URI: http://hdl.handle.net/2144/1001

Recently Added

  • Chemical probing of RNA with the hydroxyl radical at single-atom resolution 

    Ingle, Shakti; Azad, Robert N.; Jain, Swapan S.; Tullius, Thomas D. (Oxford University Press, 2014-10-13)
    While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. ...
  • GBshape: a genome browser database for DNA shape annotations 

    Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley; Parker, Stephen C.J.; Nuzhdin, Sergey V.; Tullius, Thomas D.; Rohs, Remo (Oxford University Press, 2014-10-17)
    Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative ...
  • Secondary Structure Effects on DNA Hybridization Kinetics: A Solution Versus Surface Comparison 

    Gao, Yang; Wolf, Lauren K.; Georgiadis, Rosina M. (Oxford University Press, 2006-07-05)
    The hybridization kinetics for a series of designed 25mer probe–target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution ...
  • The Role of Disorder in Interaction Networks: A Structural Analysis 

    Kim, Philip M; Sboner, Andrea; Xia, Yu; Gerstein, Mark (Nature Publishing Group, 2008-03-25)
    Recent studies have emphasized the value of including structural information into the topological analysis of protein networks. Here, we utilized structural information to investigate the role of intrinsic disorder in these ...
  • Bromido(2,2′:6′,2′′-terpyridine)platinum(II) dibromidoaurate(I) Dimethyl Sulfoxide Solvate 

    Kahn, Michael I.; Golen, James A.; Rheingold, Arnold L.; Doerrer, Linda H. (International Union of Crystallography, 2009-8-26)
    The crystal structure of the title compound, [PtBr(C15H11N3)][AuBr2]·(CH3)2SO, exhibits infinite chains of {PtAuPt}∞ metallophilic interactions along the b axis. Two cations and one anion stack in a trimer with a unique ...
  • Antitumor Activity and Mechanism of Action of the Cyclopenta[b]benzofuran, Silvestrol 

    Cencic, Regina; Carrier, Marilyn; Galicia-Vázquez, Gabriela; Bordeleau, Marie-Eve; Sukarieh, Rami; Bourdeau, Annie; Brem, Brigitte; Teodoro, Jose G.; Greger, Harald; Tremblay, Michel L.; Porco, John A.; Pelletier, Jerry (Public Library of Science, 2009-4-29)
    BACKGROUND. Flavaglines are a family of natural products from the genus Aglaia that exhibit anti-cancer activity in vitro and in vivo and inhibit translation initiation. They have been shown to modulate the activity of ...
  • Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate 

    Xia, Yu; Franzosa, Eric A.; Gerstein, Mark B. (Public Library of Science, 2009-6-12)
    Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to rigorously assess the ...
  • Spectral affinity in protein networks 

    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 ...
  • Finding Local Communities in Protein Networks 

    Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu (BioMed Central, 2009-9-18)
    BACKGROUND. Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is ...
  • Predicting Eukaryotic Transcriptional Cooperativity by Bayesian Network Integration of Genome-Wide Data 

    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 ...
  • Protein Evolution in Yeast Transcription Factor Subnetworks 

    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 ...
  • Discovering Causal Signaling Pathways through Gene-Expression Patterns 

    Parikh, Jignesh R.; Klinger, Bertram; Xia, Yu; Marto, Jarrod A.; Blüthgen, Nils (Oxford University Press, 2010-5-21)
    High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various ...
  • Survey of Human Mitochondrial Diseases Using New Genomic/Proteomic Tools 

    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 ...
  • Genome-Wide Prioritization of Disease Genes and Identification of Disease-Disease Associations from an Integrated Human Functional Linkage Network 

    Linghu, Bolan; Snitkin, Evan S.; Hu, Zhenjun; Xia, Yu; DeLisi, Charles (BioMed Central, 2009-09-03)
    An evidence-weighted functional-linkage network of human genes reveals associations among diseases that share no known disease genes and have dissimilar phenotypes. We integrate 16 genomic features to construct an ...
  • Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison 

    Gao, Yang; Wolf, Lauren K.; Georgiadis, Rosina M. (2006)
    The hybridization kinetics for a series of designed 25mer probe�target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy ...