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OpenBU

Browsing Bioinformatics by Title

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  • Reddy, Timothy E; DeLisi, Charles; Shakhnovich, Boris E (Public Library of Science, 2007-5-11)
    Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem. Determination of binding positions is a prerequisite for research in gene regulation, ...
  • Yu, Wen-Han; Hu, Han; Zhou, Qingde; Xia, Yu; Amar, Salomon (Public Library of Science, 2010-12-23)
    BACKGROUND. Periodontitis is the most common human infection affecting tooth-supporting structures. It was shown to play a role in aggravating atherosclerosis. To deepen our understanding of the pathogenesis of this disease, ...
  • Dotan-Cohen, Dikla; Letovsky, Stan; Melkman, Avraham A.; Kasif, Simon (Public Library of Science, 2009-4-23)
    BACKGROUND. The traditional approach to studying complex biological networks is based on the identification of interactions between internal components of signaling or metabolic pathways. By comparison, little is known ...
  • Lehár, Joseph; Zimmermann, Grant R; Krueger, Andrew S; Molnar, Raymond A; Ledell, Jebediah T; Heilbut, Adrian M; Short, Glenn F; Giusti, Leanne C; Nolan, Garry P; Magid, Omar A; Lee, Margaret S; Borisy, Alexis A; Stockwell, Brent R; Keith, Curtis T (2007-02-27)
    Efforts to construct therapeutically useful models of biological systems require large and diverse sets of data on functional connections between their components. Here we show that cellular responses to combinations of ...
  • Owens, Christopher M; Mawhinney, Christina; Grenier, Jill M; Altmeyer, Ralf; Lee, Margaret S; Borisy, Alexis A; Lehár, Joseph; Johansen, Lisa M (Nature Publishing Group, 2010-06-08)
    The search for effective Hepatitis C antiviral therapies has recently focused on host sterol metabolism and protein prenylation pathways that indirectly affect viral replication. However, inhibition of the sterol pathway ...
  • Holloway, Dustin T; Kon, Mark; DeLisi, Charles (BioMed Central, 2008-5-30)
    BACKGROUND. An important goal in post-genomic research is discovering the network of interactions between transcription factors (TFs) and the genes they regulate. We have previously reported the development of a ...
  • Ryan, Joseph F; Burton, Patrick M; Mazza, Maureen E; Kwong, Grace K; Mullikin, James C; Finnerty, John R (BioMed Central, 2006-07-24)
    The first near-complete set of homeodomains from a non-bilaterian animal is described. BACKGROUND. Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass ...
  • Roberts, Richard J.; Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John N.; Anton, Brian P.; Pokrzywa, Revonda M.; Choi, Han-Pil; Faller, Lina L.; Guleria, Jyotsna; Housman, Genevieve; Klitgord, Niels; Mazumdar, Varun; McGettrick, Mark G.; Osmani, Lais; Swaminathan, Rajeswari; Tao, Kevin R.; Letovsky, Stan; Vitkup, Dennis; Segrè, Daniel; Salzberg, Steven L.; Delisi, Charles; Steffen, Martin; Kasif, Simon (2010-11-20)
    COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists ...
  • Snitkin, Evan S; Gustafson, Adam M; Mellor, Joseph; Wu, Jie; DeLisi, Charles (BioMed Central, 2006-9-27)
    BACKGROUND. The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced ...
  • Steiling, Katrina; Kadar, Aran Y.; Bergerat, Agnes; Flanigon, James; Sridhar, Sriram; Shah, Vishal; Ahmad, Q. Rushdy; Brody, Jerome S.; Lenburg, Marc E.; Steffen, Martin; Spira, Avrum (Public Libary of Science, 2009-4-9)
    BACKGROUND. Although prior studies have demonstrated a smoking-induced field of molecular injury throughout the lung and airway, the impact of smoking on the airway epithelial proteome and its relationship to smoking-related ...
  • Rachlin, John; Ding, Chunming; Cantor, Charles; Kasif, Simon (BioMed Central, 2005-7-25)
    BACKGROUND: Multiplex PCR is a key technology for detecting infectious microorganisms, whole-genome sequencing, forensic analysis, and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR ...
  • Mintseris, Julian; Eisen, Michael B (BioMed Central, 2006-10-3)
    BACKGROUND. Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding ...
  • 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 ...
  • Strawbridge, Eva M.; Benson, Gary; Gelfand, Yevgeniy; Benham, Craig J. (Springer-Verlag, 2010-5-6)
    Although a variety of possible functions have been proposed for inverted repeat sequences (IRs), it is not known which of them might occur in vivo. We investigate this question by assessing the distributions and properties ...
  • Editorial 
    Benson, Gary (Oxford University Press, 2008-7-1)
  • Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D (BioMed Central, 2006-9-26)
    BACKGROUND. Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed ...
  • Shakhnovich, Boris E; Harvey, John M; Comeau, Steve; Lorenz, David; DeLisi, Charles; Shakhnovich, Eugene (BioMed Central, 2003-9-2)
    The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that allow valid ...
  • Klitgord, Niels; Segrè, Daniel (Public Library of Science, 2010-11-18)
    Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may ...
  • Yanai, Itai; Wolf, Yuri I; Koonin, Eugene V (BioMed Central, 2002-04-26)
    BACKGROUND. Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical ...
  • Imielinski, Marcin; Belta, Calin (BioMed Central, 2008-4-30)
    BACKGROUND. Biological robustness results from redundant pathways that achieve an essential objective, e.g. the production of biomass. As a consequence, the biological roles of many genes can only be revealed through ...

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