Browsing by Author "Galagan, James E"

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Browsing by Author "Galagan, James E"

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  • A Blind Deconvolution Approach to High-Resolution Mapping of Transcription Factor Binding Sites from ChIP-Seq Data
    Lun, Desmond S; Sherrid, Ashley; Weiner, Brian; Sherman, David R; Galagan, James E (BioMed Central, 2009-12-22)
    CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites. We present CSDeconv, a computational method that determines locations of ...
  • Large-Scale Identification of Genetic Design Strategies Using Local Search
    Lun, Desmond S; Rockwell, Graham; Guido, Nicholas J; Baym, Michael; Kelner, Jonathan A; Berger, Bonnie; Galagan, James E; Church, George M (Nature Publishing Group, 2009-08-18)
    In the past decade, computational methods have been shown to be well suited to unraveling the complex web of metabolic reactions in biological systems. Methods based on flux–balance analysis (FBA) and bi-level optimization ...
  • Short-Term Genome Evolution of Listeria Monocytogenes in a Non-Controlled Environment
    Orsi, Renato H; Borowsky, Mark L; Lauer, Peter; Young, Sarah K; Nusbaum, Chad; Galagan, James E; Birren, Bruce W; Ivy, Reid A; Sun, Qi; Graves, Lewis M; Swaminathan, Bala; Wiedmann, Martin (BioMed Central, 2008-11-13)
    BACKGROUND: While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus performed full genome analyses ...