Browsing Faculty - Engineering and Computer Science by Author "Brayton, Kelly A."
Now showing items 1-9 of 9
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A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network Science
Khaledian, Ehdieh; Brayton, Kelly A.; Broschat, Shira L. (Microorganisms, 2020)Reconstructing and visualizing phylogenetic relationships among living organisms is a fundamental challenge because not all organisms share the same genes. As a result, the first phylogenetic visualizations employed a ... -
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
Ashari, Zhila Esna; Dasgupta, Nairanjana; Brayton, Kelly A.; Broschat, Shira L. (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 ... -
Comparative genomics reveals multiple pathways to mutualism for tick-borne pathogens
Lockwood, Svetlana; Brayton, Kelly A.; Broschat, Shira L. (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: ... -
Dynamics of repeat-associated plasticity in the aaap gene family in Anaplasma marginale
Fallquist, Heather M.; Tao, Jin; Cheng, Xiaoya; Pierlé, Sebastian Aguilar; Broschat, Shira L.; Brayton, Kelly A. (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 ... -
Expansion of variant diversity associated with high prevalence of pathogen strain superinfection under conditions of natural transmission
Uetia, Massaro W.; Tan, Yunbing; Broschat, Shira L.; Castaneda Ortiz, Elizabeth J.; Camacho-Nuez, Minerva; Mosqueda, Juan J.; Scoles, Glen A.; Grimes, Matthew; Brayton, Kelly A.; Palmer, Guy H. (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 ... -
Identification of Anaplasma marginale type IV secretion system effector proteins
Lockwood, Svetlana; Voth, Daniel E; Brayton, Kelly A.; Beare, Paul A; Brown, Wendy C; Heinzen, Robert A; Broschat, Shira L (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 ... -
Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool
Ashari, Zhila Esna; Brayton, Kelly A.; Broschat, Shira L. (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
Ashari, Zhila Esna; Brayton, Kelly A.; Broschat, Shira L. (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. ... -
Whole proteome clustering of 2,307 Proteobacterial genomes reveals conserved proteins and significant annotation issues
Lockwood, Svetlana; Brayton, Kelly A.; Daily, Jeff A.; Broschat, Shira L. (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 ...