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ApicoAMP: The first computational model for identifying apicoplast-targeted transmembrane proteins in Apicomplexa
(Elsevier, 2013-12)
In this work, we develop a method for predicting apicoplast-targeted transmembrane proteins for multiple species of Apicomplexa, whereby several classifiers trained on different feature sets and based on different algorithms ...
Genetic relationships among 527 Gram-negative bacterial plasmids
(Elsevier, 2012)
Plasmids are mosaic in composition with a maintenance “backbone” as well as “accessory” genes obtained via horizontal gene transfer. This horizontal gene transfer complicates the study of their genetic relationships. We ...
The SSA+ for scattering from dielectric surfaces at very low grazing angles
(Taylor and Francis, 2011-02)
In this paper we develop an extension of the small slope approximation (SSA) for scattering from randomly rough Dirichlet surfaces, which includes some multiple scattering. This extension is designated by SSA+. We focus ...
Identification of Anaplasma marginale type IV secretion system effector proteins
(PLoS ONE, 2011-11)
Anaplasma marginale, an obligate intracellular alphaproteobacterium in the order Rickettsiales, is a tick-borne pathogen and the leading cause of anaplasmosis in cattle worldwide. Complete genome sequencing of A. marginale ...
ApicoAP: The first computational model for predicting apicoplast-targeted proteins for multiple species of Apicomplexa
(PLoS ONE, 2012-05)
Most of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast. This organelle is important not only for the survival of the parasite, but its unique properties make it ...
Genotypic-phenotypic discrepancies between antibiotic resistance characteristics of Escherichia coli from calves in high and low antibiotic use management settings
(Applied and Environmental Microbiology, 2011-05)
We hypothesized that bacterial populations growing in the absence of antibiotics will accumulate more resistance gene mutations than bacterial populations growing in the presence of antibiotics. If this is so, the prevalence ...
Primary structural variation in Anaplasma marginale Msp2 efficiently generates immune escape variants
(Infection and Immunity, 2015-11)
Antigenic variation allows microbial pathogens to evade immune clearance and establish persistent infection. Anaplasma marginale utilizes gene conversion of a repertoire of silent msp2 alleles into a single active expression ...
Expansion of variant diversity associated with high prevalence of pathogen strain superinfection under conditions of natural transmission
(Infection and Immunity, 2012-07)
Superinfection occurs when a second, genetically distinct pathogen strain infects a host that has already mounted an immune response to a primary strain. For antigenically variant pathogens, the primary strain itself ...
Improved identification of epidemiologically related strains of Salmonella enterica by use of a fusion algorithm based on pulsed-field gel electrophoresis and multiple-locus variable-number tandemrepeat analysis
(Journal of Clinical Microbiology, 2010-11)
Pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem-repeat analysis (MLVA) are used to assess genetic similarity between bacterial strains. There are cases, however, when neither of these ...
Automated training for algorithms that learn from genomic data
(BioMed Research International, 2015-01)
Supervised machine learning algorithms are used by life scientists for a variety of objectives. Expert-curated public gene and protein databases are major resources for gathering data to train these algorithms. While these ...