Functional Evolutionary Genomics Group

Members

In the "Functional evolutionary genomics" team, one of our ovearching aims is understanding the genomic basis of phenotypic evolution. We are particularly interested in convergent phenotypic evolution events. We study a wide range of phenotypic traits, including morphological traits, sensory traits, physiological traits. Our aim is to identify the genomic changes that accompany phenotypic evolution. We also aim to characterize the evolutionary processes that underlie phenotypic changes, by searching for instances of lineage-specific positive selection or relaxation of purifying selection.

We study both protein-coding gene evolution and non-coding DNA evolution, in particular regulatory elements that control gene expression. We aim to develop new methods for this purpose, and rely on statistical inference, including deep learning.

Publications

Display of 121 to 136 publications on 136 in total

Démasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN

Perrine Portier, Denis Costechareyre, Daniel Muller, David Chapulliot, Christine Oger, Guy Perrière...

7. Colloque national du Bureau des Ressources Génétiques . 7

Conference paper

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Parallel Adaptations to High Temperatures in the Archean Eon

Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy

Nature . 456 ( 7224 ) : 942-945

DOI: 10.1038/nature07393

Journal article

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A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

A. Necşulea, J.R. Lobry

Molecular Biology and Evolution . 24 : 2169-2179

Journal article

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Horizontal Gene Transfer Regulation in Bacteria as a ‘‘Spandrel'' of DNA Repair Mechanisms

Saliou Fall, Anne Mercier, Franck Bertolla, Alexandra Calteau, Laurent Gueguen, Guy Perrière...

PLoS ONE . 2 ( 10 ) : e1055-e1066

DOI: 10.1371/journal.pone.0001055

Journal article

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MareyMap: an R-based tool with graphical interface for estimating recombination rates

C. Rezvoy, D. Charif, Laurent Guéguen, Gabriel Marais

Bioinformatics . 23 : 2188-2189

Journal article

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A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

A. Necşulea, J.R. Lobry

incollection . 7 : 379-381

Journal article

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A Markovian Approach for the Analysis of the Gene Structure

C. Melodelima, Laurent Guéguen, Christian Gautier, D. Piau

Prague stringology conference . 19 ( 1 ) : 19-35

Conference paper

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A computational prediction of isochores based on hidden Markov models

C. Melodelima, Laurent Guéguen, D. Piau, Christian Gautier

Gene . 385 : 41-49

Journal article

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UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes

L. Palmeira, Laurent Guéguen, J.R. Lobry

Molecular Biology and Evolution . 23 : 2214-2219

Journal article

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Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

J.R. Lobry, A. Necşulea

Gene . 385 : 128-136

Journal article

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Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major

A. Necşulea, J.R. Lobry

Gene . 385 : 28-40

Journal article

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Sarment: Python modules for HMM analysis and partitioning of sequences

Laurent Guéguen

Bioinformatics . 21 : 3427-3428

Journal article

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Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

M. Robinson-Rechavi, Bastien Boussau, V. Laudet

Molecular Biology and Evolution . 21 : 580-586

Journal article

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Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

M. Robinson-Rechavi, B. Boussau, V. Laudet

Molecular Biology and Evolution . 21 ( 3 ) : 580-586

Journal article

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Computational inference of scenarios for alpha-proteobacterial genome evolution

Bastien Boussau, E.O. Karlberg, A.C. Frank, B.A. Legault, S.G. Andersson

Proceedings of the National Academy of Sciences of the United States of America . 101 : 9722-9727

Journal article

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