Journal Articles (Agricultural, Food and Nutritional Science)
Items in this Collection
- 11Stothard, Paul
- 5Liao, Xiaoping
- 4Shrivastava, Savita
- 4Wishart, David S.
- 3Dennis, Jonathan J.
- 3Lynch, Karlene H.
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2005
Wishart, David S., Shrivastava, Savita, Ellison, Michael, Guo, Anchi, Cruz, Joseph, van Domselaar, Gary, O'Neill, Brian, Stothard, Paul
BacMap is an interactive visual database containing fully labeled, zoomable and searchable chromosome maps from more than 170 bacterial (archaebacterial and eubacterial) species. It uses a recently developed visualization tool (CGView) to generate high-resolution circular genome maps from...
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2005
Dong, Xaoli, Wishart, David S., Stothard, Paul, Greiner, Russ, Guo, AnChi, van Domselaar, Gary H., Szafron, Duane, Shrivastava, Savita, Cruz, Joseph A., Lu, Paul
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 and an optional list of gene identification information and provides extensive textual annotation and...
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Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages
Download2012
Stothard, Paul, Dennis, Jonathan J., Lynch, Karlene H.
Background Genomic analysis of bacteriophages infecting the Burkholderia cepacia complex (BCC) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. The objective of this study was to characterize KL1 (vBBceSKL1) and AH2 (vBBceSAH2),...
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Genome sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex
Download2008
Lynch, Karlene H., Shrivastava, Savita, Seed, Kimberley D., Goudie, Amanda D., Wishart, David S., Stothard, Paul, Dennis, Jonathan J.
Background The Burkholderia cepacia complex (BCC) is a versatile group of Gram negative organisms that can be found throughout the environment in sources such as soil, water, and plants. While BCC bacteria can be involved in beneficial interactions with plants, they are also considered...
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2010
Dennis, Jonathan J., Stothard, Paul, Lynch, Karlene H.
Background The Burkholderia cepacia complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment...
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Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)
Download2015
Moore, Stephen S., Miller, Joshua M., Coltman, David W., Liao, Xiaoping, Stothard, Paul
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction...
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2007
Sawhney, Summit, Greiner, Russ, Querengesser, Lori, Shrivastava, Savita, Vogel, Hans J., Arndt, David, Macinnis, Glen D., Natalie, Zhang, Gavin E., Ying, Duggan, Tang, Peter, Amegbey, Godwin, Jewell, Kevin, Wagner, James, Clements, Tzur, Dan, Bamforth, Fiona, Young, Nelson, Miniaci, Jessica, Nikolai, Lisa, Eisner, Roman, Coutouly, Marie-Aude, Clive, Derrick, Li, Liang, Marrie, Tom, Block, David, Hau, David D., Cheng, Dean, Melisa, Gebremedhin, Stothard, Paul, Forsythe, Ian, Weljie, Alim M., Dowlatabadi, Reza, Wishart, David S., Sykes, Brian D., Fung, Chris, Knox, Craig, Jeroncic, Kevin, Mulu, Guo, Lewis, Mike, Guo, An Chi
The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles...
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2014
Bamforth, Fiona, Stothard, Paul, Peng, Fred, Sergi, Consolato, Chan, Alicia, Bahitham, Wesam, Stone, Bradley, Mason, Andrew, Liao, Xiaoping
Cholangiocellular carcinoma (CCA) of the liver was the target of more interest, recently, due mainly to its increased incidence and possible association to new environmental factors. Somatic mitochondrial DNA (mtDNA) mutations have been found in several cancers. Some of these malignancies contain...
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2011
Liao, Xiaoping, Choi, Jung-Woo, Stothard, Paul, Basu, Urmila, Sumner-Thomson, Jennifer M., Meng, Yan, Moore, Stephen S.
Background One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or...
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Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing
Download2014
Kim, Tae-Hun, Oh, Jae-Don, Han, Kwang-Jin, Choi, Jung-Woo, Choi, So-Young, Lee, Hak-Kyo, Stothard, Paul, Jeon, Heoyn-Jeong, Lee, Kyung-Tai, Lee, Jeong-Koo, Jeong, Dongkee, Kim, Namshin, Chung, Won-Hyong, Kim, Hyeong-Cheol, Liao, Xiaoping, Yang, Bokyoung, Miller, Stephen P., Lee, Sung-Jin
A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing...