Now showing items 21-40 of 454

    • A rapid conditional enumeration haplotyping method in pedigrees 

      Gao, Guimin; Hoeschele, Ina (2008-01-15)
      Haplotyping in pedigrees provides valuable information for genetic studies (e.g., linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large ...
    • The landscape of human proteins interacting with viruses and other pathogens 

      Dyer, Matthew D.; Murali, T. M.; Sobal, Bruno W. (Public Library of Science, 2008-02-15)
      Infectious diseases result in millions of deaths each year. Mechanisms of infection have been studied in detail for many pathogens. However, many questions are relatively unexplored. What are the properties of human proteins ...
    • Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction 

      Yang, Kuan; Zhang, Liqing (2008-03)
      Phylogenetic tree reconstruction requires construction of a multiple sequence alignment (MSA) from sequences. Computationally, it is difficult to achieve an optimal MSA for many sequences. Moreover, even if an optimal MSA ...
    • Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages 

      Mian, MA Rouf; Zhang, Yan; Wang, Zeng-Yu; Zhang, Ji-Yi; Cheng, Xiaofei; Chen, Lei; Chekhovskiy, Konstantin; Dai, Xinbin; Mao, Chunhong; Cheung, Foo; Zhao, Xuechun; He, Ji; Scott, Angela D; Town, Christopher D; May, Gregory D (2008-03-04)
      Background Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence ...
    • Modeling targeted layered containment of an influenza pandemic in the United States 

      Halloran, Elizabeth M.; Ferguson, Neil M.; Eubank, Stephen; Longini Jr., Ira M.; Cummings, Derek A.T.; Lewis, Bryan; Xu, Shufu; Fraser, Christophe; Vullikanti, Anil; Germann, Timothy C.; Wagener, Diane; Beckman, Richard; Kadau, Kai; Barrett, Christopher L.; Macken, Catherine A.; Burke, Donald S.; Cooley, Philip (NAS, 2008-03-25)
      Planning a response to an outbreak of a pandemic strain of influenza is a high public health priority. Three research groups using different individual-based, stochastic simulation models have examined the consequences of ...
    • Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life 

      Gillespie, Joseph J.; Williams, Kelly; Shukla, Maulik; Snyder, Eric E.; Nordberg, Eric K.; Ceraul, Shane M.; Dharmanolla, Chitti; Rainey, Daphne; Soneja, Jeetendra; Shallom, Joshua M.; Vishnubhat, Nataraj Dongre; Wattam, Rebecca; Purkayastha, Anjan; Czar, Michael; Crasta, Oswald; Setubal, João C.; Azad, Abdu F.; Sobral, Bruno S. (Public Library of Science, 2008-04-16)
      Background: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular α-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In ...
    • HDP - A novel heme detoxification protein from the malaria parasite 

      Dewal, Jani; Nagarkatti, Rana; Beatty, Wandy; Angel, Ross; Slebodnick, Carla; Anderson, John; Kumar, Sanjai; Rathore, Dharmendar (Public Library of Science, 2008-04-25)
      When malaria parasites infect host red blood cells (RBC) and proteolyze hemoglobin, a unique, albeit poorly understood parasite-specific mechanism, detoxifies released heme into hemozoin (Hz). Here, we report the identification ...
    • Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system 

      Mao, Chunhong; Evans, Clive; Jensen, Roderick V; Sobral, Bruno WS (2008-05-02)
      Background Sinorhizobium meliloti is an agriculturally important model symbiont. There is an ongoing need to update and improve its genome annotation. In this study, we used a high-throughput pyrosequencing approach to ...
    • Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes 

      Crasta, Oswald R.; Folkerts, Otto; Fei, Zhangjun; Mane ,Shrinivasrao P.; Evans, Clive; Martino-Catt, Susan; Bricker, Betsy; Yu, GongXin; Du, Lei; Sobral, Bruno W. (Public Library of Science, 2008-05-14)
      The Brucella abortus strain S19, a spontaneously attenuated strain, has been used as a vaccine strain in vaccination of cattle against brucellosis for six decades. Despite many studies, the physiological and molecular ...
    • The effect of negative feedback loops on the dynamics of Boolean networks 

      Sontag, Eduardo; Veliz-Cuba, Alan; Laubenbacher, Reinhard; Jarrah, Abdul Salam (CELL PRESS, 2008-07)
      Feedback loops play an important role in determining the dynamics of biological networks. To study the role of negative feedback loops, this article introduces the notion of distance-to-positive-feedback which, in essence, ...
    • Targeted Development of Registries of Biological Parts 

      Peccoud, Jean; Blauvelt, Megan F.; Cai, Yizhi; Cooper, Kristal L.; Crasta, Oswald; DeLalla, Emily C.; Evans, Clive; Folkerts, Otto; Lyons, Blair M.; Mane, Shrinivasrao P.; Shelton, Rebecca; Sweede, Matthew A.; Waldon, Sally A. (Public Library of Science, 2008-07-16)
      The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to ...
    • Enzymatic, immunological and phylogenetic characterization of Brucella suis urease 

      Contreras-Rodriguez, Araceli; Quiroz-Limon, Jose; Martins, Ana M.; Peralta, Humberto; Avila-Calderon, Eric; Sriranganathan, Nammalwar; Boyle, Stephen M.; Lopez-Merino, Ahide (2008-07-19)
      Background The sequenced genomes of the Brucella spp. have two urease operons, ure-1 and ure-2, but there is evidence that only one is responsible for encoding an active urease. The present work describes the purification ...
    • Deja vu: a database of highly similar citations in the scientific literature 

      Errami, Mounir; Sun, Zhaohui; Long, Tara C.; George, Angela C.; Garner, Harold R. (Oxford University Press, 2008-08-09)
      In the scientific research community, plagiarism and covert multiple publications of the same data are considered unacceptable because they undermine the public confidence in the scientific integrity. Yet, little has been ...
    • Insertion polymorphisms of SINE200 retrotransposons within speciation islands of Anopheles gambiae molecular forms 

      Santolamazza, Federica; Mancini, Emiliano; Simard, Frédéric; Qi, Yumin; Tu, Zhijian; della Torre, Alessandra (Biomed Central Ltd, 2008-08-25)
      Background SINEs (Short INterspersed Elements) are homoplasy-free and co-dominant genetic markers which are considered to represent useful tools for population genetic studies, and could help clarifying the speciation ...
    • RNA Interference of Trypanosoma brucei Cathepsin B and L Affects Disease Progression in a Mouse Model 

      Abdulla, M-H; O'Brien, T; Mackey, ZB; Sajid, M; Grab, DJ; McKerrow, JH (PLOS, 2008-09-01)
    • Tandemly Arrayed Genes in Vertebrate Genomes 

      Pan, Deng; Zhang, Liqing (Hindawi, 2008-09-21)
      Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available ...
    • A Sterol-Regulatory Element Binding Protein Is Required for Cell Polarity, Hypoxia Adaptation, Azole Drug Resistance, and Virulence in Aspergillus fumigatus 

      Willger, Sven D.; Puttikamonkul, Srisombat|Kim, Kwang-Hyung; Burritt, James B.; Grahl, Nora; Metzler, Laurel J.; Barbuch, Robert; Bard, Martin; Lawrence, Christopher B.; Cramer Jr., Robert A. (Public Library of Science, 2008-11-07)
      At the site of microbial infections, the significant influx of immune effector cells and the necrosis of tissue by the invading pathogen generate hypoxic microenvironments in which both the pathogen and host cells must ...
    • PIG-the pathogen interaction gateway 

      Driscoll, Tim; Dyer, Matthew D.; Murali, T. M.; Sobral, Bruno W. (2009-01)
      Protein-protein interactions (PPIs) play a vital role in initiating infection in a number of pathogens. Identifying which interactions allow a pathogen to infect its host can help us to understand methods of pathogenesis ...
    • Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation 

      Csikasz-Nagy, A.; Kapuy, O.; Toth, A.; Pal, C.; Jensen, L. J.; Uhlmann, F.; Tyson, John J.; Novak, B. (Nature Publishing Group, 2009-01-01)
    • An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors 

      Wendelsdorf, Katherine V.; Song, Zhuo; Samuels, David C. (Public Library of Science, 2009-01-09)
      Nucleoside analogs used in antiretroviral treatment have been associated with mitochondrial toxicity. The polymerase-gamma hypothesis states that this toxicity stems from the analogs' inhibition of the mitochondrial DNA ...