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Benoit Nabholz - Publications

Affiliations: 
2005-2008 ISEM, Université Montpellier 
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48 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 Gabrielli M, Leroy T, Salmona J, Nabholz B, Milá B, Thébaud C. Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole-genome sequencing. Molecular Ecology. e17243. PMID 38108507 DOI: 10.1111/mec.17243  0.358
2023 Marino A, Reboud EL, Chevalier E, Tilak MK, Contreras-Garduño J, Nabholz B, Condamine FL. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 (Bethesda, Md.). PMID 37847748 DOI: 10.1093/g3journal/jkad239  0.489
2023 Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. Journal of Evolutionary Biology. PMID 37485603 DOI: 10.1111/jeb.14200  0.405
2023 Reboud EL, Nabholz B, Chevalier E, Tilak MK, Bito D, Condamine FL. Genomics, population divergence and historical demography of the world's largest and endangered butterfly, the Queen Alexandra's birdwing. Genome Biology and Evolution. PMID 36896590 DOI: 10.1093/gbe/evad040  0.42
2021 Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. Elife. 10. PMID 33599612 DOI: 10.7554/eLife.63167  0.462
2021 Leroy T, Rousselle M, Tilak MK, Caizergues AE, Scornavacca C, Recuerda M, Fuchs J, Illera JC, De Swardt DH, Blanco G, Thébaud C, Milá B, Nabholz B. Island songbirds as windows into evolution in small populations. Current Biology : Cb. PMID 33476557 DOI: 10.1016/j.cub.2020.12.040  0.475
2021 Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nature Communications. 12: 354. PMID 33441560 DOI: 10.1038/s41467-020-20507-3  0.321
2020 Rousselle M, Simion P, Tilak MK, Figuet E, Nabholz B, Galtier N. Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. Plos Genetics. 16: e1008668. PMID 32251427 DOI: 10.1371/Journal.Pgen.1008668  0.495
2020 Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Molecular Ecology Resources. 20: 892-905. PMID 32243090 DOI: 10.1111/1755-0998.13160  0.494
2020 Gabrielli M, Nabholz B, Leroy T, Milá B, Thébaud C. Within-island diversification in a passerine bird. Proceedings. Biological Sciences. 287: 20192999. PMID 32183633 DOI: 10.1098/Rspb.2019.2999  0.489
2019 Rousselle M, Laverré A, Figuet E, Nabholz B, Galtier N. Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds. Molecular Biology and Evolution. 36: 458-471. PMID 30590692 DOI: 10.1093/Molbev/Msy243  0.48
2018 Rousselle M, Mollion M, Nabholz B, Bataillon T, Galtier N. Overestimation of the adaptive substitution rate in fluctuating populations. Biology Letters. 14. PMID 29743267 DOI: 10.1098/Rsbl.2018.0055  0.453
2018 Tilak MK, Botero-Castro F, Galtier N, Nabholz B. Illumina library preparation for sequencing the GC-rich fraction of heterogeneous genomic DNA. Genome Biology and Evolution. PMID 29385572 DOI: 10.1093/Gbe/Evy022  0.432
2018 Condamine FL, Nabholz B, Clamens A, Dupuis JR, Sperling FAH. Mitochondrial phylogenomics, the origin of swallowtail butterflies, and the impact of the number of clocks in Bayesian molecular dating Systematic Entomology. 43: 460-480. DOI: 10.1111/Syen.12284  0.43
2017 Allio R, Donega S, Galtier N, Nabholz B. Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker. Molecular Biology and Evolution. PMID 28981721 DOI: 10.1093/Molbev/Msx197  0.51
2017 Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N. Avian genomes revisited: hidden genes uncovered and the rates vs. traits paradox in birds. Molecular Biology and Evolution. PMID 28962031 DOI: 10.1093/Molbev/Msx236  0.505
2017 Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, et al. Evolutionary forces affecting synonymous variations in plant genomes. Plos Genetics. 13: e1006799. PMID 28531201 DOI: 10.1371/Journal.Pgen.1006799  0.707
2016 Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, et al. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources. PMID 27487989 DOI: 10.1111/1755-0998.12587  0.684
2016 Nabholz B, Lanfear R, Fuchs J. Body mass-corrected molecular rate for bird mitochondrial DNA. Molecular Ecology. PMID 27483387 DOI: 10.1111/Mec.13780  0.496
2016 Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N. Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Molecular Biology and Evolution. PMID 26944704 DOI: 10.1093/Molbev/Msw033  0.496
2015 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, Alfaro-Núñez A, Narula N, et al. Phylogenomic analyses data of the avian phylogenomics project. Gigascience. 4: 4. PMID 25741440 DOI: 10.1186/S13742-014-0038-1  0.509
2014 Weber CC, Nabholz B, Romiguier J, Ellegren H. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biology. 15: 542. PMID 25607475 DOI: 10.1186/S13059-014-0542-8  0.376
2014 Clément Y, Fustier MA, Nabholz B, Glémin S. The bimodal distribution of genic GC content is ancestral to monocot species. Genome Biology and Evolution. 7: 336-48. PMID 25527839 DOI: 10.1093/Gbe/Evu278  0.685
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, 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  0.548
2014 Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, et al. Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature. 515: 261-3. PMID 25141177 DOI: 10.1038/Nature13685  0.503
2014 Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Molecular Ecology. 23: 2210-27. PMID 24684265 DOI: 10.1111/Mec.12738  0.4
2013 Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM, Galtier N. Population genomics of the endangered giant Galápagos tortoise. Genome Biology. 14: R136. PMID 24342523 DOI: 10.1186/Gb-2013-14-12-R136  0.538
2013 Nabholz B, Uwimana N, Lartillot N. Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds. Genome Biology and Evolution. 5: 1273-90. PMID 23711670 DOI: 10.1093/Gbe/Evt083  0.524
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  0.709
2013 Gayral P, Melo-Ferreira J, Glémin S, Bierne N, Carneiro M, Nabholz B, Lourenco JM, Alves PC, Ballenghien M, Faivre N, Belkhir K, Cahais V, Loire E, Bernard A, Galtier N. Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap. Plos Genetics. 9: e1003457. PMID 23593039 DOI: 10.1371/Journal.Pgen.1003457  0.733
2013 Mugal CF, Nabholz B, Ellegren H. Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. Bmc Genomics. 14: 86. PMID 23394684 DOI: 10.1186/1471-2164-14-86  0.516
2013 Nabholz B, Ellegren H, Wolf JB. High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes. Molecular Biology and Evolution. 30: 272-84. PMID 23071102 DOI: 10.1093/Molbev/Mss238  0.397
2011 Künstner A, Nabholz B, Ellegren H. Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection. Genome Biology and Evolution. 3: 1381-9. PMID 22042333 DOI: 10.1093/Gbe/Evr112  0.498
2011 Nygren K, Strandberg R, Wallberg A, Nabholz B, Gustafsson T, García D, Cano J, Guarro J, Johannesson H. A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi. Molecular Phylogenetics and Evolution. 59: 649-63. PMID 21439389 DOI: 10.1016/J.Ympev.2011.03.023  0.448
2011 Nabholz B, Künstner A, Wang R, Jarvis ED, Ellegren H. Dynamic evolution of base composition: causes and consequences in avian phylogenomics. Molecular Biology and Evolution. 28: 2197-210. PMID 21393604 DOI: 10.1093/Molbev/Msr047  0.575
2011 Künstner A, Nabholz B, Ellegren H. Evolutionary constraint in flanking regions of avian genes. Molecular Biology and Evolution. 28: 2481-9. PMID 21393603 DOI: 10.1093/Molbev/Msr066  0.445
2010 Nabholz B, Jarvis ED, Ellegren H. Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Molecular Phylogenetics and Evolution. 57: 466-70. PMID 20601014 DOI: 10.1016/J.Ympev.2010.06.009  0.533
2010 Nam K, Mugal C, Nabholz B, Schielzeth H, Wolf JB, Backström N, Künstner A, Balakrishnan CN, Heger A, Ponting CP, Clayton DF, Ellegren H. Molecular evolution of genes in avian genomes. Genome Biology. 11: R68. PMID 20573239 DOI: 10.1186/Gb-2010-11-6-R68  0.522
2010 Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, ... ... Nabholz B, et al. The genome of a songbird. Nature. 464: 757-62. PMID 20360741 DOI: 10.1038/Nature08819  0.469
2010 Jobson RW, Nabholz B, Galtier N. An evolutionary genome scan for longevity-related natural selection in mammals. Molecular Biology and Evolution. 27: 840-7. PMID 19955481 DOI: 10.1093/Molbev/Msp293  0.477
2010 Künstner A, Nabholz B, Ellegren H. Strong selection in 3' flanking regions: Evidence from avian genomics F1000research. 1. DOI: 10.7490/F1000Research.237.1  0.424
2009 Galtier N, Nabholz B, Glémin S, Hurst GD. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology. 18: 4541-50. PMID 19821901 DOI: 10.1111/J.1365-294X.2009.04380.X  0.67
2009 Galtier N, Jobson RW, Nabholz B, Glémin S, Blier PU. Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biology Letters. 5: 413-6. PMID 19324654 DOI: 10.1098/Rsbl.2008.0662  0.454
2009 Nabholz B, Glémin S, Galtier N. The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals. Bmc Evolutionary Biology. 9: 54. PMID 19284537 DOI: 10.1186/1471-2148-9-54  0.694
2009 Galtier N, Blier PU, Nabholz B. Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds. Mitochondrion. 9: 51-7. PMID 19154799 DOI: 10.1016/J.Mito.2008.11.006  0.504
2008 Nabholz B, Mauffrey JF, Bazin E, Galtier N, Glemin S. Determination of mitochondrial genetic diversity in mammals. Genetics. 178: 351-61. PMID 18202378 DOI: 10.1534/Genetics.107.073346  0.695
2008 Nabholz B, Glémin S, Galtier N. Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis. Molecular Biology and Evolution. 25: 120-30. PMID 17998254 DOI: 10.1093/Molbev/Msm248  0.686
2008 Nabholz B, Glémin S, Galtier N. Extreme variation of mtDNA neutral substitution rate across mammalian species - The longevity hypothesis (Molecular Biology and Evolution (2008) 25, (120-130) DOI: 10.1093/molbev/msm248) Molecular Biology and Evolution. 25: 795. DOI: 10.1093/Molbev/Msn033  0.625
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