| The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? EJP Douzery, EA Snell, E Bapteste, F Delsuc, H Philippe Proceedings of the National Academy of Sciences 101 (43), 15386-15391, 2004 | 623 | 2004 |
| Pattern pluralism and the Tree of Life hypothesis WF Doolittle, E Bapteste Proceedings of the National Academy of Sciences 104 (7), 2043-2049, 2007 | 526 | 2007 |
| The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba E Bapteste, H Brinkmann, JA Lee, DV Moore, CW Sensen, P Gordon, ... Proceedings of the National Academy of Sciences 99 (3), 1414-1419, 2002 | 476 | 2002 |
| Phylogenomics of eukaryotes: impact of missing data on large alignments H Philippe, EA Snell, E Bapteste, P Lopez, PWH Holland, D Casane Molecular biology and evolution 21 (9), 1740-1752, 2004 | 430 | 2004 |
| The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea EF Mongodin, KE Nelson, S Daugherty, RT Deboy, J Wister, H Khouri, ... Proceedings of the National Academy of Sciences 102 (50), 18147-18152, 2005 | 320 | 2005 |
| Network analyses structure genetic diversity in independent genetic worlds S Halary, JW Leigh, B Cheaib, P Lopez, E Bapteste Proceedings of the National Academy of Sciences 107 (1), 127-132, 2010 | 267 | 2010 |
| Prokaryotic evolution and the tree of life are two different things E Bapteste, MA O'Malley, RG Beiko, M Ereshefsky, JP Gogarten, ... Biology direct 4 (1), 1-20, 2009 | 256 | 2009 |
| Higher-level classification of the Archaea: evolution of methanogenesis and methanogens É Bapteste, C Brochier, Y Boucher Archaea 1 (5), 353-363, 2005 | 255 | 2005 |
| Do orthologous gene phylogenies really support tree-thinking? E Bapteste, E Susko, J Leigh, D MacLeod, RL Charlebois, WF Doolittle BMC Evolutionary Biology 5 (1), 1-10, 2005 | 195 | 2005 |
| Eubacterial phylogeny based on translational apparatus proteins C Brochier, E Bapteste, D Moreira, H Philippe TRENDS in Genetics 18 (1), 1-5, 2002 | 186 | 2002 |
| Networks: expanding evolutionary thinking E Bapteste, L van Iersel, A Janke, S Kelchner, S Kelk, JO McInerney, ... Trends in Genetics 29 (8), 439-441, 2013 | 161 | 2013 |
| Phylogenetic reconstruction and lateral gene transfer E Bapteste, Y Boucher, J Leigh, WF Doolittle Trends in microbiology 12 (9), 406-411, 2004 | 150 | 2004 |
| Network-thinking: graphs to analyze microbial complexity and evolution E Corel, P Lopez, R Méheust, E Bapteste Trends in Microbiology 24 (3), 224-237, 2016 | 100 | 2016 |
| The potential value of indels as phylogenetic markers: position of trichomonads as a case study E Bapteste, H Philippe Molecular biology and evolution 19 (6), 972-977, 2002 | 96 | 2002 |
| The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure E Bapteste, RL Charlebois, D MacLeod, C Brochier Genome biology 6 (10), 1-15, 2005 | 95 | 2005 |
| Evolutionary analyses of non-genealogical bonds produced by introgressive descent E Bapteste, P Lopez, F Bouchard, F Baquero, JO McInerney, RM Burian Proceedings of the National Academy of Sciences 109 (45), 18266-18272, 2012 | 94 | 2012 |
| Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations Y Boucher, OX Cordero, A Takemura, DE Hunt, K Schliep, E Bapteste, ... MBio 2 (2), e00335-10, 2011 | 94 | 2011 |
| Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement D MacLeod, RL Charlebois, F Doolittle, E Bapteste BMC evolutionary biology 5 (1), 1-11, 2005 | 91 | 2005 |
| Towards a processual microbial ontology E Bapteste, J Dupré Biology & Philosophy 28 (2), 379-404, 2013 | 89 | 2013 |
| Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome RG Dorrell, G Gile, G Mccallum, R Méheust, EP Bapteste, CM Klinger, ... elife 6, e23717, 2017 | 88 | 2017 |
