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  1. Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
    • Nikolaos Vakirlis,
    • Véronique Sarilar,
    • Guénola Drillon,
    • Aubin Fleiss,
    • Nicolas Agier,
    • Jean-Philippe Meyniel,
    • Lou Blanpain,
    • Alessandra Carbone,
    • Hugo Devillers,
    • Kenny Dubois,
    • Alexandre Gillet-Markowska,
    • Stéphane Graziani,
    • Nguyen Huu-Vang,
    • Marion Poirel,
    • Cyrielle Reisser,
    • Jonathan Schott,
    • Joseph Schacherer,
    • Ingrid Lafontaine,
    • Bertrand Llorente,
    • Cécile Neuvéglise,
    • and Gilles Fischer
    Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
    ...Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus Nikolaos Vakirlis 1 , 6 , Véronique Sarilar 2 , 6 , Guénola Drillon 1 , 6 , Aubin Fleiss 1 , Nicolas Agier...
  2. LETTER: Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
    • Olga Zhaxybayeva,
    • J. Peter Gogarten,
    • Robert L. Charlebois,
    • W. Ford Doolittle,
    • and R. Thane Papke
    Genome Res. September 2006 16: 1099-1108; Published in Advance August 9, 2006, doi:10.1101/gr.5322306
    ...and Archaeal domains. Phylogenetic analysis of such “extended data sets” identifies putative instances of horizontal gene transfer from/to the cyanobacteria. Out of 1128 data sets, 879 had detectable homologs in selected prokaryotic s, and the remaining 249 data sets were “cyanobacteria-specific” (and...
  3. Methods: Estimating the tempo and mode of gene family evolution from comparative genomic data
    • Matthew W. Hahn,
    • Tijl De Bie,
    • Jason E. Stajich,
    • Chi Nguyen,
    • and Nello Cristianini
    Genome Res. August 2005 15: 1153-1160; doi:10.1101/gr.3567505
    ...within angiosperms. Evolution 57 : 460 –479. ↵ Slatkin, M. and Rannala, B. 1997 . Estimating the age of alleles by use of intrallelic variability. Am. J. Hum. Genet. 60 : 447 –458. ↵ Snel, B., Bork, P., and Huynen, M. 2002 . Genomes in flux: The evolution of archaeal and proteobacterial gene content...
  4. LETTER: Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
    • Dmitri M. Krylov,
    • Yuri I. Wolf,
    • Igor B. Rogozin,
    • and Eugene V. Koonin
    Genome Res. October 2003 13: 2229-2235; doi:10.1101/gr.1589103
    ...., and Hurst, L.D. 2001 . Highly expressed genes in yeast evolve slowly. Genetics 158 : 927 -931. ↵ ____. 2003 . Genomic function: Rate of evolution and gene dispensability. Nature 421 : 496 -497. ↵ Snel, B., Bork, P., and Huynen, M.A. 2002 . Genomes in flux: The evolution of archaeal and proteobacterial gene...
  5. PERSPECTIVE: Insights on biology and evolution from microbial genome sequencing
    • Claire M. Fraser-Liggett
    Genome Res. December 2005 15: 1603-1610; doi:10.1101/gr.3724205
    ...assembly: ϕX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. 100 : 15440 -15445. ↵ Snel, B., Bork, P., and Huynen, M.A. 2002 . Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res. 12 : 17 -25. ↵ Tatusov, R.L., Fedorova, N.D., Jackson, J...
  6. LETTER: The Balance of Driving Forces During Genome Evolution in Prokaryotes
    • Victor Kunin and
    • Christos A. Ouzounis
    Genome Res. July 2003 13: 1589-1594; doi:10.1101/gr.1092603
    ....A. 2001 . Detection of lateral gene transfer among microbial s. Curr. Opin. Genet. Dev. 11 : 620 -626. ↵ Snel, B., Bork, P., and Huynen, M.A. 1999 . Genome phylogeny based on gene content. Nat. Genet. 21 : 108 -110. ↵ Snel, B., Bork, P., and Huynen, M.A. 2002 . Genomes in flux: The evolution of archaeal...
  7. LETTER: Computing prokaryotic gene ubiquity: Rescuing the core from extinction
    • Robert L. Charlebois and
    • W. Ford Doolittle
    Genome Res. December 2004 14: 2469-2477; doi:10.1101/gr.3024704
    ...reading frames among bacterial phyla: Implications for vertical and lateral transmission. Int. J. Syst. Evol. Microbiol. 52 : 777 -787. ↵ Snel, B., Bork, P., and Huynen, M.A. 2002 . Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res. 12 : 17 -25. ↵ Tatusov, R...
  8. Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
    • Eyal Elyashiv,
    • Kevin Bullaughey,
    • Shmuel Sattath,
    • Yosef Rinott,
    • Molly Przeworski,
    • and Guy Sella
    Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
    .... As a first step toward understanding the processes generating these patterns, we sought to tease apart the relative importance of systematic, genome-wide changes in the efficacy of selection, such as those expected from demographic processes and of gene-specific changes, which may be expected after a shift...
  9. LETTER: The Genetic Core of the Universal Ancestor
    • J. Kirk Harris,
    • Scott T. Kelley,
    • George B. Spiegelman,
    • and Norman R. Pace
    Genome Res. March 1, 2003 13: 407-412; Published in Advance February 12, 2003, doi:10.1101/gr.652803
    .... , Woese C.R. ( 1997 ) Archaeal genomics: An overview. Cell 89 : 991 – 994 . ↵ Ouzounis C. , Kyrpides N. ( 1996 ) The emergence of major cellular processes in evolution. FEBS Lett. 390 : 119 – 123 . ↵ Snel B. , Bork P. , Huynen M.A. ( 2002 ) Genomes in flux: The evolution of archaeal and proteobacterial...
  10. LETTER: The fate of laterally transferred genes: Life in the fast lane to adaptation or death
    • Weilong Hao and
    • G. Brian Golding
    Genome Res. May 2006 16: 636-643; doi:10.1101/gr.4746406
    .... Genet. 21 : 108 – 110 . ↵ Snel B. , Bork P. , Huynen M.A. ( 2002 ) Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res. 12 : 17 – 25 . ↵ Stoebel D.M. ( 2005 ) Lack of evidence for horizontal transfer of the lac operon into Escherichia coli. Mol. Biol. Evol. 22 : 683...
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