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  1. Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
    • Sira Sriswasdi,
    • Masako Takashima,
    • Ri-ichiroh Manabe,
    • Moriya Ohkuma,
    • Takashi Sugita,
    • and Wataru Iwasaki
    Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
    ...-8568, Japan; 6Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba 277-8564, Japan Corresponding authors: sirasris@bs.s.u-tokyo.ac.jp , iwasaki@bs.s.u-tokyo.ac.jp Abstract Polyploidization events such as whole-genome duplication and inter...
  2. LETTER: Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
    • Romain A. Studer,
    • Simon Penel,
    • Laurent Duret,
    • and Marc Robinson-Rechavi
    Genome Res. September 2008 18: 1393-1402; Published in Advance June 18, 2008, doi:10.1101/gr.076992.108
    ...: Between 0.9% and 4.7% of sites are affected by positive selection depending on the branches. No functional category was overrepresented among genes under positive selection. Surprisingly, whole genome duplication had no effect on the prevalence of positive selection, whether the fish-specific genome...
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  3. Resource: ECHO: A reference-free short-read error correction algorithm
    • Wei-Chun Kao,
    • Andrew H. Chan,
    • and Yun S. Song
    Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
    ...coverage depth and the position in the read. The improvement is most pronounced toward the end of the read, where previous methods become noticeably less effective. Using a whole-genome yeast data set, it is demonstrated here that ECHO is capable of coping with nonuniform coverage. Also, it is shown...
  4. PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
    • LaDeana W. Hillier,
    • Alan Coulson,
    • John I. Murray,
    • Zhirong Bao,
    • John E. Sulston,
    • and Robert H. Waterston
    Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
    ...of these regions in large insert clone libraries, we turned to a strategy of directly subcloning and shotgunsequencing a restriction fragment from whole genomic DNA for these internal gaps and the uncloned telomere from Chromosome II right. The regions containing the internal gaps and the remaining telomere were...
  5. ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
    • Stephen Richards,
    • Yue Liu,
    • Brian R. Bettencourt,
    • Pavel Hradecky,
    • Stan Letovsky,
    • Rasmus Nielsen,
    • Kevin Thornton,
    • Melissa J. Hubisz,
    • Rui Chen,
    • Richard P. Meisel,
    • Olivier Couronne,
    • Sujun Hua,
    • Mark A. Smith,
    • Peili Zhang,
    • Jing Liu,
    • Harmen J. Bussemaker,
    • Marinus F. van Batenburg,
    • Sally L. Howells,
    • Steven E. Scherer,
    • Erica Sodergren,
    • Beverly B. Matthews,
    • Madeline A. Crosby,
    • Andrew J. Schroeder,
    • Daniel Ortiz-Barrientos,
    • Catharine M. Rives,
    • Michael L. Metzker,
    • Donna M. Muzny,
    • Graham Scott,
    • David Steffen,
    • David A. Wheeler,
    • Kim C. Worley,
    • Paul Havlak,
    • K. James Durbin,
    • Amy Egan,
    • Rachel Gill,
    • Jennifer Hume,
    • Margaret B. Morgan,
    • George Miner,
    • Cerissa Hamilton,
    • Yanmei Huang,
    • Lenée Waldron,
    • Daniel Verduzco,
    • Kerstin P. Clerc-Blankenburg,
    • Inna Dubchak,
    • Mohamed A.F. Noor,
    • Wyatt Anderson,
    • Kevin P. White,
    • Andrew G. Clark,
    • Stephen W. Schaeffer,
    • William Gelbart,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
    ....genome.org. The annotated whole genome project has been deposited into DDBJ/EMBL/GenBank under the project accession AADE00000000. The version described in this paper is the first version, AADE01000000. The sequences of the proximal and distal Arrowhead breakpoints have been deposited in GenBank with accession nos. AY...
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