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- 25Biological Sciences, Department of/Journal Articles (Biological Sciences)
- 16Roy Berg Kinsella Research Ranch
- 16Roy Berg Kinsella Research Ranch/Journal Articles (Kinsella Ranch)
- 2Oil Sands Research and Information Network (OSRIN)
- 2Oil Sands Research and Information Network (OSRIN)/OSRIN Technical Reports
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2014-03-17
Liang, J., Gamal El-Din, M., Estrada, L.P., Tumpa, F., Liu, Y.
The accumulation of mature fine tailings (MFT) in tailings ponds with very slow natural consolidation rate has been a concern for decades. Previous studies and current practices for tailings consolidation focus on the addition of various inorganic and organic additives to reduce MFT production...
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PA-GOSUB: A searchable database of model organism protein sequences with their predicted GO molecular function and subcellular localization
Download2005
Poulin, B., Lu, P., Wishart, D.S., Szafron, D., Lamb, N., Eisner, R., Pearcy, B., Ngo, D., Fyshe, A., Grenier, R.
PA-GOSUB (Proteome Analyst: Gene Ontology Molecular Function and Subcellular Localization) is a publicly available, web-based, searchable and downloadable database that contains the sequences, predicted GO molecular functions and predicted subcellular localizations of more than 107 000 proteins...
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2004
Wishart, D.S., Stothard, P., Dong, X., Forsythe, I.
PlasMapper is a comprehensive web server that automatically generates and annotates high-quality circular plasmid maps. Taking only the plasmid/vector DNA sequence as input, PlasMapper uses sequence pattern matching and BLAST alignment to automatically identify and label common promoters,...
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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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2006
Wishart, D.S., Neal, S., Berjanskii, M.V.
Every year between 500 and 1000 peptide and protein structures are determined by NMR and deposited into the Protein Data Bank. However, the process of NMR structure determination continues to be a manually intensive and time-consuming task. One of the most tedious and error-prone aspects of this...
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PROTEUS2: A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation
Download2008
Shrivistava, S., Berjanskii, M., Wishart, D.S., Cruz, J.A., Arndt, D., Montgomerie, S.
PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary...
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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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Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping
Download2009
Janzen, R.P., Dong, X., Gordon, P.M., Soh, J., Wishart, D.S., Sabhaney, A., Turinsky, A.L., Sensen, C.W., Chang, J., Hau, D., Xia, J., Trinh, Q.M.
We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data and pharmacokinetic data, respectively, we demonstrate how existing knowledge bases for molecular...