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Now showing items 1-20 of 146

    • Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich 

      Bradshaw, Patrick C; Rathi, Anand; Samuels, David C (2005-09-26)
      Background Eukaryotic organisms contain mitochondria, organelles capable of producing large amounts of ATP by oxidative phosphorylation. Each cell contains many mitochondria with many copies of mitochondrial DNA in each ...
    • The distribution of SNPs in human gene regulatory regions 

      Guo, Yongjian; Jamison, D Curtis (2005-10-06)
      Background As a result of high-throughput genotyping methods, millions of human genetic variants have been reported in recent years. To efficiently identify those with significant biological functions, a practical strategy ...
    • The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison 

      Sioson, Allan A; Mane, Shrinivasrao P; Li, Pinghua; Sha, Wei; Heath, Lenwood S.; Bohnert, Hans J; Grene, Ruth (2006-04-20)
      Background Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance ...
    • GenomeBlast: a web tool for small genome comparison 

      Lu, Guoqing; Jiang, Liying; Helikar, Resa MK; Rowley, Thaine W; Zhang, Luwen; Chen, Xianfeng; Moriyama, Etsuko N (2006-12-12)
      Background Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. ...
    • Bayesian estimation of genetic parameters for multivariate threshold and continuous phenotypes and molecular genetic data in simulated horse populations using Gibbs sampling 

      Stock, Kathrin F; Distl, Ottmar; Hoeschele, Ina (2007-05-09)
      Background Requirements for successful implementation of multivariate animal threshold models including phenotypic and genotypic information are not known yet. Here simulated horse data were used to investigate the properties ...
    • Role of information and communication networks in malaria survival 

      Mozumder, Pallab; Marathe, Achla (2007-10-10)
      Background Quite often symptoms of malaria go unrecognized or untreated. According to the Multilateral Initiative on Malaria, 70% of the malaria cases that are treated at home are mismanaged. Up to 82% of all malaria ...
    • Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions 

      Venancio, Thiago M.; DeMarco, Ricardo; Almeida, Giulliana T.; Oliveira, Katia C.; Setubal, João C.; Verjovski-Almeida, Sergio (2007-11-08)
      Background: Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite ...
    • Detecting epistatic interactions contributing to human gene expression using the CEPH family data 

      Li, Hua; Gao, Guimin; Li, Jian; Page, Grier P; Zhang, Kui (2007-12-18)
      It is believed that epistatic interactions among loci contribute to variations in quantitative traits. Several methods are available to detect epistasis using population-based data. However, methods to characterize epistasis ...
    • 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 ...
    • A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells 

      Li, Shenghua; Brazhnik, Paul; Sobral, Bruno; Tyson, John J. (Public Library of Science, 2008-01-25)
      The cell cycle is the sequence of events by which a growing cell replicates all its components and divides them more or less evenly between two daughter cells. The timing and spatial organization of these events are ...
    • 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 ...
    • 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 ...
    • 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, E.; Veliz-Cuba, A.; Laubenbacher, R.; Jarrahy, A. S. (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 ...