition of chromosomal boundaries between core and subtelomeric regions as well as a precise quantification of their relative evolutionary rates of genome dynamics.

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January 1, 2017

The Diatom Functional Genomics Team (Angela Falciatore and Antonio E. Fortunato) contributed to the manuscript “Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus”,  published on Nature in January 2017. This study, coordinated by Prof. Thomas Mock, University of East Anglia, Norwich, has revealed the existence of highly diverged alleles in the genome of this polar diatom species that may be involved in adaptation to environmental fluctuations in the Southern Ocean.

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October 31, 2016

A new publication of F. Devaux Team in NAR:
The discovery of novel specific ribosome-associated factors challenges the assumption that translation relies on standardized molecular machinery. In this work, we demonstrate that Tma108, an uncharacterized translation machinery-associated factor in yeast, is a specific nascent-chain associated factor selectively recruited during the translation of less than 200 mRNAs encoding proteins with ATP or Zinc binding domains. Tma108 is a unique example of a nascent chain-associated factor with high selectivity and its study illustrates the existence of other specific translation-associated factors besides RNA binding proteins.

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September 15, 2016

The LCQB laboratory is in the CNRS Journal for his project MetaSUB Paris.

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July 8, 2016

We published a new generation domain annotation approach, demonstrating that "multi-source" domain modelling is more appropriate than "mono-source" domain modelling for capturing remote homology. We re-annotate the Plasmodium falciparum genome.

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July 5, 2016

F. Devaux's team published one of the first ChIP-seq-based description of the transcriptional regulatory networks in the pathogenic yeast Candida glabrata. This work, which was performed in collaboration with J-M. Camadro and G. Lelandais from the Jacques Monod Institute and with the NGS platform directed by S. Le Crom, is the first publication from a larger ANR project aiming at a comprehensive description of stress response regulatory networks in this emerging human pathogen.

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.

May 2, 2016

The team of Diatom Functional Genomics just published a paper describing how marine diatoms efficiently attune acclimation responses in highly variable ocean environments. L.Taddei*, G.R. Stella*, A. Rogato, B. Bailleul, A.E. Fortunato, R. Annunziata, R. Sanges, M. Thaler, B. Lepetit, J. Lavaud, M. Jaubert, G. Finazzi, J.P. Bouly, A. Falciatore. Multi-signal control of expression of the LHCX protein family in marine diatom Phaeodactylum tricornutum.  Journal Experimental Botany, in press.

*co-first-authors

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).

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