| Bio++: efficient extensible libraries and tools for computational molecular evolution L Guéguen, S Gaillard, B Boussau, M Gouy, M Groussin, NC Rochette, ... Molecular biology and evolution 30 (8), 1745-1750, 2013 | 150 | 2013 |
| Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens F Lassalle, T Campillo, L Vial, J Baude, D Costechareyre, D Chapulliot, ... Genome Biology and Evolution 3, 762-781, 2011 | 130 | 2011 |
| MareyMap: an R-based tool with graphical interface for estimating recombination rates C Rezvoy, D Charif, L Guéguen, GAB Marais Bioinformatics 23 (16), 2188-2189, 2007 | 101 | 2007 |
| Horizontal gene transfer regulation in bacteria as a “spandrel” of DNA repair mechanisms S Fall, A Mercier, F Bertolla, A Calteau, L Gueguen, G Perriere, TM Vogel, ... PLoS One 2 (10), e1055, 2007 | 94 | 2007 |
| Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria B Boussau, L Guéguen, M Gouy BMC evolutionary biology 8 (1), 1-18, 2008 | 92 | 2008 |
| Less effective selection leads to larger genomes T Lefébure, C Morvan, F Malard, C François, L Konecny-Dupré, ... Genome Research 27 (6), 1016-1028, 2017 | 59 | 2017 |
| Efficient gene tree correction guided by genome evolution E Noutahi, M Semeria, M Lafond, J Seguin, B Boussau, L Guéguen, ... PLoS One 11 (8), e0159559, 2016 | 49* | 2016 |
| Breaking good: accounting for fragility of genomic regions in rearrangement distance estimation P Biller, L Guéguen, C Knibbe, E Tannier Genome biology and evolution 8 (5), 1427-1439, 2016 | 45* | 2016 |
| Accurate detection of convergent amino-acid evolution with PCOC C Rey, L Guéguen, M Sémon, B Boussau Molecular Biology and Evolution 35 (9), 2296-2306, 2018 | 43 | 2018 |
| Unbiased estimate of synonymous and nonsynonymous substitution rates with nonstationary base composition L Guéguen, L Duret Molecular Biology and Evolution 35 (3), 734-742, 2018 | 38 | 2018 |
| Segmentation by maximal predictive partitioning according to composition biases L Guéguen Computational Biology: First International Conference on Biology …, 2001 | 33 | 2001 |
| Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium F Lassalle, R Planel, S Penel, D Chapulliot, V Barbe, A Dubost, A Calteau, ... Genome biology and evolution 9 (12), 3413-3431, 2017 | 28 | 2017 |
| Duplication, rearrangement and reconciliation: a follow-up 13 years later C Chauve, N El-Mabrouk, L Guéguen, M Semeria, E Tannier Models and algorithms for genome evolution, 47-62, 2013 | 28 | 2013 |
| Sarment: Python modules for HMM analysis and partitioning of sequences L Guéguen Bioinformatics 21 (16), 3427-3428, 2005 | 26 | 2005 |
| Treerecs: an integrated phylogenetic tool, from sequences to reconciliations N Comte, B Morel, D Hasić, L Guéguen, B Boussau, V Daubin, S Penel, ... Bioinformatics 36 (18), 4822-4824, 2020 | 24 | 2020 |
| Patterns of molecular evolution in dioecious and non‐dioecious Silene J Käfer, M Talianová, T Bigot, E Michu, L Guéguen, A Widmer, J Žlůvová, ... Journal of Evolutionary Biology 26 (2), 335-346, 2013 | 24 | 2013 |
| Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context J Bérard, L Guéguen Systematic biology 61 (3), 510-521, 2012 | 24 | 2012 |
| GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes P Bolívar, L Guéguen, L Duret, H Ellegren, CF Mugal Genome Biology 20 (1), 1-13, 2019 | 23 | 2019 |
| UV-targeted dinucleotides are not depleted in light-exposed prokaryotic genomes L Palmeira, L Guéguen, JR Lobry Molecular biology and evolution 23 (11), 2214-2219, 2006 | 23 | 2006 |
| A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies B Boussau, L Guéguen, M Gouy Evolutionary Bioinformatics 5, EBO. S2242, 2009 | 22 | 2009 |
