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Browsing ENG: Biomedical Engineering: Scholarly Papers by Issue Date

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Browsing ENG: Biomedical Engineering: Scholarly Papers by Issue Date

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  • Liu, Manway; Liberzon, Arthur; Kong, Sek Won; Lai, Weil R; Park, Peter J; Kohane, Isaac S; Kasif, Simon (Public Library of SCience, 2007-6-15)
    Type 2 diabetes mellitus is a complex disorder associated with multiple genetic, epigenetic, developmental, and environmental factors. Animal models of type 2 diabetes differ based on diet, drug treatment, and gene knockouts, ...
  • Xi, Hualin; Shulha, Hennady P; Lin, Jane M; Vales, Teresa R; Fu, Yutao; Bodine, David M; McKay, Ronald D. G; Chenoweth, Josh G; Tesar, Paul J; Furey, Terrence S; Ren, Bing; Weng, Zhiping; Crawford, Gregory E (Public Library of Science, 2007-8-17)
    The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites ...
  • Dalgin, Gul S; Alexe, Gabriela; Scanfeld, Daniel; Tamayo, Pablo; Mesirov, Jill P; Ganesan, Shridar; DeLisi, Charles; Bhanot, Gyan (BioMed Central, 2007-8-6)
    BACKGROUND. Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper, we describe a new method based ...
  • Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi (BioMed Central, 2007-9-18)
    BACKGROUND. Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard ...
  • 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 ...
  • Weng, Zhiping; Guigó, Roderic (BioMed Central, 2008-02-25)
    A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007.
  • Naxerova, Kamila; Bult, Carol J; Peaston, Anne; Fancher, Karen; Knowles, Barbara B; Kasif, Simon; Kohane, Isaac S (BioMed Central, 2008-07-08)
    A systematic analysis of the relationship between the neoplastic and developmental transcriptome provides an outline of global trends in cancer gene expression. BACKGROUND. In recent years, the molecular underpinnings of ...
  • Lehár, Joseph; Krueger, Andrew; Zimmermann, Grant; Borisy, Alexis (Nature Publishing Group, 2008-08-05)
    Biological systems are robust, in that they can maintain stable phenotypes under varying conditions or attacks. Biological systems are also complex, being organized into many functional modules that communicate through ...
  • Snitkin, Evan S; Dudley, Aimée M; Janse, Daniel M; Wong, Kaisheen; Church, George M; Segrè, Daniel (BioMed Central, 2008-09-22)
    An iterative approach that integrates high-throughput measurements of yeast deletion mutants and flux balance model predictions improves understanding of both experimental and computational results. BACKGROUND. Understanding ...
  • Faith, Jeremiah J.; Driscoll, Michael E.; Fusaro, Vincent A.; Cosgrove, Elissa J.; Hayete, Boris; Juhn, Frank S.; Schneider, Stephen J.; Gardner, Timothy S. (Oxford University Press, 2008-1)
    Many Microbe Microarrays Database (M3D) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. M3D contains over a thousand Affymetrix microarrays for ...
  • Vazquez, Alexei; Beg, Qasim K; deMenezes, Marcio A; Ernst, Jason; Bar-Joseph, Ziv; Barabási, Albert-László; Boros, László G; Oltvai, Zoltán N (BioMed Central, 2008-1-23)
    BACKGROUND. Obtaining quantitative predictions for cellular metabolic activities requires the identification and modeling of the physicochemical constraints that are relevant at physiological growth conditions. Molecular ...
  • 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 ...
  • Ku, Manching; Koche, Richard P.; Rheinbay, Esther; Mendenhall, Eric M.; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Presser, Aviva; Nusbaum, Chad; Xie, Xiaohui; Chi, Andrew S.; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Cowan, Chad A.; Lander, Eric S.; Koseki, Haruhiko; Bernstein, Bradley E. (Public Library of Science, 2008-10-31)
    In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...
  • 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 ...
  • 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 ...
  • Chen, Jing; Yoshida, Tatsuro; Bitensky, Mark W. (Molecular Vision, 2008-12-29)
    PURPOSE. Cyclic GMP phosphodiesterase (PDE) is the light-regulated effector enzyme of vertebrate rods. Upon photo-activation of rhodopsin followed by activation of transducin/GTP, PDE rapidly hydrolyzes 3′, 5′-cyclic GMP ...
  • Kuhn, Heiko; Frank-Kamenetskii, Maxim D. (Oxford University Press, 2008-4)
    We describe a new approach for labeling of unique sequences within dsDNA under nondenaturing conditions. The method is based on the site-specific formation of vicinal nicks, which are created by nicking endonucleases ...
  • 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 ...
  • Fu, Yutao; Sinha, Manisha; Peterson, Craig L.; Weng, Zhiping (Public Library of Science, 2008-7-25)
    Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by ...

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