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Browsing College of Engineering by Issue Date

OpenBU

Browsing College of Engineering by Issue Date

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  • Mellor, Joe; DeLisi, Charles (BioMed Central, 2006-6-8)
    A systematic curation of the literature on Saccharomyces cerevisiae has yielded a comprehensive collection of experimentally observed interactions. This new resource augments current views of the topological structure of ...
  • Millien, Guetchyn; Spira, Avrum; Hinds, Anne; Wang, Junling; Williams, Mary C; Ramirez, Maria I (BioMed Central, 2006-7-25)
    BACKGROUND. Development of lung alveolar sacs of normal structure and size at late gestation is necessary for the gas exchange process that sustains respiration at birth. Mice lacking the lung differentiation gene T1α ...
  • Li, Jian-Liang; Hayden, Michael R; Warby, Simon C; Durr, Alexandra; Morrison, Patrick J; Nance, Martha; Ross, Christopher A; Margolis, Russell L; Rosenblatt, Adam; Squitieri, Ferdinando; Frati, Luigi; Gómez-Tortosa, Estrella; García, Carmen Ayuso; Suchowersky, Oksana; Klimek, Mary Lou; Trent, Ronald JA; McCusker, Elizabeth; Novelletto, Andrea; Frontali, Marina; Paulsen, Jane S; Jones, Randi; Ashizawa, Tetsuo; Lazzarini, Alice; Wheeler, Vanessa C; Prakash, Ranjana; Xu, Gang; Djoussé, Luc; Mysore, Jayalakshmi Srinidhi; Gillis, Tammy; Hakky, Michael; Cupples, L Adrienne; Saint-Hilaire, Marie H; Cha, Jang-Ho J; Hersch, Steven M; Penney, John B; Harrison, Madaline B; Perlman, Susan L; Zanko, Andrea; Abramson, Ruth K; Lechich, Anthony J; Duckett, Ayana; Marder, Karen; Conneally, P Michael; Gusella, James F; MacDonald, Marcy E; Myers, Richard H (BioMed Central, 2006-8-17)
    BACKGROUND: Age at onset of Huntington's disease (HD) is correlated with the size of the abnormal CAG repeat expansion in the HD gene; however, several studies have indicated that other genetic factors also contribute to ...
  • 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 ...
  • 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 ...
  • Dwyer, Daniel J; Kohanski, Michael A; Hayete, Boris; Collins, James J (2007)
    Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap ...
  • Farny, Caleb Hooper (Boston University, 2007)
    For high-intensity focused ultrasound (HIFU) to continue to gain acceptance for cancer treatment it is necessary to understand how the applied ultrasound interacts with gas trapped in the tissue. The presence of bubbles ...
  • Richards, Michael Scott (Boston University, 2007)
    Neoplastic tissue is typically highly vascularized, contains abnormal concentrations of extracellular proteins (e.g. collagen, proteoglycans) and has a high interstitial fluid pres- sure compared to most normal tissues. ...
  • Holmes, Jason David (Boston University, 2007)
    Sound propagation in shallow water is characterized by interaction with the oceans surface, volume, and bottom. In many coastal margin regions, including the Eastern U.S. continental shelf and the coastal seas of China, ...
  • 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 ...
  • Ergün, Ayla; Lawrence, Carolyn A; Kohanski, Michael A; Brennan, Timothy A; Collins, James J (2007-02-13)
    There is a need to identify genetic mediators of solid-tumor cancers, such as prostate cancer, where invasion and distant metastases determine the clinical outcome of the disease. Whole-genome expression profiling offers ...
  • Hayete, Boris; Gardner, Timothy S; Collins, James J (2007-02-13)
  • 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 ...
  • Dwyer, Daniel J; Kohanski, Michael A; Hayete, Boris; Collins, James J (2007-03-13)
    Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase ...
  • Eichler, Gabriel S; Reimers, Mark; Kane, David; Weinstein, John N (BioMed Central, 2007-09-10)
    The LeFE algorithm has been developed to address the complex, non-linear regulation of gene expression. Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear ...
  • 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, ...
  • Ryan, Joseph F.; Mazza, Maureen E.; Pang, Kevin; Matus, David Q.; Baxevanis, Andreas D.; Martindale, Mark Q.; Finnerty, John R. (Public Library of Science, 2007-1-24)
    BACKGROUND. Hox genes were critical to many morphological innovations of bilaterian animals. However, early Hox evolution remains obscure. Phylogenetic, developmental, and genomic analyses on the cnidarian sea anemone ...
  • Burroughs, A Maxwell; Balaji, S; Iyer, Lakshminarayan M; Aravind, L (BioMed Central, 2007-1-24)
    BACKGROUND. Domains containing the β-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS. Using sensitive ...
  • Faith, Jeremiah J; Hayete, Boris; Thaden, Joshua T; Mogno, Ilaria; Wierzbowski, Jamey; Cottarel, Guillaume; Kasif, Simon; Collins, James J; Gardner, Timothy S (Public Library of Science, 2007-1-9)
    Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance ...
  • 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. ...

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