Browsing ENG: Biomedical Engineering: Scholarly Papers by Title

OpenBU

Browsing ENG: Biomedical Engineering: Scholarly Papers by Title

Sort by: Order: Results:

  • Landon, Melissa R; Amaro, Rommie E; Baron, Riccardo; Ngan, Chi Ho; Ozonoff, David; Andrew McCammon, J; Vajda, Sandor (Blackwell Publishing Ltd, 2011-12-29)
    The influenza virus subtype H5N1 has raised concerns of a possible human pandemic threat because of its high virulence and mutation rate. Although several approved anti-influenza drugs effectively target the neuraminidase, ...
  • Cosgrove, Elissa J; Gardner, Timothy S; Kolaczyk, Eric D (BioMed Central, 2010-9-9)
    BACKGROUND. Transcriptional regulatory network inference (TRNI) from large compendia of DNA microarrays has become a fundamental approach for discovering transcription factor (TF)-gene interactions at the genome-wide level. ...
  • Pulim, Vinay; Berger, Bonnie; Bienkowska, Jadwiga (Oxford University Press, 2008-8-18)
    The long-standing problem of constructing protein structure alignments is of central importance in computational biology. The main goal is to provide an alignment of residue correspondences, in order to identify homologous ...
  • Caffrey, Daniel R; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E; Somaroo, Shyamal; Caffrey, Brian E; Potluri, Shobha; Huang, Enoch S (BioMed Central, 2007-10-11)
    BACKGROUND. By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. ...
  • Zheng, Yu; Anton, Brian P; Roberts, Richard J; Kasif, Simon (BioMed Central, 2005-10-3)
    BACKGROUND. Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional ...
  • 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 ...
  • Reddy, Timothy E.; Shakhnovich, Boris E.; Roberts, Daniel S.; Russek, Shelley J.; DeLisi, Charles (Oxford University Press, 2007-01-03)
    Understanding transcription factor (TF) mediated control of gene expression remains a major challenge at the interface of computational and experimental biology. Computational techniques predicting TF-binding site specificity ...
  • 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 (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 ...
  • 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 ...
  • 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. (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 ...
  • 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 ...
  • 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 ...

Search OpenBU


Advanced Search

Browse

Deposit Materials