URI: http://hdl.handle.net/2144/987

Recently Added

  • Microfluidic chip for molecular amplification of influenza A RNA in human respiratory specimens 

    Mahalanabis, Madhumita; Chang, Jessie; Carey, Brendan; Hsieh, Christopher; Stanley, Ahjegannie; Feldman, James; Mitchell, Patricia; Klapperich, Catherine; Odell, Christine A.; Pollock, Nira R.; Qingqing, Cao (2012-03-22)
    A rapid, low cost, accurate point-of-care (POC) device to detect influenza virus is needed for effective treatment and control of both seasonal and pandemic strains. We developed a single-use microfluidic chip that integrates ...
  • Awareness, interest, and preferences of primary care providers in using point-of-care cancer screening technology 

    Vanture, Sarah; Cho, Margaret; Wang, Catharine; Klapperich, Catherine; Huang, Franklin W.; Kim, Chloe S. (2016-01-15)
    Well-developed point-of-care (POC) cancer screening tools have the potential to provide better cancer care to patients in both developed and developing countries. However, new medical technology will not be adopted by ...
  • VisANT 3.5: Multi-Scale Network Visualization, Analysis and Inference Based on the Gene Ontology 

    Hu, Zhenjun; Hung, Jui-Hung; Wang, Yan; Chang, Yi-Chien; Huang, Chia-Ling; Huyck, Matt; DeLisi, Charles (2009-7-1)
    Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on ...
  • Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites 

    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, ...
  • Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes 

    Shen, Yang; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Vajda, Sandor (Public Library of Science, 2008-10-10)
    Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic ...
  • Many Microbe Microarrays Database: Uniformly Normalized Affymetrix Compendia with Structured Experimental Metadata 

    Faith, Jeremiah J.; Driscoll, Michael E.; Fusaro, Vincent A.; Cosgrove, Elissa J.; Hayete, Boris; Juhn, Frank S.; Schneider, Stephen J.; Gardner, Timothy S. (Oxford University Press, 2008-1)
    Many Microbe Microarrays Database (M3D) is designed to facilitate the analysis and visualization of expression data in compendia compiled from multiple laboratories. M3D contains over a thousand Affymetrix microarrays for ...
  • Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies 

    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 ...
  • Biological Process Linkage Networks 

    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 ...
  • Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation 

    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 ...
  • The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome 

    Fu, Yutao; Sinha, Manisha; Peterson, Craig L.; Weng, Zhiping (Public Library of Science, 2008-7-25)
    Chromatin structure plays an important role in modulating the accessibility of genomic DNA to regulatory proteins in eukaryotic cells. We performed an integrative analysis on dozens of recent datasets generated by ...
  • Trichomonas Transmembrane Cyclases Result from Massive Gene Duplication and Concomitant Development of Pseudogenes 

    Cui, Jike; Das, Suchismita; Smith, Temple F.; Samuelson, John (Public Library of Science, 2010-8-3)
    BACKGROUND. Trichomonas vaginalis has an unusually large genome (∼160 Mb) encoding ∼60,000 proteins. With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here ...
  • Distinct Functions for the Drosophila piRNA Pathway in Genome Maintenance and Telomere Protection 

    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 ...
  • Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains 

    Ku, Manching; Koche, Richard P.; Rheinbay, Esther; Mendenhall, Eric M.; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Presser, Aviva; Nusbaum, Chad; Xie, Xiaohui; Chi, Andrew S.; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Cowan, Chad A.; Lander, Eric S.; Koseki, Haruhiko; Bernstein, Bradley E. (Public Library of Science, 2008-10-31)
    In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...
  • A Predictive Phosphorylation Signature of Lung Cancer 

    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 ...
  • Long-Range Correlations in Rectal Temperature Fluctuations of Healthy Infants during Maturation 

    Stern, Georgette; Beel, Julia; Suki, Béla; Silverman, Mike; Westaway, Jenny; Cernelc, Mateja; Baldwin, David; Frey, Urs (Public Library of Science, 2009-7-29)
    BACKGROUND. Control of breathing, heart rate, and body temperature are interdependent in infants, where instabilities in thermoregulation can contribute to apneas or even life-threatening events. Identifying abnormalities ...
  • Molecular Weight Assessment of Proteins in Total Proteome Profiles using 1D-PAGE and LC/MS/MS 

    Ahmad, Q. Rushdy; Nguyen, Dat H.; Wingerd, Mark A.; Church, George M.; Steffen, Martin A. (BioMed Central, 2005-6-8)
    BACKGROUND. The observed molecular weight of a protein on a 1D polyacrylamide gel can provide meaningful insight into its biological function. Differences between a protein's observed molecular weight and that predicted ...
  • Experimental Validation of the Influence of White Matter Anisotropy on the Intracranial EEG Forward Solution 

    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 ...
  • Chemical Combination Effects Predict Connectivity in Biological Systems 

    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 ...
  • Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome 

    Xi, Hualin; Shulha, Hennaed P.; Lin, Jane M.; Vales, Teresa R.; Fu, Yutao; Bodine, David M.; McKay, Ronald D. G.; Chenoweth, Josh G.; Tesar, Paul J.; Furey, Terrence S.; Ren, Bing; Weng, Zhiping; Crawford, Gregory E. (Public Library of Science, 2007-8-17)
    The identification of regulatory elements from different cell types is necessary for understanding the mechanisms controlling cell type–specific and housekeeping gene expression. Mapping DNaseI hypersensitive (HS) sites ...
  • COMBREX: A Project to Accelerate the Functional Annotation of Prokaryotic Genomes 

    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 ...

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