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Browsing ENG: Biomedical Engineering: Scholarly Papers by Title

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Browsing ENG: Biomedical Engineering: Scholarly Papers by Title

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  • Wang, Xuewei; Wu, Ming; Li, Zheng; Chan, Christina (BioMed Central, 2008-7-7)
    The detection and analysis of steady-state gene expression has become routine. Time-series microarrays are of growing interest to systems biologists for deciphering the dynamic nature and complex regulation of biosystems. ...
  • 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 ...
  • Shah, Vishal; Sridhar, Sriram; Beane, Jennifer; Brody, Jerome S.; Spira, Avrum (2005-01-01)
    The SIEGE (Smoking Induced Epithelial Gene Expression) database is a clinical resource for compiling and analyzing gene expression data from epithelial cells of the human intra-thoracic airway. This ...
  • Riehl, William J.; Krapivsky, Paul L.; Redner, Sidney; Segrè, Daniel (Public Library of Science, 2010-4-1)
    Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding ...
  • Hayete, Boris; Gardner, Timothy S; Collins, James J (2007-02-13)
  • Yanai, Itai; DeLisi, Charles (BioMed Central, 2002-10-25)
    Comparative genomics provides at least three methods for identifying functional links between genes: examination of phylogenetic distributions, analysis of conserved proximity and observations of fusions of genes into a ...
  • Oşan, Remus; Zhu, Liping; Shoham, Shy; Tsien, Joe Z. (Public Library of Science, 2007-5-2)
    Recent advances in large-scale ensemble recordings allow monitoring of activity patterns of several hundreds of neurons in freely behaving animals. The emergence of such high-dimensional datasets poses challenges for the ...
  • Plasterer, Thomas N; Smith, Temple F; Mohr, Scott C (BioMed Central, 2001-06-01)
    BACKGROUND. We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein ...
  • Li, Zheng; Chan, Christina (BioMed Central, 2009-3-10)
    Drug-induced liver toxicity is one of the leading causes of acute liver failure in the United States, exceeding all other causes combined. The objective of this paper is to describe systems biology methods for identifying ...
  • Reddy, T. B. K.; Riley, Robert; Wymore, Farrell; Montgomery, Phillip; DeCaprio, Dave; Engels, Reinhard; Gellesch, Marcel; Hubble, Jeremy; Jen, Dennis; Jin, Heng; Koehrsen, Michael; Larson, Lisa; Mao, Maria; Nitzberg, Michael; Sisk, Peter; Stolte, Christian; Weiner, Brian; White, Jared; Zachariah, Zachariah K.; Sherlock, Gavin; Galagan, James E.; Ball, Catherine A.; Schoolnik, Gary K. (Nucleic Acids Research, 2009-1)
    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. ...
  • Gustafson, Adam M; Snitkin, Evan S; Parker, Stephen CJ; DeLisi, Charles; Kasif, Simon (BioMed Central, 2006-10-19)
    BACKGROUND: The identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in the identification of potential ...
  • Bais, Manish; McLean, Jody; Sebastiani, Paola; Young, Megan; Wigner, Nathan; Smith, Temple; Kotton, Darrell N.; Einhorn, Thomas A.; Gerstenfeld, Louis C. (Public Library of Science, 2009-5-5)
    Fractures are among the most common human traumas. Fracture healing represents a unique temporarily definable post-natal process in which to study the complex interactions of multiple molecular events that regulate ...
  • Peterson, Matthew W; Colosimo, Marc E (BioMed Central, 2007-10-31)
    BACKGROUND. Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization ...
  • Cui, Jike; Das, Suchismita; Smith, Temple F.; Samuelson, John (Public Library of Science, 2010-8-3)
    BACKGROUND. Trichomonas vaginalis has an unusually large genome (∼160 Mb) encoding ∼60,000 proteins. With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here ...
  • Murphy, Kevin F.; Adams, Rhys M.; Wang, Xiao; Balázsi, Gábor; Collins, James J. (Oxford University Press, 2010-03-08)
    Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise. Accordingly, ...
  • Fregosi, Ralph F; Quan, Stuart F; Jackson, Andrew C; Kaemingk, Kris L; Morgan, Wayne J; Goodwin, Jamie L; Reeder, Jenny C; Cabrera, Rosaria K; Antonio, Elena (BioMed Central, 2004-4-29)
    BACKGROUND. We tested the hypothesis that ventilatory drive in hypoxia and hypercapnia is inversely correlated with the number of hypopneas and obstructive apneas per hour of sleep (obstructive apnea hypopnea index, OAHI) ...
  • Hu, Zhenjun; Hung, Jui-Hung; Wang, Yan; Chang, Yi-Chien; Huang, Chia-Ling; Huyck, Matt; DeLisi, Charles (2009-7-1)
    Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on ...
  • Hu, Zhenjun; Mellor, Joseph; Wu, Jie; DeLisi, Charles (BioMed Central, 2004-2-19)
    BACKGROUND. New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed ...
  • Hu, Zhenjun; Mellor, Joe; Wu, Jie; Yamada, Takuji; Holloway, Dustin; DeLisi, Charles (Oxford University Press, 2005-06-27)
    VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing many types of biological ...

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