Searching journal content for articles similar to Ohler 10 (4): 539.

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  1. Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
    • Stephen J. Salipante,
    • David J. Roach,
    • Jacob O. Kitzman,
    • Matthew W. Snyder,
    • Bethany Stackhouse,
    • Susan M. Butler-Wu,
    • Choli Lee,
    • Brad T. Cookson,
    • and Jay Shendure
    Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
    ...were identified are highlighted. Isolates from patients 1 and 29 are indicated by blue text. The group corresponding to subclone ST131-H30 is indicated. Colored ring as in A. Scale bars are expressed in changes per site for both panels. Large-scale clinical E. col i genomic sequencing Genome Research...
  2. LETTER: Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals
    • Ines Hellmann,
    • Yuan Mang,
    • Zhiping Gu,
    • Peter Li,
    • Francisco M. de la Vega,
    • Andrew G. Clark,
    • and Rasmus Nielsen
    Genome Res. July 2008 18: 1020-1029; Published in Advance April 14, 2008, doi:10.1101/gr.074187.107
    ...of composite likelihood estimators (CLEs). CLEs are becoming popular for dealing with large-scale data in population genetics. They form the basis for a number of recent methods for analyzing large-scale population genetic data, including methods for estimating changes in population size (e.g., Nielsen 2000...
  3. Research: A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast
    • Judith B. Zaugg and
    • Nicholas M. Luscombe
    Genome Res. January 2012 22: 84-94; Published in Advance September 19, 2011, doi:10.1101/gr.124099.111
    ...-remodeling enzymes are primarily responsible for the nucleosome architecture. Our model for promoter nucleosome architecture reconciles genome-scale findings with molecular studies; in doing so, we establish principles for nucleosome positioning and gene expression that apply not only to individual genes, but across...
    OPEN ACCESS ARTICLE
  4. Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
    • Viola Nolte,
    • Ram Vinay Pandey,
    • Robert Kofler,
    • and Christian Schlötterer
    Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
    ...variability suggests that these sweeps have been caused by genes involved in genomic conflict. Results The recent advances in sequencing technology provide the opportunity to perform population genetic analyses on a scale. Even for species with no available reference , it has become feasible to generate draft...
    OPEN ACCESS ARTICLE
  5. Methods: Generic eukaryotic core promoter prediction using structural features of DNA
    • Thomas Abeel,
    • Yvan Saeys,
    • Eric Bonnet,
    • Pierre Rouzé,
    • and Yves Van de Peer
    Genome Res. February 2008 18: 310-323; Published in Advance December 20, 2007, doi:10.1101/gr.6991408
    ...methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale...
  6. INSIGHT/OUTLOOK: Transposon-Induced Hotspots for Genomic Instability
    • Margaret G. Kidwell and
    • Andrew J. Holyoake
    Genome Res. August 1, 2001 11: 1321-1322; doi:10.1101/gr.201201
    ...of laboratory experiments, estimates of the frequency and evolutionary importance of such events in natural populations have been difficult to come by. Now, with the ability to obtain nucleotide sequence data on a large scale, we are starting to learn about the nature and frequency of TE-induced changes...
  7. METHODS: Drosophila Genomic Sequence Annotation Using the BLOCKS+ Database
    • Jorja G. Henikoff and
    • Steven Henikoff
    Genome Res. April 1, 2000 10: 543-546; doi:10.1101/gr.10.4.543
    ...and general homology-based method for gene finding was applied to the 2.9-Mb Drosophila melanogaster Adh region, the target sequence of the Genome Annotation Assessment Project (GASP). Each strand of the entire sequence was used as query of the BLOCKS+ database of conserved regions of proteins. This led...
  8. PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
    • Michael Ashburner and
    • Casey M. Bergman
    Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
    ...of useful constructs) ( http://www.fruitfly.org/EST/ ; S. Celniker, pers. comm.), and perhaps even to the availability of full-length cDNAs from every alternatively spliced transcript. Likewise, the genomic sequence has enabled the design of antisense RNA reagents that are now allowing large-scale...
  9. LETTER: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
    • Natalie C. Duarte,
    • Markus J. Herrgård,
    • and Bernhard Ø. Palsson
    Genome Res. July 2004 14: 1298-1309; Published in Advance June 14, 2004, doi:10.1101/gr.2250904
    ...assembly is preferred because it allows for the inclusion of disparate data sources, such as annotations, gene expression experiments, enzymatic assays, and physiological data, rather than exclusively genomic data ( Covert et al. 2001 ). Genome-scale metabolic networks have been manually reconstructed...
  10. METHODS: Ab initio Gene Finding in Drosophila Genomic DNA
    • Asaf A. Salamov and
    • Victor V. Solovyev
    Genome Res. April 1, 2000 10: 516-522; doi:10.1101/gr.10.4.516
    ...of predictions. Therefore, we decided not to use EST information to make additional improvements testing the system to predict genes in which the information about the transcript sequences is practically absent. The suggested scheme is designed to expedite initial analysis of large-scale genomic sequences...
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