Browsing Faculty - Engineering and Computer Science by Title
Now showing items 27-42 of 42
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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 ... -
Identifying predictors of antimicrobial exposure in hospitalized patients using a machine learning approach
(Journal of Applied Microbiology, 2019)Aims: Analysis and tracking of antimicrobial utilization (AU) are crucial in antimicrobial stewardship efforts which are used to find effective interventions for controlling antimicrobial resistance. In antimicrobial ... -
Implementation of transparent sources embedded in acoustic finite-difference time-domain grids
(Journal of the Acoustical Society of America, 1998-01)The finite-difference time-domain (FDTD) method is a simple but powerful numerical method which has been used to perform a wide variety of complex simulations. One of the considerations in using this method is modeling the ... -
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 ... -
Inverse imaging of the breast with a material classification technique
(Journal of the Acoustical Society of America, 1998-03)In recent publications [Chew et al., IEEE Trans. Blomed. Eng. BME-9, 218–225 (1990); Borup et al., Ultrason. Imaging14, 69–85 (1992)] the inverse imaging problem has been solved by means of a two-step iterative method. In ... -
Optical reflectance assay for the detection of biofilm formation
(Journal of Biomedical Optics, 2005-08)We describe the protocol for an inexpensive and nondestructive optical reflectance assay for the measurement of biofilm formation. Reflectance data are obtained using an Ocean Optics !Dunedin, Florida" USB 2000 spectrometer ... -
PARGT: a software tool for predicting antimicrobial resistance in bacteria
(Scientific Reports, 2020-07)With the ever-increasing availability of whole-genome sequences, machine-learning approaches can be used as an alternative to traditional alignment-based methods for identifying new antimicrobial-resistance genes. Such ... -
Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool
(Frontiers in Microbiology, 2019)Type IV secretion systems (T4SS) are used by a number of bacterial pathogens to attack the host cell. The complex protein structure of the T4SS is used to directly translocate effector proteins into host cells, often causing ... -
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 ... -
The method of the local parabolic approximation for rough surface scattering
(Journal of the Acoustical Society of America, 1993-10)A method for evaluation of scattering from rough surfaces which is similar to the Kirchhoff approximation is considered. However, it is based on a local parabolic approximation of the surface irregularities rather than a ... -
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 ... -
Using an optimal set of features with a machine learning-based approach to predict effector proteins for Legionella pneumophila
(PLoS ONE, 2019)Type IV secretion systems exist in a number of bacterial pathogens and are used to secrete effector proteins directly into host cells in order to change their environment making the environment hospitable for the bacteria. ... -
Using protein clusters from whole proteomes to construct and augment a dendrogram
(Advances in Bioinformatics, 2013-01)In this paper we present a new ab initio approach for constructing an unrooted dendrogram using protein clusters, an approach that has the potential for estimating relationships among several thousands of species based on ... -
Validation of mixed-genome microarrays as a method for genetic discrimination
(Applied and Environmental Microbiology, 2007-03)Comparative genomic hybridizations have been used to examine genetic relationships among bacteria. The microarrays used in these experiments may have open reading frames from one or more reference strains (whole-genome ... -
Whole proteome clustering of 2,307 Proteobacterial genomes reveals conserved proteins and significant annotation issues
(Frontiers in Microbiology, 2019)We clustered 8.76 M protein sequences deduced from 2,307 completely sequenced Proteobacterial genomes resulting in 707,311 clusters of one or more sequences of which 224,442 ranged in size from 2 to 2,894 sequences. To our ... -
Whole-proteome analysis of twelve species of Alphaproteobacteria links four pathogens
(Pathogens, 2013-01)Thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. This wealth of ...