Structural and functional-annotation of an equine whole genome oligoarray (2009)
Bright, Lauren A, Burgess, Shane C, Chowdhary, Bhanu, Swiderski, Cyprianna E, McCarthy, Fiona M
Abstract Background The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression...
Facilitating functional annotation of chicken microarray data (2009)
Buza, Teresia J, Kumar, Ranjit, Gresham, Cathy R, Burgess, Shane C, McCarthy, Fiona M
Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken...
An automated proteomic data analysis workflow for mass spectrometry (2009)
Pendarvis, Ken, Kumar, Ranjit, Burgess, Shane C, Nanduri, Bindu
Abstract Background Mass spectrometry-based protein identification methods are fundamental to proteomics. Biological experiments are usually performed in replicates and proteomic analyses generate...
The chicken gene nomenclature committee report (2009)
Burt, David W, Carrë, Wilfrid, Fell, Mark, Law, Andy S, Antin, Parker B, Maglott, Donna R, ...
Abstract Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species....
The transcriptional response of Pasteurella multocidato three classes of antibiotics (2009)
Nanduri, Bindu, Shack, Leslie A, Burgess, Shane C, Lawrence, Mark L
Abstract Background Pasteurella multocida is a gram-negative bacterial pathogen that has a broad host range. One of the diseases it causes is fowl cholera in poultry. The availability of the genome...
Introduction to the Proceedings of the Avian Genomics and Gene Ontology Annotation Workshop (2009)
Bridges, Susan M, Burgess, Shane C, McCarthy, Fiona M
Abstract The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery...
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays (2009)
Van Den Berg, Bart HJ, Konieczka, Jay H, McCarthy, Fiona M, Burgess, Shane C
Abstract Background Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for...
Bmc Bioinformatics, William S S, Susan M Bridges, Fiona M Mccarthy, Bindu N, Shane C Burgess, ...
Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental set level
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research (2008)
Dandass, Yoginder S, Burgess, Shane C, Lawrence, Mark, Bridges, Susan M
Abstract Background This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The...
Peddinti, Divyaswetha, Nanduri, Bindu, Kaya, Abdullah, Feugang, Jean M, Burgess, Shane C, Memili, Erdogan
Abstract Background Male infertility is a major problem for mammalian reproduction. However, molecular details including the underlying mechanisms of male fertility are still not known. A thorough...
Bindu Nanduri, Mark L. Lawrence, Divya Swetha Peddinti, Shane C. Burgess
To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved...
Bindu Nanduri, Mark L. Lawrence, Divya Swetha Peddinti, Shane C. Burgess
To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved...
Gene Ontology annotation quality analysis in model eukaryotes (2008)
Buza, Teresia J., McCarthy, Fiona M., Wang, Nan, Bridges, Susan M., Burgess, Shane C.
Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different...
Dail, Mary B., Shack, L. Allen, Chambers, Janice E., Burgess, Shane C.
A global proteomics approach was applied to model the hepatic response elicited by the toxicologically well-characterized xenobiotic phenobarbital (PB), a prototypical inducer of hepatic xenobiotic...
BMC Systems Biology BioMed Central (2008)
Divyaswetha Peddinti, Bindu N, Abdullah Kaya, Jean M Feugang, Shane C Burgess, Erdogan Memili
Research article Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility
Buza, Teresia J, McCarthy, Fiona M, Burgess, Shane C
Abstract Background The chicken genome was sequenced because of its phylogenetic position as a non-mammalian vertebrate, its use as a biomedical model especially to study embryology and development,...
Prediction of peptides observable by mass spectrometry applied at the experimental set level (2007)
Sanders, William S, Bridges, Susan M, McCarthy, Fiona M, Nanduri, Bindu, Burgess, Shane C
Abstract Background When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides associated...
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data (2007)
Bridges, Susan M, Magee, G Bryce, Wang, Nan, Williams, W Paul, Burgess, Shane C, Nanduri, Bindu
Abstract Background Effective and economical methods for quantitative analysis of high throughput mass spectrometry data are essential to meet the goals of directly identifying, characterizing, and...
Dail, Mary B., Burgess, Shane C., Meek, Edward C., Wagner, Jennifer, Baravik, Jeffrey, Chambers, Janice E.
Traditionally, the liver has been considered a homogeneous organ, but literature suggests that the cytochromes P450 are differentially distributed among the hepatocytes and that the pattern of this...
AgBase: a unified resource for functional analysis in agriculture (2007)
McCarthy, Fiona M., Bridges, Susan M., Wang, Nan, Magee, G. Bryce, Williams, W. Paul, Luthe, Dawn S., ...
Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional...
AgBase: a functional genomics resource for agriculture (2006)
McCarthy, Fiona M, Wang, Nan, Magee, G Bryce, Nanduri, Bindu, Lawrence, Mark L, Camon, Evelyn B, ...
Abstract Background Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals...
Shane C. Burgess, Timmothy S. Cummings, Larry A. Hanson, Donna C. Sullivan, Rathel L. Nolan
Human infections caused by Enterococcus species are increasing; they are the third most common cause of nosocomial infections. E. faecium, though a relatively rare Enterococcal nosocomial infection,...
Enterococcus faecium: SNPs in One Specific 16-23S rRNA Intergenic Region]]> (2006)
Shane C. Burgess, Timmothy S. Cummings, Larry A. Hanson, Donna C. Sullivan, Rathel L. Nolan
E. faecium, though a relatively rare Enterococcal nosocomial infection, is very commonly resistant to multiple antibiotics. Quinupristin/Dalfopristin, a Streptogramin, is an antibiotic of "last...
Shane C. Burgess, Timmothy S. Cummings, Larry A. Hanson, Donna C. Sullivan, Rathel L. Nolan
Human infections caused by Enterococcus species are increasing; they are the third most common cause of nosocomial infections. <I>E. faecium, </I>though a relatively rare Enterococcal...
BMC Genomics BioMed Central Database AgBase: a functional genomics resource for agriculture (2006)
Fiona M Mccarthy, Nan Wang, G Bryce Magee, Bindu N, Mark L Lawrence, Evelyn B Camon, ...
© 2006 McCarthy et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Betancourt, Angela M., Burgess, Shane C., Carr, Russell L.
Chlorpyrifos (CPS), a known neurotoxicant, is a widely used agricultural organophosphorus insecticide. The effects of postnatal exposure to CPS on the expression of mRNA for two factors critical to...
Betancourt, Angela M., Burgess, Shane C., Carr, Russell L.
Chlorpyrifos (CPS), a known neurotoxicant, is a widely used agricultural organophosphorus insecticide. The effects of postnatal exposure to CPS on the expression of mRNA for two factors critical to...
Burgess, Shane C., Davison, T. Fred
Understanding the interactions between herpesviruses and their host cells and also the interactions between neoplastically transformed cells and the host immune system is fundamental to understanding...
AgBase: a functional genomics resource for agriculture
McCarthy, Fiona M, Wang, Nan, Magee, G Bryce, Nanduri, Bindu, Lawrence, Mark L, Camon, Evelyn B, ...
Burgess, Shane C., Davison, T. Fred
Understanding the interactions between herpesviruses and their host cells and also the interactions between neoplastically transformed cells and the host immune system is fundamental to understanding...
AgBase: a functional genomics resource for agriculture
McCarthy, Fiona M, Wang, Nan, Magee, G Bryce, Nanduri, Bindu, Lawrence, Mark L, Camon, Evelyn B, ...
AgBase: a unified resource for functional analysis in agriculture
McCarthy, Fiona M., Bridges, Susan M., Wang, Nan, Magee, G. Bryce, Williams, W. Paul, Luthe, Dawn S., ...
Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional...
Prediction of peptides observable by mass spectrometry applied at the experimental set level
Sanders, William S, Bridges, Susan M, McCarthy, Fiona M, Nanduri, Bindu, Burgess, Shane C
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
Bridges, Susan M, Magee, G Bryce, Wang, Nan, Williams, W Paul, Burgess, Shane C, Nanduri, Bindu
Gene Ontology annotation quality analysis in model eukaryotes
Buza, Teresia J., McCarthy, Fiona M., Wang, Nan, Bridges, Susan M., Burgess, Shane C.
Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different...
Peddinti, Divyaswetha, Nanduri, Bindu, Kaya, Abdullah, Feugang, Jean M, Burgess, Shane C, Memili, Erdogan
Nanduri, Bindu, Lawrence, Mark L., Peddinti, Divya Swetha, Burgess, Shane C.
To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved...
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research
Dandass, Yoginder S, Burgess, Shane C, Lawrence, Mark, Bridges, Susan M
Kunec, Dusan, Hanson, Larry A., Van Haren, Sandra, Nieuwenhuizen, I. F., Burgess, Shane C.
Herpesviruses are important pathogens of humans and other animals. Herpesvirus infectious clones that can reconstitute phenotypically wild-type (wt) virus are extremely valuable tools for elucidating...
Genome Sequence of the Chemolithoautotrophic Bacterium Oligotropha carboxidovorans OM5T▿
Paul, Debarati, Bridges, Susan, Burgess, Shane C., Dandass, Yoginder, Lawrence, Mark L.
Oligotropha carboxidovorans OM5T (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium with the capability to utilize carbon monoxide, carbon dioxide, and hydrogen. It is also capable of...
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays
Van Den Berg, Bart HJ, Konieczka, Jay H, McCarthy, Fiona M, Burgess, Shane C
Comparative Proteomic Analysis of Listeria monocytogenes Strains F2365 and EGD▿ †
Donaldson, Janet R., Nanduri, Bindu, Burgess, Shane C., Lawrence, Mark L.
Listeria monocytogenes is a gram-positive, food-borne pathogen that causes disease in both humans and animals. There are three major genetic lineages of L. monocytogenes and 13 serovars. To further...