article :
Guéguen L, Duret L (2018)
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Molecular biology and evolution, vol. 35 pp.734-742.
Rey C, Gueguen L, Semon M, Boussau B (2018)
Accurate detection of convergent amino-acid evolution with PCOC, Molecular biology and evolution, vol. 35 pp.2296-2306.
Lefebure T, Morvan C, Malard F, Francois C, Konecny-Dupre L, Gueguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier N P, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ (2017)
Less effective selection leads to larger genomes, Genome research, vol. 27 pp.1016-1028.
Pantalacci S, Guéguen L, Petit C, Lambert A, Peterkova R, Sémon M (2017)
Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology, Genome biology, vol. 18 pp.29-29.
Siberchicot A, Bessy A, Gueguen L, Marais GAB (2017)
MareyMap Online: A User-Friendly Web Application and Database Service for Estimating Recombination Rates Using Physical and Genetic Maps, Genome biology and evolution, vol. 9 pp.2506-2509.
Biller P, Gueguen L, Knibbe C, Tannier E (2016)
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, Genome Biology and Evolution, vol. 8 pp.1427-39.
Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Gueguen L, El-Mabrouk N, Tannier E (2016)
Efficient Gene Tree Correction Guided by Genome Evolution, PLoS One, vol. 11 pp.e0159559-e0159559.
Pouyet F, Bailly-Bechet M, Mouchiroud D, Gueguen L (2016)
SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage, Genome Biology and Evolution, vol. 8 pp.2427-41.
Biller P, Gueguen L, Tannier E (2015)
Moments of genome evolution by Double Cut-and-Join, BMC Bioinformatics, vol. 16 Suppl 14 pp.S7-S7.
Semeria M, Tannier E, Gueguen L (2015)
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies, BMC Bioinformatics, vol. 16 Suppl 14 pp.S5-S5.
Gueguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette N, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil J Y (2013)
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution, Molecular Biology and Evolution, vol. 30 pp.1745-1750.
Kafer J, Talianova M, Bigot T, Michu E, Guéguen L, Widmer A, Zluvova J, Glemin S, Marais GA (2013)
Patterns of molecular evolution in dioecious and non-dioecious Silene, Journal of Evolutionary Biology, vol. 26 pp.335-46.
Bérard J, Guéguen L (2012)
Accurate Estimation of Substitution Rates with Neighbor-Dependent Modelsina Phylogenetic Context, Systematic Biology, vol. 61 pp.510-521.
Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X (2011)
Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens, Genome Biology and Evolution, vol. 3 pp.762-781.
Boussau B, Guéguen L, Gouy M (2009)
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies, Evolutionary Bioinformatics, vol. 5 pp.67-79.
Boussau B, Guéguen L, Gouy M (2008)
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria, BMC Evolutionary Biology, vol. 8 pp.272-272.
Mugnier N, Gueguen L, Vieira C, Biémont C (2008)
The heterochromatic copies of the LTR retrotransposons as a record of the genomic events that have shaped the Drosophila melanogaster genome, Gene, vol. 411 pp.87-93.
Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel TM , Simonet P (2007)
Horizontal Gene Transfer Regulation in Bacteria as a "Spandrel" of DNA Repair Mechanisms, PLoS One, vol. 2 pp.e1055-e1055.
Rezvoy C, Charif D, Guéguen L , Marais GAB (2007)
MareyMap: an R-based tool with graphical interface for estimating recombination rates, Bioinformatics, vol. 23 pp.2188-2189.
Melodelima C, Guéguen L, Piau D, Gautier C (2006)
A computational prediction of isochores based on hidden Markov models, Gene, vol. 385 pp.41-49.
Palmeira L, Guéguen L, Lobry JR (2006)
UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes, Molecular Biology and Evolution, vol. 23 pp.2214-2219.
Guéguen L (2005)
Sarment: Python modules for HMM analysis and partitioning of sequences, Bioinformatics, vol. 21 pp.3427-3428.
inbook :
Chauve C, El-Mabrouk N, Guéguen L, Semeria M, Tannier E (2013)
Duplication Rearrangement and Reconciliation: A Follow-Up 13 Years Later
in: Models and Algorithmes for Genome Evolution, Computentional BIology, pp.47-62.
inproceedings :
Pouyet F, Jacquemetton J, Bailly-Bechet M, Guéguen L (2013)
Codon usage in E. coli: an evolutionary approach, JOBIM 2013, pp.2427-41.
Melodelima C, Guéguen L, Gautier C, Piau D (2006)
A Markovian Approach for the Analysis of the Gene Structure, Proceedings of the Prague Stringology Conference, , vol. 19(1) pp.19-35.
