Browsing Faculty - Engineering and Computer Science by Author "Call, Douglas R."
Now showing items 1-12 of 12
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A Java-based tool for the design of classification microarrays
Broschat, Shira L.; Meng, Da; Call, Douglas R. (Oxford University Press, 2008-08)Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, ... -
Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature Evaluation
Chowdhury, Abu Sayed; Call, Douglas R.; Broschat, Shira L. (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, ... -
BlaCMY-2 positive Inc A/C plasmids from Escherichia coli and Salmonella enterica are a distinct component of a larger lineage of plasmids
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 (Antimicrobial Agents and Chemotherapy, 2009-11)Large multidrug resistance plasmids of the A/C incompatibility complex (IncA/C) have been found in a diverse group of Gram-negative commensal and pathogenic bacteria. We present three completed sequences from IncA/C plasmids ... -
Comparison of the reflectance and Crystal Violet assays for measurement of biofilm formation by Enterococcus
Broschat, Shira L.; Call, Douglas R.; Kuhn, Edward; Loge, Frank J. (Biofilms, 2005-07)In previous work, we described a protocol for measuring biofilm formation on opaque and non-opaque surfaces using reflected light. In the present work, we used the reflectance assay to assess biofilm formation for 14 strains ... -
Genetic relationships among 527 Gram-negative bacterial plasmids
Broschat, Shira L.; Zhou, Yunyun; Call, Douglas R. (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 ... -
Genotypic-phenotypic discrepancies between antibiotic resistance characteristics of Escherichia coli from calves in high and low antibiotic use management settings
Davis, Margaret A.; Besser, Thomas E.; Orfe, Lisa H.; Baker, Katherine N. K.; Lanier, Amelia S.; Broschat, Shira L.; New, Daniel; Call, Douglas R (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 ... -
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
Broschat, Shira L.; Call, Douglas R.; Davis, Margaret A.; Meng, Da; Lockwood, S.; Ahmed, R.; Besser, Thomas E (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 ... -
Optical reflectance assay for the detection of biofilm formation
Broschat, Shira L.; Loge, Frank J.; Peppin, Jason D.; White, David; Call, Douglas R.; Kuhn, Edward (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
Chowdhury, Abu Sayed; Call, Douglas R.; Broschat, Shira L. (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 ... -
Using protein clusters from whole proteomes to construct and augment a dendrogram
Zhou, Yunyun; Call, Douglas R.; Broschat, Shira L.; Van de Peer, Yves (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
Wan, Yan; Broschat, Shira L.; Call, Douglas R. (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 analysis of twelve species of Alphaproteobacteria links four pathogens
Zhou, Yunyun; Call, Douglas R.; Broschat, Shira L. (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 ...