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Browsing ENG: Biomedical Engineering: Scholarly Papers by Title

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Browsing ENG: Biomedical Engineering: Scholarly Papers by Title

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  • 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 ...
  • Lun, Desmond S; Sherrid, Ashley; Weiner, Brian; Sherman, David R; Galagan, James E (BioMed Central, 2009-12-22)
    CSdeconv is a novel method for determining the location of transcription factor binding from ChIP-seq data that discriminates closely-spaced sites. We present CSDeconv, a computational method that determines locations of ...
  • 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 ...
  • 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 ...
  • Champion, Mia D.; Zeng, Qiandong; Nix, Eli B.; Nano, Francis E.; Keim, Paul; Kodira, Chinnappa D.; Borowsky, Mark; Young, Sarah; Koehrsen, Michael; Engels, Reinhard; Pearson, Matthew; Howarth, Clint; Larson, Lisa; White, Jared; Alvarado, Lucia; Forsman, Mats; Bearden, Scott W.; Sjöstedt, Anders; Titball, Richard; Michell, Stephen L.; Birren, Bruce; Galagan, James (Public Library of Science Pathogens, 2009-5-29)
    Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its ...
  • Wu, Jie; Xie, Xiaohui (BioMed Central, 2006-09-26)
    Using comparative sequence analysis, a network among REST, CREB and brain-related miRNAs is propsed to mediate neuronal gene expression. BACKGROUND. Two distinct classes of regulators have been implicated in regulating ...
  • Spencer, Jean L.; Bernanke, Joel A.; Buczek-Thomas, Jo Ann; Nugent, Matthew A. (Public Library of Science, 2010-2-23)
    BACKGROUND. Increasing evidence has revealed important roles for complex glycans as mediators of normal and pathological processes. Glycosaminoglycans are a class of glycans that bind and regulate the function of a wide ...
  • 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 ...
  • Lee, Shane; Sen, Kamal; Kopell, Nancy (Public Library of Science, 2009-12-11)
    Spike timing dependent plasticity (STDP) has been observed experimentally in vitro and is a widely studied neural algorithm for synaptic modification. While the functional role of STDP has been investigated extensively, ...
  • Alexe, G.; Dalgin, G.S.; Ramaswamy, R.; DeLisi, C.; Bhanot, G. (Libertas Academica, 2007-2-19)
    Molecular stratification of disease based on expression levels of sets of genes can help guide therapeutic decisions if such classifications can be shown to be stable against variations in sample source and data perturbation. ...
  • Rosen, Jennifer; Suh, Hyunsuk; Lee, Stephanie; Aamar, Ousama; Bigio, Irving (BioMed Central, 2010-10-29)
  • Jain, Abhishek; Munn, Lance L. (Public Library of Science, 2009-9-21)
    Microfabrication of polydimethylsiloxane (PDMS) devices has provided a new set of tools for studying fluid dynamics of blood at the scale of real microvessels. However, we are only starting to understand the power and ...
  • 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 ...
  • Khurana, Jaspreet S.; Xu, Jia; Weng, Zhiping; Theurkauf, William E. (Public Library of Science, 2010-12-16)
    Transposons and other selfish DNA elements can be found in all phyla, and mobilization of these elements can compromise genome integrity. The piRNA (PIWI-interacting RNA) pathway silences transposons in the germline, but ...
  • Esue, Osigwe; Rupprecht, Laura; Sun, Sean X.; Wirtz, Denis (Public Library of Science, 2010-1-25)
    BACKGROUND. Crescentin, the recently discovered bacterial intermediate filament protein, organizes into an extended filamentous structure that spans the length of the bacterium Caulobacter crescentus and plays a critical ...
  • 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 ...
  • Bangera, Nitin B.; Schomer, Donald L.; Dehghani, Nima; Ulbert, Istvan; Cash, Sydney; Papavasiliou, Steve; Eisenberg, Solomon R.; Dale, Anders M.; Halgren, Eric (Springer US, 2010-1-9)
    Forward solutions with different levels of complexity are employed for localization of current generators, which are responsible for the electric and magnetic fields measured from the human brain. The influence of brain ...

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