Now showing items 1-17 of 17

    • 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)
      We present CSDeconv, a computational method that determines locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows ...
    • Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis 

      Weiner, Brian; Raman, Sahadevan; Dolganov, Gregory; Peterson, Matthew; Riley, Robert; Abeel, Thomas; White, Jared; Sisk, Peter; Stolte, Christian; Koehrsen, Mike; Yamamoto, Robert T; Iacobelli-Martinez, Milena; Kidd, Matthew J; Maer, Andreia M; Schoolnik, Gary K; Regev, Aviv; McGuire, Abigail Manson; Park, Sang T.; Wapinski, Ilan Neustat; Zucker, Jeremy Daniel Hofeld; Galagan, James E. (BioMed Central, 2012)
      Background: The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains ...
    • Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies 

      Champion, Mia D.; Zeng, Qiandong; Nix, Eli B.; Nano, Francis E.; Keim, Paul; Kodira, Chinnappa D.; Koehrsen, Michael; Pearson, Matthew; Howarth, Clint; Larson, Lisa; White, Jared; Alvarado, Lucia; Forsman, Mats; Bearden, Scott W.; Sjöstedt, Anders; Titball, Richard; Michell, Stephen L.; Birren, Bruce; Borowsky, Mark L; Young, Sarah U.; Engels, Reinhard; Galagan, James E (Public Library of Science, 2009)
      Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its ...
    • Cross-kingdom patterns of alternative splicing and splice recognition 

      McGuire, Abigail M; Pearson, Matthew D; Neafsey, Daniel Edward; Galagan, James E (BioMed Central, 2008)
      Background: Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition ...
    • Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication 

      Ma, Li-Jun; Ibrahim, Ashraf S.; Skory, Christopher; Grabherr, Manfred G.; Burger, Gertraud; Butler, Margi; Elias, Marek; Idnurm, Alexander; Lang, B. Franz; Sone, Teruo; Abe, Ayumi; Corrochano, Luis M.; Fu, Jianmin; Hansberg, Wilhelm; Kim, Jung-Mi; Kodira, Chinnappa D.; Koehrsen, Michael J.; Miranda-Saavedra, Diego; O'Leary, Sinead; Ortiz-Castellanos, Lucila; Poulter, Russell; Rodriguez-Romero, Julio; Ruiz-Herrera, José; Shen, Yao-Qing; Zeng, Qiandong; Birren, Bruce W.; Cuomo, Christina A.; Wickes, Brian L.; Calvo, Sarah E; Engels, Reinhard; Galagan, James E; Liu, Bo (Public Library of Science, 2009)
      Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic ...
    • How Accurate Can Genetic Predictions Be? 

      Dreyfuss, Jonathan M; Levner, Daniel; Galagan, James E; Church, George McDonald; Ramoni, Marco F (BioMed Central, 2012)
      Background: Pre-symptomatic prediction of disease and drug response based on genetic testing is a critical component of personalized medicine. Previous work has demonstrated that the predictive capacity of genetic testing ...
    • Independent Large Scale Duplications in Multiple M. tuberculosis Lineages Overlapping the Same Genomic Region 

      Weiner, Brian; Victor, Thomas C.; Warren, Robert M.; Plikaytis, Bonnie B.; Posey, James E.; van Helden, Paul D.; Gey van Pittius, Nicolass C.; Koehrsen, Michael; Sisk, Peter; Stolte, Christian; White, Jared; Gagneux, Sebastien; Birren, Bruce; Gomez, James E.; Sloutsky, Alexander; Hung, Deborah Tan; Murray, Megan Blanche; Galagan, James E (Public Library of Science, 2012)
      Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, ...
    • Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models 

      Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn; Zucker, Jeremy Daniel Hofeld; Colijn, Caroline; Weiner, Brian; Galagan, James E. (Public Library of Science, 2012)
      Background: Bacteria have evolved the ability to efficiently and resourcefully adapt to changing environments. A key means by which they optimize their use of available nutrients is through adjustments in gene expression ...
    • Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production 

      Colijn, Caroline; Brandes, Aaron; Zucker, Jeremy Daniel Hofeld; Lun, Desmond S.; Weiner, Brian; Farhat, Maha Reda; Cheng, Tan-Yun; Moody, D Branch; Murray, Megan Blanche; Galagan, James E (Public Library of Science, 2009)
      Metabolism is central to cell physiology, and metabolic disturbances play a role in numerous disease states. Despite its importance, the ability to study metabolism at a global scale using genomic technologies is limited. ...
    • Large-scale identification of genetic design strategies using local search 

      Lun, Desmond S; Rockwell, Graham; Guido, Nicholas; Baym, Michael Hartmann; Kelner, Jonathan A; Berger, Bonnie; Galagan, James E; Church, George McDonald (Nature Publishing Group, 2009)
      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 ...
    • Mechanisms of Intron Gain and Loss in Cryptococcus 

      Sharpton, Thomas J; Neafsey, Daniel Edward; Galagan, James E; Taylor, John W (BioMed Central, 2008)
      Background: Genome comparisons across deep phylogenetic divergences have revealed that spliceosomal intron gain and loss are common evolutionary events. However, because of the deep divergences involved in these comparisons, ...
    • Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence 

      Weinberger, Daniel M.; Trzciński, Krzysztof; Lu, Ying-Jie; Bogaert, Debby; Brandes, Aaron; Galagan, James E; Anderson, Porter; Malley, Richard; Lipsitch, Marc (Public Library of Science, 2009)
      There are 91 known capsular serotypes of Streptococcus pneumoniae. The nasopharyngeal carriage prevalence of particular serotypes is relatively stable worldwide, but the host and bacterial factors that maintain these ...
    • Positive Selection for Unpreferred Codon Usage in Eukaryotic Genomes 

      Neafsey, Daniel Edward; Galagan, James E (BioMed Central, 2007)
      Background: Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral ...
    • Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM 

      Dreyfuss, Jonathan M.; Zucker, Jeremy D.; Hood, Heather M.; Ocasio, Linda R.; Sachs, Matthew S.; Galagan, James E. (Public Library of Science, 2013)
      The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. Here, ...
    • Resource Competition May Lead to Effective Treatment of Antibiotic Resistant Infections 

      Gomes, Antonio L. C.; Galagan, James E.; Segrè, Daniel (Public Library of Science, 2013)
      Drug resistance is a common problem in the fight against infectious diseases. Recent studies have shown conditions (which we call antiR) that select against resistant strains. However, no specific drug administration ...
    • Short-Term Genome Evolution of Listeria Monocytogenes in a Non-Controlled Environment 

      Orsi, Renato H; Lauer, Peter; Nusbaum, Chad; Birren, Bruce W; Ivy, Reid A; Graves, Lewis M; Swaminathan, Bala; Wiedmann, Martin; Borowsky, Mark L; Young, Sarah K.; Galagan, James E; Sun, Qi (BioMed Central, 2008)
      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 ...
    • TB database: An Integrated Platform for Tuberculosis Research 

      Reddy, T. B. K.; Riley, Robert; Wymore, Farrell; Montgomery, Phillip; DeCaprio, Dave; Gellesch, Marcel; Hubble, Jeremy; Jen, Dennis; Jin, Heng; Koehrsen, Michael; Larson, Lisa; Nitzberg, Michael; Sisk, Peter; Stolte, Christian; Weiner, Brian; White, Jared; Zachariah, Zachariah K.; Sherlock, Gavin; Ball, Catherine A.; Schoolnik, Gary K.; Engels, Reinhard; Mao, Maria; Galagan, James E (Oxford University Press, 2009)
      The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. ...