Browsing Faculty - Engineering and Computer Science by Author "Broschat, Shira L."
Now showing items 1-20 of 42
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A comparison of material classification techniques for ultrasound inverse imaging
Zhang, Xiaodong; Broschat, Shira L.; Flynn, Patrick J. (Journal of the Acoustical Society of America, 2002-01)The conjugate gradient method with edge preserving regularization (CGEP) is applied to the ultrasoundinverse scattering problem for the early detection of breast tumors. To accelerate image reconstruction, several different ... -
A conjugate gradient-neural network technique for ultrasound inverse imaging
Broschat, Shira L.; Zhang, Xiaodong; Flynn, Patrick J. (World Scientific Publishing, 2002-06)In this paper, a new technique for solving the two-dimensional inverse scattering problem for ultrasound inverse imaging is presented. Reconstruction of a two-dimensional object is accomplished using an iterative algorithm ... -
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions
Abnousi, Armen; Broschat, Shira L.; Kalyanaraman, Ananth (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 ... -
A finite-difference time-domain solution to scattering from a rough pressure-release surface
Hastings, Frank D.; Schneider, John B.; Broschat, Shira L. (Journal of the Acoustical Society of America, 1997-12)The finite-difference time-domain (FDTD) method is a numerical technique that makes no explicit physical approximations to the underlying problem. The quality of a FDTD-based solution typically is determined by the ... -
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, ... -
A numerical study of conjugate gradient directions for an ultrasound inverse problem
Broschat, Shira L.; Zhang, Xiaodong; Flynn, Patrick J. (World Scientific Publishing, 2004-12)In ultrasound inverse problems, the integral equation can be nonlinear, ill-posed, and computationally expensive. One approach to solving such problems is the conjugate gradient (CG) method. A key parameter in the CG method ... -
A practical cross section for scattering from rough surfaces at very low grazing angles in both the forward and backward directions
Broschat, Shira L.; Wang, Yanqiu (Taylor and Francis, 2009-08)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 ... -
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 ... -
Acoustic scattering from a fluid-elastic solid interface using the small slope approximation
Yang, Taiqian; Broschat, Shira L. (Journal of the Acoustical Society of America, 1994-09)In this paper the small slope approximation is applied to acoustic scattering from a randomly rough fluid–elastic?solid interface. Expressions for the zeroth?, first?, and second?order bistatic scattering cross sections ... -
Alignment-free clustering of large datasets of unannotated protein conserved regions using minhashing
Abnousi, Armen; Broschat, Shira L.; Kalyanaraman, Ananth (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 ... -
An investigation of the small slope approximation for scattering from rough surfaces: Part I: Theory
Thorsos, Eric I.; Broschat, Shira L. (Journal of the Acoustical Society of America, 1995-04)The small slope approximation (SSA) of Voronovich [Sov. Phys. JETP 62, 65–70 (1985)] is a promising method for application to scattering from many natural surfaces. The theory gives a systematic expansion that can be ... -
An investigation of the small slope approximation for scattering from rough surfaces: Part II: Numerical studies
Thorsos, Eric I.; Broschat, Shira L. (Journal of the Acoustical Society of America, 1997-05)The small slope approximation (SSA) of Voronovich [Sov. Phys. JETP 62, 65–70 (1985)] is a promising method for modeling wave scattering from rough surfaces. The SSA T-matrix series, which can be interpreted as an expansion ... -
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 ... -
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, ... -
ApicoAMP: The first computational model for identifying apicoplast-targeted transmembrane proteins in Apicomplexa
Cilingir, Gokcen; Lau, Audrey O.T.; Broschat, Shira L. (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 ... -
ApicoAP: The first computational model for predicting apicoplast-targeted proteins for multiple species of Apicomplexa
Cilingir, Gokcen; Broschat, Shira L; Lau, Audrey O T (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 ... -
Application of the perfectly matched layer (PML) absorbing boundary condition to elastic wave propagation
Hastings, Frank D.; Schneider, John B.; Broschat, Shira L. (Journal of the Acoustical Society of America, 1996-11)A method is presented for application of the perfectly matched layer (PML) absorbing boundary condition (ABC) to the P?SV velocity–stress finite?difference method. The PML consists of a nonphysical material, containing ... -
Automated training for algorithms that learn from genomic data
Cilingir, Gokcen; Broschat, Shira L. (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 ... -
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 ... -
Capreomycin resistance prediction in two species of Mycobacterium using a stacked ensemble method
Chowdhury, Abu Sayed; Khaledian, Ehdieh; Broschat, Shira L. (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 ...