Browsing Faculty - Engineering and Computer Science by Issue Date
Now showing items 21-40 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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions
(Microorganisms, 2016)Background: Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to ... -
Comparative genomics reveals multiple pathways to mutualism for tick-borne pathogens
(BMC Genomics, 2016)Background: Multiple important human and livestock pathogens employ ticks as their primary host vectors. It is not currently known whether this means of infecting a host arose once or many times during evolution. Results: ... -
An optimal set of features for predicting type IV secretion system effector proteins for a subset of species based on a multi-level feature selection approach
(PLoS ONE, 2018)Type IV secretion systems (T4SS) are multi-protein complexes in a number of bacterial pathogens that can translocate proteins and DNA to the host. Most T4SSs function in conjugation and translocate DNA; however, approximately ... -
Alignment-free clustering of large datasets of unannotated protein conserved regions using minhashing
(BMC Bioinformatics, 2018)Background Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput ... -
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 ... -
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. ... -
Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature Evaluation
(Scientific Reports, 2019)The increasing prevalence of antimicrobial-resistant bacteria drives the need for advanced methods to identify antimicrobial-resistance (AMR) genes in bacterial pathogens. With the availability of whole genome sequences, ... -
Dynamics of repeat-associated plasticity in the aaap gene family in Anaplasma marginale
(Gene X, 2019)Anaplasmosis, the most prevalent tick-transmitted disease of cattle, is caused by the rickettsial intracellular parasite Anaplasma marginale. The pathogen replicates within a parasitophorous vacuole formed from the ... -
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 ... -
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 ... -
Capreomycin resistance prediction in two species of Mycobacterium using a stacked ensemble method
(Journal of Applied Microbiology, 2019)Aims: Predicting bacterial resistance provides valuable information that can assist in clinical decisions. With recent advances in whole genome sequencing technology, the detection of antibiotic resistance (AR) proteins ...