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OpenBU

Browsing Bioinformatics by Title

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  • 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 ...
  • Wang, Yong; Zhang, Xiang-Sun; Xia, Yu (2009-10)
    Transcriptional cooperativity among several transcription factors (TFs) is believed to be the main mechanism of complexity and precision in transcriptional regulatory programs. Here, we present a Bayesian network framework ...
  • 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. ...
  • Iyer, Lakshminarayan M; Burroughs, A Maxwell; Aravind, L (BioMed Central, 2006-07-19)
    A systematic analysis of prokaryotic ubiquitin-related beta-grasp fold proteins provides new insights into the Ubiquitin family functional history. BACKGROUND. Ubiquitin (Ub)-mediated signaling is one of the hallmarks of ...
  • 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 ...
  • Kim, Byoung Woo; Kennedy, David N.; Lehár, Joseph; Lee, Myung Joo; Blood, Anne J.; Lee, Sang; Perlis, Roy H.; Smoller, Jordan W.; Morris, Robert; Fava, Maurizio; Breiter, Hans C. (Public Library of Science, 2010-5-26)
    BACKGROUND. Approach and avoidance behavior provide a means for assessing the rewarding or aversive value of stimuli, and can be quantified by a keypress procedure whereby subjects work to increase (approach), decrease ...
  • Beane, Jennifer; Sebastiani, Paola; Liu, Gang; Brody, Jerome S; Lenburg, Marc E; Spira, Avrum (BioMed Central, 2007-09-25)
    Oligonucleotide microarray analysis revealed 175 genes that are differentially expressed in large airway epithelial cells of people who currently smoke compared with those who never smoked, with 28 classified as irreversible, ...
  • 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" ...
  • Shah, Vishal; Sridhar, Sriram; Beane, Jennifer; Brody, Jerome S.; Spira, Avrum (Oxford University Press, 2004-12-17)
    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 database supports a ...
  • 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 ...
  • Ding, Chunming; Maier, Esther; Roscher, Adelbert A; Braun, Andreas; Cantor, Charles R (BioMed Central, 2004-5-5)
    BACKGROUND. For a diploid organism such as human, the two alleles of a particular gene can be expressed at different levels due to X chromosome inactivation, gene imprinting, different local promoter activity, or mRNA ...
  • Hayete, Boris; Gardner, Timothy S; Collins, James J (2007-02-13)
  • Burroughs, A Maxwell; Balaji, S; Iyer, Lakshminarayan M; Aravind, L (BioMed Central, 2007-7-2)
    BACKGROUND. The β-grasp fold (β-GF), prototyped by ubiquitin (UB), has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active ...
  • Sridhar, Sriram; Schembri, Frank; Zeskind, Julie; Shah, Vishal; Gustafson, Adam M; Steiling, Katrina; Liu, Gang; Dumas, Yves-Martine; Zhang, Xiaohui; Brody, Jerome S; Lenburg, Marc E; Spira, Avrum (BioMed Central, 2008-5-30)
    BACKGROUND: Cigarette smoking is a leading cause of preventable death and a significant cause of lung cancer and chronic obstructive pulmonary disease. Prior studies have demonstrated that smoking creates a field of molecular ...
  • 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 ...
  • Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-11-29)
    BACKGROUND. Protein-protein interaction (PPI) networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network ...

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