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- 16Biological 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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Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Download2014
Stothard, P., Fritz-Waters, E., Choi, I., Abrams, S. M., Kommadath, A., Hosseini, A., Plastow, G. S., Guan, L. L., Tuggle, C. K., Bao, H., Meng, Y., Lunney, J. K., Reecy, J. M., Sun, X.
Background Transcriptome analysis of porcine whole blood has several applications, which include deciphering genetic mechanisms for host responses to viral infection and vaccination. The abundance of alpha- and beta-globin transcripts in blood, however, impedes the ability to cost-effectively...
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2004
Chan, C., Cutumisu, M., Szafron, D., Lu, P.
Java has multiple inheritance of interfaces, but only single inheritance of code via classes. This situation results in duplicated code in Java library classes and application code. We describe a generalization to the Java language syntax and the Java Virtual Machine (JVM) to support multiple...
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MicroRNA Buffering and Altered Variance of Gene Expression in Response to Salmonella Infection
Download2014
Plastow, G. S., Bao, H., Kommadath, A., Guan, L. L., Tuggle, C. K., Stothard, P.
One potential role of miRNAs is to buffer variation in gene expression, although conflicting results have been reported. To investigate the buffering role of miRNAs in response to Salmonella infection in pigs, we sequenced miRNA and mRNA in whole blood from 15 pig samples before and after...
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2009
Xu, J., Goebel, R. A., Cai, Z., Sabaai, H., Lin, G., Wang, Z., Wang, Y., Stothard, P.
Background The \"common disease – common variant\" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on...
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Oil Sands Mature Fine Tailings Consolidation Through Microbial Induced Calcite Precipitation
Download2014-12-21
Liang, J., Liu, Y., Deng, L., Guo, Z.
The accumulation of mature fine tailings (MFT) in tailings ponds has been a concern of the oil sands industry and regulators for decades. Previous studies and current practices for fine tailings consolidation focus on the addition of inorganic and organic additives to reduce MFT production and...
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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...