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Items: 36


Processing and Analyzing Multiple Genomes Alignments with MafFilter.

Dutheil JY.

Methods Mol Biol. 2020;2090:21-48. doi: 10.1007/978-1-0716-0199-0_2.


A Population Genomics Lexicon.

Barroso GV, Moutinho AF, Dutheil JY.

Methods Mol Biol. 2020;2090:3-17. doi: 10.1007/978-1-0716-0199-0_1.


Inference of recombination maps from a single pair of genomes and its application to ancient samples.

V Barroso G, Puzović N, Dutheil JY.

PLoS Genet. 2019 Nov 14;15(11):e1008449. doi: 10.1371/journal.pgen.1008449. eCollection 2019 Nov.


Ancestral Population Genomics.

Dutheil JY, Hobolth A.

Methods Mol Biol. 2019;1910:555-589. doi: 10.1007/978-1-4939-9074-0_18. Review.


The genomic determinants of adaptive evolution in a fungal pathogen.

Grandaubert J, Dutheil JY, Stukenbrock EH.

Evol Lett. 2019 May 1;3(3):299-312. doi: 10.1002/evl3.117. eCollection 2019 Jun.


The Impact of Protein Architecture on Adaptive Evolution.

Moutinho AF, Trancoso FF, Dutheil JY.

Mol Biol Evol. 2019 Sep 1;36(9):2013-2028. doi: 10.1093/molbev/msz134.


Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum.

Schweizer G, Münch K, Mannhaupt G, Schirawski J, Kahmann R, Dutheil JY.

Genome Biol Evol. 2018 Feb 1;10(2):629-645. doi: 10.1093/gbe/evy023. Erratum in: Genome Biol Evol. 2018 Apr 1;10(5):1247.


Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

Stukenbrock EH, Dutheil JY.

Genetics. 2018 Mar;208(3):1209-1229. doi: 10.1534/genetics.117.300502. Epub 2017 Dec 20.


The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level.

Barroso GV, Puzovic N, Dutheil JY.

Genetics. 2018 Jan;208(1):173-189. doi: 10.1534/genetics.117.300467. Epub 2017 Nov 2.


Hidden Markov Models in Population Genomics.

Dutheil JY.

Methods Mol Biol. 2017;1552:149-164. doi: 10.1007/978-1-4939-6753-7_11.


The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis.

Tollot M, Assmann D, Becker C, Altmüller J, Dutheil JY, Wegner CE, Kahmann R.

PLoS Pathog. 2016 Jun 22;12(6):e1005697. doi: 10.1371/journal.ppat.1005697. eCollection 2016 Jun.


hotspot: software to support sperm-typing for investigating recombination hotspots.

Odenthal-Hesse L, Dutheil JY, Klötzl F, Haubold B.

Bioinformatics. 2016 Aug 15;32(16):2554-5. doi: 10.1093/bioinformatics/btw195. Epub 2016 Apr 13.


A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi.

Dutheil JY, Mannhaupt G, Schweizer G, M K Sieber C, Münsterkötter M, Güldener U, Schirawski J, Kahmann R.

Genome Biol Evol. 2016 Feb 12;8(3):681-704. doi: 10.1093/gbe/evw026.


Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.

Dutheil JY, Munch K, Nam K, Mailund T, Schierup MH.

PLoS Genet. 2015 Aug 14;11(8):e1005451. doi: 10.1371/journal.pgen.1005451. eCollection 2015 Aug.


Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off.

Dutheil JY, Figuet E.

BMC Bioinformatics. 2015 Jun 9;16:190. doi: 10.1186/s12859-015-0619-8.


Extreme selective sweeps independently targeted the X chromosomes of the great apes.

Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF; Great Ape Genome Diversity Project, Mailund T, Schierup MH.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6413-8. doi: 10.1073/pnas.1419306112. Epub 2015 May 4.


Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals.

Figuet E, Romiguier J, Dutheil JY, Galtier N.

J Evol Biol. 2014 May;27(5):899-910. doi: 10.1111/jeb.12361. Epub 2014 Apr 10.


MafFilter: a highly flexible and extensible multiple genome alignment files processor.

Dutheil JY, Gaillard S, Stukenbrock EH.

BMC Genomics. 2014 Jan 22;15:53. doi: 10.1186/1471-2164-15-53.


A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion.

Munch K, Mailund T, Dutheil JY, Schierup MH.

Genome Res. 2014 Mar;24(3):467-74. doi: 10.1101/gr.158469.113. Epub 2013 Nov 4.


Bio++: efficient extensible libraries and tools for computational molecular evolution.

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, Galtier N, Belkhir K, Dutheil JY.

Mol Biol Evol. 2013 Aug;30(8):1745-50. doi: 10.1093/molbev/mst097. Epub 2013 May 21.


A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH.

PLoS Genet. 2012;8(12):e1003125. doi: 10.1371/journal.pgen.1003125. Epub 2012 Dec 20.


Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species.

Stukenbrock EH, Christiansen FB, Hansen TT, Dutheil JY, Schierup MH.

Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10954-9. doi: 10.1073/pnas.1201403109. Epub 2012 Jun 18.


Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Romiguier J, Figuet E, Galtier N, Douzery EJ, Boussau B, Dutheil JY, Ranwez V.

PLoS One. 2012;7(3):e33852. doi: 10.1371/journal.pone.0033852. Epub 2012 Mar 27.


Ancestral population genomics.

Dutheil JY, Hobolth A.

Methods Mol Biol. 2012;856:293-313. doi: 10.1007/978-1-61779-585-5_12. Review.


Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.


Efficient selection of branch-specific models of sequence evolution.

Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B.

Mol Biol Evol. 2012 Jul;29(7):1861-74. doi: 10.1093/molbev/mss059. Epub 2012 Feb 2.


Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.

Corbi J, Dutheil JY, Damerval C, Tenaillon MI, Manicacci D.

Ann Bot. 2012 Mar;109(4):693-708. doi: 10.1093/aob/mcr303. Epub 2012 Feb 2.


Comparing fungal genomes: insight into functional and evolutionary processes.

Stukenbrock EH, Dutheil JY.

Methods Mol Biol. 2012;835:531-48. doi: 10.1007/978-1-61779-501-5_33.


The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species.

Stukenbrock EH, Bataillon T, Dutheil JY, Hansen TT, Li R, Zala M, McDonald BA, Wang J, Schierup MH.

Genome Res. 2011 Dec;21(12):2157-66. doi: 10.1101/gr.118851.110. Epub 2011 Oct 12.


Detecting coevolving positions in a molecule: why and how to account for phylogeny.

Dutheil JY.

Brief Bioinform. 2012 Mar;13(2):228-43. doi: 10.1093/bib/bbr048. Epub 2011 Sep 24. Review.


IMPACT: integrated multiprogram platform for analyses in ConTest.

Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A.

J Hered. 2011 May-Jun;102(3):366-9. doi: 10.1093/jhered/esr003. Epub 2011 Mar 16.


Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model.

Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH.

PLoS Genet. 2011 Mar;7(3):e1001319. doi: 10.1371/journal.pgen.1001319. Epub 2011 Mar 3.


Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.


Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection.

Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T.

Genome Res. 2011 Mar;21(3):349-56. doi: 10.1101/gr.114751.110. Epub 2011 Jan 26.


Base pairing constraints drive structural epistasis in ribosomal RNA sequences.

Dutheil JY, Jossinet F, Westhof E.

Mol Biol Evol. 2010 Aug;27(8):1868-76. doi: 10.1093/molbev/msq069. Epub 2010 Mar 8.


Ancestral population genomics: the coalescent hidden Markov model approach.

Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH.

Genetics. 2009 Sep;183(1):259-74. doi: 10.1534/genetics.109.103010. Epub 2009 Jul 6.

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