A5059930476- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Bacteriophages and microbial interactions
- Animal Virus Infections Studies
- Animal Genetics and Reproduction
- Microbial Community Ecology and Physiology
- Effects of Environmental Stressors on Livestock
- Ruminant Nutrition and Digestive Physiology
- Viral gastroenteritis research and epidemiology
- RNA and protein synthesis mechanisms
- Infant Nutrition and Health
- Genetics and Plant Breeding
- Molecular Biology Techniques and Applications
- Chromosomal and Genetic Variations
- Virus-based gene therapy research
- Reproductive Physiology in Livestock
- Animal health and immunology
- Plant Virus Research Studies
- Plant Pathogenic Bacteria Studies
- Microbial infections and disease research
- Spectroscopy and Chemometric Analyses
- Genomic variations and chromosomal abnormalities
- Gut microbiota and health
University of Alberta
2016-2025
Food & Nutrition
2012-2024
California Polytechnic State University
2022
Agriculture and Agri-Food Canada
2021
Universidade Estadual de Campinas (UNICAMP)
2012
Genoa (Brazil)
2012
Public Health Agency of Canada
2010-2011
National Institute for Nanotechnology
2008-2010
University of Manitoba
2010
The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite metabolism data in world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands books, journal articles electronic databases. In addition to its literature-derived data, HMDB also an extensive experimental concentration compiled hundreds mass spectra (MS) Nuclear Magnetic resonance (NMR) metabolomic analyses performed on...
The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature information submitted the form GFF (General Feature Format) files. server uses BLAST to compare primary up three comparison sets. are converted a map showing entire sequence, an expanded more detailed view region interest. Several options included control...
To understand the biology and evolution of ruminants, cattle genome was sequenced to about sevenfold coverage. The contains a minimum 22,000 genes, with core set 14,345 orthologs shared among seven mammalian species which 1217 are absent or undetected in noneutherian (marsupial monotreme) genomes. Cattle-specific evolutionary breakpoint regions chromosomes have higher density segmental duplications, enrichment repetitive elements, species-specific variations genes associated lactation immune...
Abstract Summary: CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes. It converts XML or tab-delimited input into graphical map (PNG, JPG Scalable Vector Graphics format), complete with sequence features, labels, legends footnotes. In addition to the default full view map, program can generate series hyperlinked showing expanded views. The linked be explored using any Web browser, allowing rapid genome browsing...
Abstract Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, visualizing bacterial genomes. accepts Illumina sequence reads as compressed FASTQ files or pre-assembled contigs in raw, FASTA, GenBank format. Alternatively, can supply accession previously generated map JSON then performs assembly (for raw data), generates graphical map, an interface customizing the launching further analysis jobs. Notable...
Abstract Summary: GView is a Java application for viewing and examining prokaryotic genomes in circular or linear context. It accepts standard sequence file formats an optional style specification to generate customizable, publication quality genome maps bitmap scalable vector graphics formats. features interactive pan-and-zoom interface, command-line interface incorporation analysis pipelines, public Application Programming Interface other applications. Availability: freely available...
Abstract Background Continued sequencing efforts coupled with advances in technology will lead to the completion of a vast number small genomes. Whole-genome comparisons represent an important part analysis any new genome sequence, as they can provide better understanding biology and evolution source organism. Visualization results is important, it allows information from variety sources be integrated interpreted. However, existing graphical comparison tools lack features needed for...
Abstract PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to PHAST and PHASTER prophage finding web servers. designed support rapid identification, annotation visualization of sequences within bacterial genomes plasmids. also supports interactive all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in genomes. Given that genome sequencing has become so routine, need for fast tools comprehensively annotate progressively more important. not only...
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data an optional list gene identification information provides extensive textual hyperlinked image output. uses >30 programs to determine ∼60 subfields for each gene, including gene/protein name, GO function, COG possible paralogues orthologues, molecular weight, isoelectric point, operon structure, subcellular...
A particular challenge in biomedical text mining is to find ways of handling 'comprehensive' or 'associative' queries such as 'Find all genes associated with breast cancer'. Given that many genomics, proteomics metabolomics involve these kind comprehensive searches we believe a web-based tool could support would be quite useful. In response this need, have developed the PolySearch web server. supports >50 different classes against nearly dozen types text, scientific abstract bioinformatic...
Abstract Background Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine organization which will allow the design studies to associate genetic variation with economically important traits and also provides background extent long range in Results Linkage was assessed using r 2 among all pairs syntenic markers within cattle from Bos taurus indicus subspecies. included Angus, Charolais, Dutch...
Abstract Background One of the goals livestock genomics research is to identify genetic differences responsible for variation in phenotypic traits, particularly those economic importance. Characterizing species an important step towards linking genes or genomic regions with phenotypes. The completion bovine genome sequence and recent advances DNA sequencing technology allow in-depth characterization variations present cattle. Here we describe whole-genome resequencing two Bos taurus bulls...
Genome-wide association studies (GWAS) are a powerful tool for detecting genomic regions explaining variation in phenotype. The objectives of the present study were to identify or refine positions affecting milk production, components and fertility traits Canadian Holstein cattle, use these genes pathways that may influence traits. Several QTL detected production (MILK), fat (FAT), protein (PROT) deviation (FATD, PROTD respectively). identified (including production) support previous...
Cattle are divided into 2 groups referred to as taurine and indicine, both of which have been under strong artificial selection due their importance for human nutrition. A side effect this domestication includes a loss genetic diversity within each specialized breed. Recently, the first genome was sequenced assembled, allowing better understanding ruminant species. However, information from indicine breeds has limited. Here, we present sequence an breed (Nellore) generated with 52X coverage...
Feed efficient cattle consume less feed and produce environmental waste than inefficient cattle. Many factors are known to contribute differences in efficiency, however the underlying molecular mechanisms largely unknown. Our study aimed understand how host gene expression rumen epithelium contributes residual intake (RFI), a measure of using transcriptome profiling based approach. The epithelial from highly (low (L-) RFI, n = 9) (high (H-) Hereford x Angus steers was obtained...
This study aimed to investigate the potential regulatory role of miRNAs in development gastrointestinal tract (GIT) during early life dairy calves. Rumen and small intestinal (mid-jejunum ileum) tissue samples were collected from newborn (30 min after birth; n = 3), 7-day-old (n 6), 21-day-old 42-day-old 6) The miRNA profiling was performed using Illumina RNA-sequencing temporal regional differentially expressed further validated qRT-PCR. Analysis 16S rRNA gene copy numbers used quantify...
Selecting for lower methane (CH4) emitting animals is one of the best approaches to reduce CH4 given that genetic progress permanent and cumulative over generations. As selection requires a large number with records few countries actively record CH4, combining data from different could help expedite accurate parameters traits build future genomic reference population. Additionally, if we want include in breeding goal, it important know correlations other economically traits. Therefore, aim...
Abstract This study explored the potential of circulatory serum metabolite profiles to increase understanding physiology feed efficiency and identify biomarkers predict residual intake (RFI) in lactating Holsteins. Serum were compared high ( n = 20) low RFI cows at early, mid, late lactation stages. The had decreased P < 0.05) concentrations dodecanoylcarnitine, dodecenoylcarnitine, dodecanedioylcarnitine, tetradecanoylcarnitine, succinic acid, trimethylamine N-oxide, betaine, increased...
Polaromonas sp. strain JS666 can grow on cis-1,2-dichloroethene (cDCE) as a sole carbon and energy source may be useful for bioremediation of chlorinated solvent-contaminated sites. Analysis the genome sequence (5.9 Mb) shows bacterium well adapted to pollution that carries many genes likely involved in hydrocarbon xenobiotic catabolism metal resistance. Clusters coding haloalkane, haloalkanoate, n-alkane, alicyclic acid, cyclic alcohol, aromatic were analyzed detail, growth acetate,...