Year |
Citation |
Score |
2023 |
Trost J, Haag J, Höhler D, Jacob L, Stamatakis A, Boussau B. Simulations of sequence evolution: how (un)realistic they are and why. Molecular Biology and Evolution. PMID 38124381 DOI: 10.1093/molbev/msad277 |
0.305 |
|
2022 |
Borges R, Boussau B, Szöllősi GJ, Kosiol C. Nucleotide Usage Biases Distort Inferences of the Species Tree. Genome Biology and Evolution. 14. PMID 34983052 DOI: 10.1093/gbe/evab290 |
0.369 |
|
2021 |
Szöllősi GJ, Höhna S, Williams TA, Schrempf D, Daubin V, Boussau B. Relative time constraints improve molecular dating. Systematic Biology. PMID 34668564 DOI: 10.1093/sysbio/syab084 |
0.664 |
|
2020 |
Comte N, Morel B, Hasić D, Guéguen L, Boussau B, Daubin V, Penel S, Scornavacca C, Gouy M, Stamatakis A, Tannier E, Parsons DP. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Bioinformatics (Oxford, England). PMID 33085745 DOI: 10.1093/Bioinformatics/Btaa615 |
0.791 |
|
2019 |
Rey C, Lanore V, Veber P, Guéguen L, Lartillot N, Sémon M, Boussau B. Detecting adaptive convergent amino acid evolution. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 374: 20180234. PMID 31154974 DOI: 10.1098/Rstb.2018.0234 |
0.383 |
|
2018 |
Rey C, Veber P, Boussau B, Sémon M. CAARS: comparative assembly and annotation of RNA-Seq data. Bioinformatics (Oxford, England). PMID 30452539 DOI: 10.1093/Bioinformatics/Bty903 |
0.404 |
|
2018 |
Rey C, Guéguen L, Sémon M, Boussau B. Accurate detection of convergent amino-acid evolution with PCOC. Molecular Biology and Evolution. PMID 29986048 DOI: 10.1093/Molbev/Msy114 |
0.33 |
|
2018 |
Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, et al. RecPhyloXML - a format for reconciled gene trees. Bioinformatics (Oxford, England). PMID 29762653 DOI: 10.1093/Bioinformatics/Bty389 |
0.718 |
|
2018 |
Davín AA, Tannier E, Williams TA, Boussau B, Daubin V, Szöllősi GJ. Gene transfers can date the tree of life. Nature Ecology & Evolution. PMID 29610471 DOI: 10.1038/S41559-018-0525-3 |
0.742 |
|
2017 |
Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM. Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proceedings of the National Academy of Sciences of the United States of America. PMID 28533395 DOI: 10.1073/Pnas.1618463114 |
0.552 |
|
2016 |
Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Guéguen L, El-Mabrouk N, Tannier E. Efficient Gene Tree Correction Guided by Genome Evolution. Plos One. 11: e0159559. PMID 27513924 DOI: 10.1371/Journal.Pone.0159559 |
0.546 |
|
2016 |
Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language. Systematic Biology. PMID 27235697 DOI: 10.1093/Sysbio/Syw021 |
0.739 |
|
2015 |
Groussin M, Boussau B, Szöllősi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V. Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. Molecular Biology and Evolution. PMID 26541173 DOI: 10.1093/Molbev/Msv249 |
0.772 |
|
2015 |
Mirarab S, Bayzid MS, Boussau B, Warnow T. Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science (New York, N.Y.). 350: 171. PMID 26450204 DOI: 10.1126/Science.Aaa7719 |
0.324 |
|
2015 |
Szöllősi GJ, Davín AA, Tannier E, Daubin V, Boussau B. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370: 20140335. PMID 26323765 DOI: 10.1098/Rstb.2014.0335 |
0.754 |
|
2015 |
Bayzid MS, Mirarab S, Boussau B, Warnow T. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. Plos One. 10: e0129183. PMID 26086579 DOI: 10.1371/Journal.Pone.0129183 |
0.515 |
|
2015 |
Chaudhary R, Boussau B, Burleigh JG, Fernández-Baca D. Assessing approaches for inferring species trees from multi-copy genes. Systematic Biology. 64: 325-39. PMID 25540456 DOI: 10.1093/Sysbio/Syu128 |
0.478 |
|
2015 |
Szöll?si GJ, Tannier E, Daubin V, Boussau B. The inference of gene trees with species trees. Systematic Biology. 64: e42-62. PMID 25070970 DOI: 10.1093/Sysbio/Syu048 |
0.767 |
|
2014 |
Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science (New York, N.Y.). 346: 1250463. PMID 25504728 DOI: 10.1126/Science.1250463 |
0.439 |
|
2014 |
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, ... ... Boussau B, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science (New York, N.Y.). 346: 1320-31. PMID 25504713 DOI: 10.1126/Science.1253451 |
0.504 |
|
2014 |
Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biology. 15: 549. PMID 25496599 DOI: 10.1186/S13059-014-0549-1 |
0.401 |
|
2014 |
Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP. Strepsiptera, phylogenomics and the long branch attraction problem. Plos One. 9: e107709. PMID 25272037 DOI: 10.1371/Journal.Pone.0107709 |
0.736 |
|
2014 |
Höhna S, Heath TA, Boussau B, Landis MJ, Ronquist F, Huelsenbeck JP. Probabilistic graphical model representation in phylogenetics. Systematic Biology. 63: 753-71. PMID 24951559 DOI: 10.1093/Sysbio/Syu039 |
0.763 |
|
2013 |
Groussin M, Boussau B, Charles S, Blanquart S, Gouy M. The molecular signal for the adaptation to cold temperature during early life on Earth. Biology Letters. 9: 20130608. PMID 24046876 DOI: 10.1098/Rsbl.2013.0608 |
0.78 |
|
2013 |
Szöllõsi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V. Efficient exploration of the space of reconciled gene trees. Systematic Biology. 62: 901-12. PMID 23925510 DOI: 10.1093/Sysbio/Syt054 |
0.755 |
|
2013 |
Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, et al. Bio++: efficient extensible libraries and tools for computational molecular evolution. Molecular Biology and Evolution. 30: 1745-50. PMID 23699471 DOI: 10.1093/Molbev/Mst097 |
0.751 |
|
2013 |
Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P. An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution; International Journal of Organic Evolution. 67: 1155-68. PMID 23550763 DOI: 10.1111/Evo.12009 |
0.466 |
|
2013 |
Groussin M, Boussau B, Gouy M. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences. Systematic Biology. 62: 523-38. PMID 23475623 DOI: 10.1093/Sysbio/Syt016 |
0.791 |
|
2013 |
Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V. Genome-scale coestimation of species and gene trees. Genome Research. 23: 323-30. PMID 23132911 DOI: 10.1101/Gr.141978.112 |
0.811 |
|
2012 |
Fong JJ, Brown JM, Fujita MK, Boussau B. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. Plos One. 7: e48990. PMID 23145043 DOI: 10.1371/Journal.Pone.0048990 |
0.626 |
|
2012 |
Szöllosi GJ, Boussau B, Abby SS, Tannier E, Daubin V. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences of the United States of America. 109: 17513-8. PMID 23043116 DOI: 10.1073/Pnas.1202997109 |
0.817 |
|
2012 |
Bérard S, Gallien C, Boussau B, Szöll?si GJ, Daubin V, Tannier E. Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics (Oxford, England). 28: i382-i388. PMID 22962456 DOI: 10.1093/Bioinformatics/Bts374 |
0.757 |
|
2012 |
Romiguier J, Figuet E, Galtier N, Douzery EJ, Boussau B, Dutheil JY, Ranwez V. Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. Plos One. 7: e33852. PMID 22479459 DOI: 10.1371/Journal.Pone.0033852 |
0.704 |
|
2012 |
Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B. Efficient selection of branch-specific models of sequence evolution. Molecular Biology and Evolution. 29: 1861-74. PMID 22319139 DOI: 10.1093/Molbev/Mss059 |
0.683 |
|
2012 |
Boussau B, Gouy M. What genomes have to say about the evolution of the Earth Gondwana Research. 21: 483-494. DOI: 10.1016/J.Gr.2011.08.002 |
0.669 |
|
2011 |
Boussau B, Brown JM, Fujita MK. Nonadaptive evolution of mitochondrial genome size. Evolution; International Journal of Organic Evolution. 65: 2706-11. PMID 21884067 DOI: 10.1111/J.1558-5646.2011.01322.X |
0.585 |
|
2010 |
Boussau B, Daubin V. Genomes as documents of evolutionary history. Trends in Ecology & Evolution. 25: 224-32. PMID 19880211 DOI: 10.1016/J.Tree.2009.09.007 |
0.747 |
|
2009 |
Boussau B, Guéguen L, Gouy M. A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies. Evolutionary Bioinformatics Online. 5: 67-79. PMID 19812727 DOI: 10.4137/Ebo.S2242 |
0.712 |
|
2008 |
Douard V, Brunet F, Boussau B, Ahrens-Fath I, Vlaeminck-Guillem V, Haendler B, Laudet V, Guiguen Y. The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event? Bmc Evolutionary Biology. 8: 336. PMID 19094205 DOI: 10.1186/1471-2148-8-336 |
0.411 |
|
2008 |
Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M. Parallel adaptations to high temperatures in the Archaean eon. Nature. 456: 942-5. PMID 19037246 DOI: 10.1038/Nature07393 |
0.654 |
|
2008 |
Boussau B, Guéguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. Bmc Evolutionary Biology. 8: 272. PMID 18834516 DOI: 10.1186/1471-2148-8-272 |
0.715 |
|
2008 |
Dutheil J, Boussau B. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. Bmc Evolutionary Biology. 8: 255. PMID 18808672 DOI: 10.1186/1471-2148-8-255 |
0.473 |
|
2008 |
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews. Microbiology. 6: 245-52. PMID 18274537 DOI: 10.1038/Nrmicro1852 |
0.41 |
|
2006 |
Boussau B, Gouy M. Efficient likelihood computations with nonreversible models of evolution. Systematic Biology. 55: 756-68. PMID 17060197 DOI: 10.1080/10635150600975218 |
0.684 |
|
2004 |
Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 101: 9722-7. PMID 15210995 DOI: 10.1073/Pnas.0400975101 |
0.459 |
|
2004 |
Robinson-Rechavi M, Boussau B, Laudet V. Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Molecular Biology and Evolution. 21: 580-6. PMID 14694077 DOI: 10.1093/Molbev/Msh046 |
0.526 |
|
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