Now showing items 309-323 of 323

    • Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status 

      Sharaf, Hazem; Rodrigues, Richard R; Moon, Jinyoung; Zhang, Bo; Mills, Kerri; Williams, Mark A (2019-04-16)
      Abstract Background Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is ...
    • Unraveling the Entry Mechanism of Oomycete and Fungal Effector Proteins into host cells 

      Kale, SD; Rumore, AC; GU, B; Shan, CB; Lawrence, D; Capelluto, D; Tyler, BM (2015-11-30)
      Oomycetes and fungi facilitate pathogenesis via secretion of effector proteins that have apoplastic and intracellular localizations. These effector proteins have a diverse array of functions that aid in pathogenesis, ...
    • Updating microbial genomic sequences: improving accuracy & innovation 

      Tae, Hongseok; Karunasena, Enusha; Bavarva, Jasmin H; Garner, Harold R. (2014-11-07)
      Background Many bacterial genome sequences completed using the Sanger method may contain assembly errors due in-part to low sequence coverage driven by cost. Findings To illustrate the need for re-sequencing of pre-nextgen ...
    • Using data-driven agent-based models for forecasting emerging infectious diseases 

      Venkatramanan, Srinivasan; Lewis, Bryan; Chen, Jiangzhuo; Higdon, Dave; Vullikanti, Anil; Marathe, Madhav (Elsevier, 2017-02-22)
      Producing timely, well-informed and reliable forecasts for an ongoing epidemic of an emerging infectious disease is a huge challenge. Epidemiologists and policy makers have to deal with poor data quality, limited understanding ...
    • Using Interpolation to Estimate System Uncertainty in Gene Expression Experiments 

      Falin, Lee J.; Tyler, Brett M. (Public Library of Science, 2011-07-22)
      The widespread use of high-throughput experimental assays designed to measure the entire complement of a cell's genes or gene products has led to vast stores of data that are extremely plentiful in terms of the number of ...
    • A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case 

      Yu, G. X.; Snyder, E. E.; Boyle, S. M.; Crasta, O. R.; Czar, M.; Mane, S. P.; Purkayastha, A.; Sobral, B.; Setubal, J. C. (2007-06)
      We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence ...
    • A virtual look at Epstein-Barr virus infection: Biological interpretations 

      Duca, Karen A.; Shapiro, Michael; Delgado-Eckert, Edgar; Hadinoto, Vey; Jarrah, Abdul S.; Laubenbacher, Reinhard; Lee, Kichol; Luzuriaga, Katherine; Polys, Nicholas F.; Thorley-Lawson, David A. (PLOS, 2007-10-19)
      The possibility of using computer simulation and mathematical modeling to gain insight into biological and other complex systems is receiving increased attention. However, it is as yet unclear to what extent these techniques ...
    • Virtual Screening as a Technique for PPAR Modulator Discovery 

      Lewis, Stephanie N.; Bassaganya-Riera, Josep; Bevan, David R. (Hindawi Publishing Corporation, 2010-01-01)
      Virtual screening (VS) is a discovery technique to identify novel compounds with therapeutic and preventive efficacy against disease. Our current focus is on the in silico screening and discovery of novel peroxisome ...
    • VMD: a community annotation database for oomycetes and microbial genomes 

      Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (2006-01-01)
      The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae ...
    • What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? 

      Kent, Edward; Neumann, Stefan; Kummer, Ursula; Mendes, Pedro (PLOS, 2013-09-14)
      Most biological models of intermediate size, and probably all large models, need to cope with the fact that many of their parameter values are unknown. In addition, it may not be possible to identify these values unambiguously ...
    • What Factors Might Have Led to the Emergence of Ebola in West Africa? 

      Alexander, Kathleen A.; Sanderson, Claire E.; Marathe, Madav; Lewis, Bryan L.; Rivers, Caitlin M.; Lofgren Eric; Eubank, Stephen; et al. (PLOS, 2015-06-04)
      An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been ...
    • What to know before forecasting the flu 

      Chakraborty, Prithwish; Lewis, Bryan; Eubank, Stephen; Brownstein, John S.; Marathe, Madhav; Ramakrishnan, Naren (PLOS, 2018-10-12)
      Accurate and timely influenza (flu) forecasting has gained significant traction in recent times. If done well, such forecasting can aid in deploying effective public health measures. Unlike other statistical or machine ...
    • Whole Exome Sequencing to Identify Genetic Variants Associated with Raised Atherosclerotic Lesions in Young Persons 

      Hixson, James E.; Jun, Goo; Shimmin, Lawrence C.; Wang, Yizhi; Yu, Guoqiang; Mao, Chunhong; Warren, Andrew S.; Howard, Timothy D.; Vander Heide, Richard S.; Van Eyk, Jennifer; Wang, Yue; Herrington, David M. (Springer Nature, 2017-06-22)
      We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified ...
    • Writing DNA with GenoCAD (TM) 

      Czar, Michael J.; Cai, Yizhi; Peccoud, Jean (2009-07-01)
      Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD (TM) (www.genocad.org) is a free web-based application to design protein expression vectors, ...
    • Zoospore interspecific signaling promotes plant infection by Phytophthora 

      Kong, P; Tyler, BM; Richardson, PA; Lee, BWK; Zhou, ZS; Hong, C (Biomed Central Ltd, 2010-12-07)
      Background Oomycetes attack a huge variety of economically and ecologically important plants. These pathogens release, detect and respond to signal molecules to coordinate their communal behaviors including the infection ...