Evolutionary Systems Biology

  • Barroso GV, Puzovic N, Dutheil JY. The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level. Genetics. 2018 Jan;208(1):173-189. [pubmed]

Genome and Genomics 

  • Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF; Great Ape Genome Diversity Project, Mailund T, Schierup MH.
    Extreme selective sweeps independently targeted the X chromosomes of the great apes.
    Proc Natl Acad Sci U S A. 2015 May 19;112(20):6413-8. [pubmed]
  • Munch K, Mailund T, Dutheil JY, Schierup MH.
    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. Genome Res. 2014 Mar;24(3):467-74. [pubmed]
  • Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH.
    A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.
    PLoS Genet. 2012;8(12):e1003125. [pubmed] [HTML]
  • Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S.
    The bonobo genome compared with the chimpanzee and human genomes.
    Nature. 2012 Jun 28;486(7404):527-31. [pubmed]
  • Stukenbrock EH, Christiansen FB, Hansen TT, Dutheil JY, Schierup MH.
    Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species.
    Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10954-9. [pubmed]
  • Dutheil JY, Hobolth A.
    Ancestral population genomics.
    Methods Mol Biol. 2012;856:293-313. [pubmed]
  • 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.
    Insights into hominid evolution from the gorilla genome sequence.
    Nature. 2012 Mar 7;483(7388):169-75. [pubmed]
  • Stukenbrock EH, Dutheil JY.
    Comparing fungal genomes: insight into functional and evolutionary processes.
    Methods Mol Biol. 2012;835:531-48. [pubmed]
  • Stukenbrock EH, Bataillon T, Dutheil JY, Hansen TT, Li R, Zala M, McDonald BA, Wang J, Schierup MH.
    The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species.
    Genome Res. 2011 Dec;21(12):2157-66. [pubmed] [HTML]
  • Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH.
    Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model.
    PLoS Genet. 2011 Mar;7(3):e1001319. [pubmed] [HTML]
  • Locke DP, et al (100 authors).
    Comparative and demographic analysis of orang-utan genomes.
    Nature. 2011 Jan 27;469(7331):529-33. [pubmed] [H TML] [PDF]
  • Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T.
    Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection.
    Genome Res. 2011 Mar;21(3):349-56. Epub 2011 Jan 26. [pubmed] [HTML]
  • Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH.
    Ancestral population genomics: the coalescent hidden Markov model approach.
    Genetics. 2009 Sep;183(1):259-74. Epub 2009 Jul 6. [pubmed] [HTML]


  • Corbi J, Dutheil JY, Damerval C, Tenaillon MI, Manicacci D.
    Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation.
    Ann Bot. 2012 Feb 2. [pubmed]
  • Dutheil JY.
    Detecting coevolving positions in a molecule: why and how to account for phylogeny.
    Brief Bioinform. 2011. [pubmed]
  • Dutheil JY, Jossinet F, Westhof E.
    Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
    Mol Biol Evol. 2010 Aug;27(8):1868-76. Epub 2010 Mar 8. [pubmed] [HTM L]
  • Dutheil J & Galtier N.
    Detecting groups of co-evolving positions in a molecule : a clustering approach.
    BMC Evolutionary Biology. 2007 Nov 30, 7(1), 242. [pubmed] [HTML] [PDF]
  • Galtier N & Dutheil J.
    Coevolution within and between genes in Gene and protein evolution.
    Genome Dyn. 2007;3:1-12. [pubmed]
  • Dutheil J, Pupko T, Jean-Marie A, Galtier N.
    A Model-Based Approach for Detecting Co-evolving Positions in a Molecule.
    Mol Biol Evol. 2005 Sep; 22(9):1919-1928 [Pubmed] [Abstract] [HTML] [PDF]

Comparative analysis

  • Lenormand T, Dutheil J.
    Recombination difference between sexes: a role for haploid selection.
    PLoS Biol. 2005 Mar;3(3):e63. [pubmed] [HTML] [PDF]


  • 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. 2012;7(3):e33852. Epub 2012 Mar 27. [pubmed] [HTML] [PDF]
  • Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B.
    Efficient Selection of Branch-Specific Models of Sequence Evolution. 
    Mol Biol Evol. 2012 Mar 22. [pubmed]
  • Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N & Pupko T.
    Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
    PLoS Comput Biol. 2008 Nov;4(11):e1000214. Epub 2008 Nov 7. [pubmed] [HTML] [PDF]
  • Dutheil J.
    Detecting site-specific biochemical constraints through substitution mapping.
    J Mol Evol. 2008 Sep;67(3):257-65. Epub 2008 Aug 12. [pubmed] [HTML] [PD F]


  • Dutheil JY, Figuet E.
    Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off.
    BMC Bioinformatics. 2015 Jun 9;16(1):190. [pubmed]
  • Dutheil JY, Gaillard S, Stukenbrock EH.
    MafFilter: a highly flexible and extensible multiple genome alignment files processor.
    BMC Genomics. 2014 Jan 22;15:53. [pubmed] [HTML]
  • 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, Du theil JY.
    Bio++: efficient, extensible libraries and tools for computational molecular evolution
    Mol. Biol. Evol. 2013 [pubmed]
  • Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A.
    IMPACT: integrated multiprogram platform for analyses in ConTest.
    J Hered. 2011 May-Jun;102(3):366-9 [pubmed]
  • Dutheil J, Boussau B.
    Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs.
    BMC Evol Biol. 2008 Sep 22;8:255. [pubmed][HTML][PDF]
  • Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.
    Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. 
    BMC Bioinformatics. 2006 Apr 4;7:188. [pubmed] [HTML] [PDF]
  • Dutheil J, Galtier N.
    BAOBAB: a Java editor for large phylogenetic trees.
    Bioinformatics. 2002 Jun;18(6):892-3. [pubmed][PDF]