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Bastien Boussau - Publications

Affiliations: 
Integrative Biology; LBBE, UMR5558 University of California, Berkeley; Université Lyon 1, Université de Lyon, Villeurbanne, Auvergne-Rhône-Alpes, France 
Area:
phylogenetics
Website:
http://fisher.berkeley.edu/cteg/members/boussau.html
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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  0.304
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  0.372
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  0.666
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  0.792
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  0.385
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  0.406
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  0.332
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  0.72
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  0.745
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  0.555
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  0.55
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  0.744
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  0.771
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  0.323
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  0.756
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  0.517
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  0.481
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  0.769
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  0.441
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  0.507
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  0.403
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  0.737
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  0.768
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  0.782
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  0.758
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  0.749
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  0.469
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  0.792
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  0.813
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  0.628
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  0.818
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  0.759
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  0.705
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  0.684
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  0.67
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  0.588
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  0.749
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  0.413
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  0.655
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  0.718
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  0.47
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  0.412
2006 Boussau B, Gouy M. Efficient likelihood computations with nonreversible models of evolution. Systematic Biology. 55: 756-68. PMID 17060197 DOI: 10.1080/10635150600975218  0.683
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  0.462
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  0.53
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