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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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  • K. Chu, Kengyeh; Lim, Daryl; Mertz, Jerome (Optical Society of America, 2010-7-16)
    Active illumination microscopy (AIM) is a method of redistributing dynamic range in a scanning microscope using real-time feedback to control illumination power on a sub-pixel time scale. We describe and demonstrate a fully ...
  • Sheu, Shu-Hsien; Lancia, David R.; Clodfelter, Karl H.; Landon, Melissa R.; Vajda, Sandor (Oxford University Press, 2004-12-17)
    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its ligands (substrate and transition state analogs, cofactors, inhibitors and ...
  • Wu, Chang-Jiun; Cai, Tianxi; Rikova, Klarisa; Merberg, David; Kasif, Simon; Steffen, Martin (Public Library of Science, 2009-11-25)
    BACKGROUND. Aberrant activation of signaling pathways drives many of the fundamental biological processes that accompany tumor initiation and progression. Inappropriate phosphorylation of intermediates in these signaling ...
  • Nariai, Naoki; Kolaczyk, Eric D.; Kasif, Simon (Public Library of Science, 2007-3-28)
    Dramatic improvements in high throughput sequencing technologies have led to a staggering growth in the number of predicted genes. However, a large fraction of these newly discovered genes do not have a functional assignment. ...
  • Shen, Yang; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Vajda, Sandor (2008-10-01)
    Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method ...
  • Shen, Yang; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Vajda, Sandor (Public Library of Science, 2008-10-10)
    Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic ...
  • Wang, Yong; Franzosa, Eric A.; Zhang, Xiang-Sun; Xia, Yu (Oxford University Press, 2010-5-13)
    When averaged over the full yeast protein–protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased ...
  • Lee, Soohyun; Kasif, Simon; Weng, Zhiping; Cantor, Charles R. (2008)
    Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded ...
  • Lee, Soohyun; Kasif, Simon; Weng, Zhiping; Cantor, Charles R. (Public Library of Science, 2008-12-18)
    BACKGROUND. Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these ...
  • Wesson, Daniel W; Carey, Ryan M; Verhagen, Justus V; Wachowiak, Matt (Public Library of Science, 2008-4-8)
    To gain insight into which parameters of neural activity are important in shaping the perception of odors, we combined a behavioral measure of odor perception with optical imaging of odor representations at the level of ...
  • Sebastiani, Paola; Montano, Monty; Puca, Annibale; Solovieff, Nadia; Kojima, Toshio; Wang, Meng C.; Melista, Efthymia; Meltzer, Micah; Fischer, Sylvia E. J.; Andersen, Stacy; Hartley, Stephen H.; Sedgewick, Amanda; Arai, Yasumichi; Bergman, Aviv; Barzilai, Nir; Terry, Dellara F.; Riva, Alberto; Anselmi, Chiara Viviani; Malovini, Alberto; Kitamoto, Aya; Sawabe, Motoji; Arai, Tomio; Gondo, Yasuyuki; Steinberg, Martin H.; Hirose, Nobuyoshi; Atzmon, Gil; Ruvkun, Gary; Baldwin, Clinton T.; Perls, Thomas T. (Public Library of Science, 2009-12-14)
    BACKGROUND. The strong familiality of living to extreme ages suggests that human longevity is genetically regulated. The majority of genes found thus far to be associated with longevity primarily function in lipoprotein ...
  • Dotan-Cohen, Dikla; Kasif, Simon; Melkman, Avraham A. (Oxford University Press, 2009-6-3)
    Motivation: There is a growing interest in improving the cluster analysis of expression data by incorporating into it prior knowledge, such as the Gene Ontology (GO) annotations of genes, in order to improve the biological ...
  • Zheng, Yu; Roberts, Richard J; Kasif, Simon (Public Library of Science, 2004-4-13)
    Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving ...
  • Hu, Zhenjun; Frith, Martin; Niu, Tianhua; Weng, Zhiping (BioMed Central, 2003-1-4)
    BACKGROUND. Many readers will sympathize with the following story. You are viewing a gene sequence in Entrez, and you want to find whether it contains a particular sequence motif. You reach for the browser's "find in page" ...
  • 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 ...

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