Shane C Burgess

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A veterinarian (Massey University, New Zealand, 1989) and Ph.D. (Bristol University Medical School, UK, 1998). His funded research and 187 published works are in human and other animal and plant systems and genomic biology, bioinformatics, high-performance computation in biology, immunology, virology, cancer biology, vaccinology, bacteriology, toxicology, bioenergy, aquaculture, parasitology, agriculture and biotechnology. His 12 patents and nine software copyrights are from nearly $55 million in competitive funding.

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Robert Flight

University of Louisville

NAARM

North Carolina State University

Francesco Mancuso

Vall d' Hebron Institute of Oncology

Chris Evelo

Maastricht University

Michael Platel

P. Guzzi

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Papers by Shane C Burgess

Explorer Facilitating functional annotation of chicken microarray data

Background: Modeling results from chicken microarray studies is challenging for researchers due t... more Background: Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to GeneOntology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results: Wehave improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%.We have also ...

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Avian Genomics Conference and Gene Ontology Annotation Workshop, Starkville, Mississippi, USA, 19-22 May 2008

BMC Genomics (www.biomedcentral.com/ bmcgenomics) is an open access journal published by BioMed C... more BMC Genomics (www.biomedcentral.com/ bmcgenomics) is an open access journal published by BioMed Central Ltd. The journal publishes original peer-reviewed research articles in all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics (ISSN 1471-2164) is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Zoological Record, Thomson Reuters (ISI) and Google Scholar.

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The Gene Ontology: enhancements for 2011

The Gene Ontology (GO) (http://www.geneontology .org) is a community bioinformatics resource that... more The Gene Ontology (GO) (http://www.geneontology .org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.

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A Comparative Analysis of Adipose Tissue Secretome in a Model System of Lean and Fat Chickens

The Endocrine Society's 92nd Annual Meeting, June 19–22, 2010 - San Diego, 2010

The chicken gene nomenclature committee report

BMC genomics, Jul 14, 2009

Comparative genomics is an essential component of the post-genomic era. The chicken genome is the... more 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. Moreover, due to its unique evolutionary niche, the chicken genome can be used to understand evolution of functional elements and gene regulation in mammalian species. However comparative biology both within avian species and within amniotes is hampered due to the difficulty of recognising functional orthologs. This ...

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Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

BMC genomics, Jan 26, 2018

The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian vi... more The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian visceral fat hardly expresses leptin, the key adipokine in mammals. Therefore, to assess the endocrine role of adipose tissue in birds, we compared the transcriptome and proteome between two metabolically different types of chickens, broilers and layers, bred towards efficient meat and egg production, respectively. Broilers and layer hens, grown up to sexual maturation under free-feeding conditions, differed 4.0-fold in weight and 1.6-fold in ovarian-follicle counts, yet the relative accumulation of visceral fat was comparable. RNA-seq and mass-spectrometry (MS) analyses of visceral fat revealed differentially expressed genes between broilers and layers, 1106 at the mRNA level (FDR ≤ 0.05), and 203 at the protein level (P ≤ 0.05). In broilers, Ingenuity Pathway Analysis revealed activation of the PTEN-pathway, and in layers increased response to external signals. The expression pattern of ...

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

Genome biology, Jun 14, 2017

Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long... more

Effects of Subminimum Inhibitory Concentrations of Antibiotics on the Pasteurella m ultocida Proteome

J Proteome Res, 2006

Avian Genomics Conference and Gene Ontology Annotation Workshop, Starkville, Mississippi, USA, 19-22 May 2008

Bmc Genomics, 2009

Laser-induced breakdown spectroscopy for specimen analysis

Structural and functional annotation to explain the horse genome

Systems toxicology identifies mechanistic impacts of 2-amino-4,6-dinitrotoluene (2A-DNT) exposure in Northern Bobwhite

BMC Genomics, 2015

Marek's disease lymphomas

Marek's Disease, 2004

Proteomics in Animal Reproduction and Breeding

Whitfield/Methods in Animal Proteomics, 2011

Laser Induced Breakdown Spectroscopy: Application to Tissue Analysis

Laser Applilcations to Chemical, Security and Environmental Analysis, 2006

Analyses of the spleen proteome of chickens infected with Marek's disease virus

Virology, 2009

Interferon-Containing Supernatants Increase Marek's Disease Herpesvirus Genomes and Gene Transcription Levels, but Not Virion Replication in Vitro

Viral Immunology, 2003

Resistance to Marek's Disease Herpesvirus-induced Lymphoma is Multiphasic and Dependent on Host Genotype

Veterinary Pathology, 2001

Genotype-dependent differences in Marek's disease (MD) susceptibility were identified using 1... more Genotype-dependent differences in Marek's disease (MD) susceptibility were identified using 14-day-old line N and 61 (resistant) and 15I and 72 (susceptible) inbred chickens infected with HPRS-16 MD virus (MDV). All line 72 chickens developed progressive MD. Line 15I had fluctuating MD-specific clinical signs and individuals recovered. A novel histologic scoring system enabled indices to be calculated for lymphocyte infiltration into nonlymphoid organs. All genotypes had increased mean lesion scores (MLSs) and mean total lesion scores after MDV infection. These differed quantitatively and qualitatively between the genotypes. Lines 61 and 72 had a similar MLS distribution in the cytolytic phase, although scores were greater in line 72. At the time lymphomas were visible in line 72, histologic lesions in line 61 were regressing. AV37+ cells were present in similar numbers in all genotypes in the cytolytic phase, suggesting that neoplastically transformed cells were present in all ...

Experimental annotation of channel catfish virus by probabilistic proteogenomic mapping

PROTEOMICS, 2009

Maternal Antibody Transfer from Dams to Their Egg Yolks, Egg Whites, and Chicks in Meat Lines of Chickens

Poultry Science, 2006

Explorer Facilitating functional annotation of chicken microarray data

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Avian Genomics Conference and Gene Ontology Annotation Workshop, Starkville, Mississippi, USA, 19-22 May 2008

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The Gene Ontology: enhancements for 2011

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A Comparative Analysis of Adipose Tissue Secretome in a Model System of Lean and Fat Chickens

The Endocrine Society's 92nd Annual Meeting, June 19–22, 2010 - San Diego, 2010