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- 7Single nucleotide polymorphisms
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- 4Linkage disequilibrium
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PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Download2008
Stothard, P., Damaraju, S., Wishart, D.S., Young, N., Cheng, D., Knox, C.
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 queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe...
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Quantitative trait loci affecting Rous Sarcoma Virus induced tumor regression trait in F2 intercross chickens
Download2009
Uemoto, Y., Mitsuhashi, T., Saburi, J., Miyata, T., Suzuki, K., Odawara, S., Yamashita, H., Yamamoto, R., Sato, S-I., Plastow, G., Kobayashi, E., Irina, C., Ohtake, T.
We performed a genome-wide linkage and quantitative trait locus (QTL) analysis to confirm the existence of QTL affecting Rous Sarcoma Virus (RSV) induced tumor regression, and to estimate their effects on phenotypic variance in an F2 resource population. The F2 population comprised 158 chickens...
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2014
Plastow, G., Stothard, P., Moore, S., Bao, H., Meng, Y., Liao, X.
Gene duplication is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary innovation. In the present study, we performed the first comprehensive analysis of duplicate genes in the bovine genome. A total of 3131 putative duplicated gene pairs...
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Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle
Download2014
Squires, J. J., Moore, S., Stothard, P., Swanson, K. C., Miller, S. P., Abo-Ismail, M. K., Vander Voort, G., Liao, X., Plastow, G., Mandell, I. B.
Background This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the...
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The CyberCell Database (CCDB): A comprehensive, self-updating relational database to coordinate and facilitate in silico modeling of Escherichia coli
Download2004
Stothard, P., Rouani, M., Sundararaj, S., Wishart, D.S., Nazhad, B.H., Guo, A., Ellison, M.
The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data...
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2003
Mitsuhashi, T., Andersson, L. , Carrion, D., Haley, C., Archibald, A., Evans, G., Plastow, G., Day, A.
We describe the characterisation of the two main coat colour determining loci (MC1R and KIT) for pigs and demonstrate how this information can be utilized for breed identification. These approaches can be useful components of quality assurance and traceability schemes which are increasingly...
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2003
Heuven, H. , Plastow, G., Peleman, J., Siggens, K., Brugmanns, B., Bagga, M.
AFLP® was utilized successfully as a tool to generate a large number (more than 100) of DNA markers in a total of 2435 individuals from the EC Pig Biodiversity project. This information was used for an initial genetic distance analysis with the results tending to group the lines and breeds as...
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Variation in Fetal Outcome, Viral Load and ORF5 Sequence Mutations in a Large Scale Study of Phenotypic Responses to Late Gestation Exposure to Type 2 Porcine Reproductive and Respiratory Syndrome Virus
Download2014
Plastow, G., Lunney, J. K., Ladinig, A., Ashley, C., Detmer, S. E., Wilkinson, A., Harding, J. C. S.
In spite of extensive research, the mechanisms of reproductive disease associated with Porcine Reproductive and Respiratory Syndrome virus (PRRSv) are still poorly understood. The objectives of this large scale study were to evaluate associations between viral load and fetal preservation,...
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2011
Nalaila, S., Li, C., Moore, S. S., Stothard, P., Wang, Z.
Quantitative trait loci (QTL) mapped to large chromosomal regions have limited utility as DNA markers for marker-assisted selection (MAS) and are less informative as a reference for the identification of the underlying causative quantitative trait nucleotides (QTN). The objective of this study...
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2007
Schnabel, R. D., Wang, Z., Mannenl, H., Gill, C. A., Van Tassell, C. P., Gao, C., Aerts, J., Williams, J. L., Neto, E. D., Moore, S. S., Matukumalli, L. K., Coppieters, W., McKay, S. D., Taylor, J. F., Crews, D., Murdoch, B. M.
Background Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and...