Search Results - "Broschat, Shira L"

PARGT: a software tool for predicting antimicrobial resistance in bacteria by Chowdhury, Abu Sayed, Call, Douglas R., Broschat, Shira L.

“…With the ever-increasing availability of whole-genome sequences, machine-learning approaches can be used as an alternative to traditional alignment-based…”
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Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool by Esna Ashari, Zhila, Brayton, Kelly A, Broschat, Shira L

“…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…”
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Using an optimal set of features with a machine learning-based approach to predict effector proteins for Legionella pneumophila by Esna Ashari, Zhila, Brayton, Kelly A, Broschat, Shira L

“…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…”
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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 by Esna Ashari, Zhila, Dasgupta, Nairanjana, Brayton, Kelly A, Broschat, Shira L

“…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…”
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Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing by Abnousi, Armen, Broschat, Shira L, Kalyanaraman, Ananth

“…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…”
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A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions by Abnousi, Armen, Broschat, Shira L, Kalyanaraman, Ananth

“…Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to…”
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Sequence determinants of human-cell entry identified in ACE2-independent bat sarbecoviruses: A combined laboratory and computational network science approach by Khaledian, Ehdieh, Ulusan, Sinem, Erickson, Jeffery, Fawcett, Stephen, Letko, Michael C., Broschat, Shira L.

“…The sarbecovirus subgenus of betacoronaviruses is widely distributed throughout bats and other mammals globally and includes human pathogens, SARS-CoV and…”
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blaCMY-2-Positive IncA/C Plasmids from Escherichia coli and Salmonella enterica Are a Distinct Component of a Larger Lineage of Plasmids by Call, Douglas R, Singer, Randall S, Meng, Da, Broschat, Shira L, Orfe, Lisa H, Anderson, Janet M, Herndon, David R, Kappmeyer, Lowell S, Daniels, Joshua B, Besser, Thomas E

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Editorial: Machine learning approaches to antimicrobials: discovery and resistance by Broschat, Shira L, Siu, Shirley W I, de la Fuente-Nunez, Cesar

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Automated Confirmation of Protein Annotation Using NLP and the UniProtKB Database by Tao, Jin, Brayton, Kelly, Broschat, Shira

“…Advances in genome sequencing technology and computing power have brought about the explosive growth of sequenced genomes in public repositories with a…”
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ApicoAP: the first computational model for identifying apicoplast-targeted proteins in multiple species of Apicomplexa by Cilingir, Gokcen, Broschat, Shira L, Lau, Audrey O T

“…Most of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast. This organelle is important not only for…”
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Whole Proteome Clustering of 2,307 Proteobacterial Genomes Reveals Conserved Proteins and Significant Annotation Issues by Lockwood, Svetlana, Brayton, Kelly A, Daily, Jeff A, Broschat, Shira L

“…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…”
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Genotypic-Phenotypic Discrepancies between Antibiotic Resistance Characteristics of Escherichia coli Isolates from Calves in Management Settings with High and Low Antibiotic Use by DAVIS, Margaret A, BESSER, Thomas E, ORFE, Lisa H, BAKER, Katherine N. K, LANIER, Amelia S, BROSCHAT, Shira L, NEW, Daniel, CALL, Douglas R

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PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks by Tao, Jin, Brayton, Kelly A, Broschat, Shira L

“…Advances in genome sequencing have accelerated the growth of sequenced genomes but at a cost in the quality of genome annotation. At the same time,…”
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A Systematic Approach to Bacterial Phylogeny Using Order Level Sampling and Identification of HGT Using Network Science by Khaledian, Ehdieh, Brayton, Kelly A, Broschat, Shira L

“…Reconstructing and visualizing phylogenetic relationships among living organisms is a fundamental challenge because not all organisms share the same genes. As…”
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Identification of Anaplasma marginale type IV secretion system effector proteins by Lockwood, Svetlana, Voth, Daniel E, Brayton, Kelly A, Beare, Paul A, Brown, Wendy C, Heinzen, Robert A, Broschat, Shira L

“…Anaplasma marginale, an obligate intracellular alphaproteobacterium in the order Rickettsiales, is a tick-borne pathogen and the leading cause of anaplasmosis…”
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Expansion of Variant Diversity Associated with a High Prevalence of Pathogen Strain Superinfection under Conditions of Natural Transmission by Ueti, Massaro W, Tan, Yunbing, Broschat, Shira L, Castañeda Ortiz, Elizabeth J, Camacho-Nuez, Minerva, Mosqueda, Juan J, Scoles, Glen A, Grimes, Matthew, Brayton, Kelly A, Palmer, Guy H

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Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature Evaluation by Chowdhury, Abu Sayed, Call, Douglas R., Broschat, Shira L.

“…The increasing prevalence of antimicrobial-resistant bacteria drives the need for advanced methods to identify antimicrobial-resistance (AMR) genes in…”
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A Java-based tool for the design of classification microarrays by Meng, Da, Broschat, Shira L, Call, Douglas R

“…Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology…”
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Validation of Mixed-Genome Microarrays as a Method for Genetic Discrimination by Wan, Yan, Broschat, Shira L, Call, Douglas R

“…Comparative genomic hybridizations have been used to examine genetic relationships among bacteria. The microarrays used in these experiments may have open…”
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