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  1. Method: Finished bacterial genomes from shotgun sequence data
    • Filipe J. Ribeiro,
    • Dariusz Przybylski,
    • Shuangye Yin,
    • Ted Sharpe,
    • Sante Gnerre,
    • Amr Abouelleil,
    • Aaron M. Berlin,
    • Anna Montmayeur,
    • Terrance P. Shea,
    • Bruce J. Walker,
    • Sarah K. Young,
    • Carsten Russ,
    • Chad Nusbaum,
    • Iain MacCallum,
    • and David B. Jaffe
    Genome Res. November 2012 22: 2270-2277; Published in Advance July 24, 2012, doi:10.1101/gr.141515.112
    ..., Nusbaum C, Jaffe DB. 2008. ALLPATHS: De novo assembly of whole shotgun microreads. Genome Res 18: 810–820. Chain PSG, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, et al. 2009. Genome project standards in a new era of sequencing. Science 326: 236...
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  2. 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...
  3. RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
    • Stephan Ossowski,
    • Korbinian Schneeberger,
    • Richard M. Clark,
    • Christa Lanz,
    • Norman Warthmann,
    • and Detlef Weigel
    Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
    ...of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany ↵ 1 These authors contributed equally to this work. Abstract Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis...
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  4. Resource: Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs
    • Amy Huei-Yi Lee,
    • Stephane Flibotte,
    • Sunita Sinha,
    • Adrianna Paiero,
    • Rachel L. Ehrlich,
    • Sergey Balashov,
    • Garth D. Ehrlich,
    • James E.A. Zlosnik,
    • Joshua Chang Mell,
    • and Corey Nislow
    Genome Res. April 2017 27: 650-662; Published in Advance March 21, 2017, doi:10.1101/gr.213363.116
    ..., Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of whole- shotgun microreads. Genome Res 18: 810–820. Cant N, Pollock N, Ford RC. 2014. CFTR structure and cystic fibrosis. Int J Biochem Cell Biol 52: 15–25. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A...
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