Journal Articles (Agricultural, Food and Nutritional Science)
Items in this Collection
- 29Stothard, Paul
- 8Wishart, David S.
- 5Liao, Xiaoping
- 5Moore, Stephen S.
- 4Shrivastava, Savita
- 3Bao, Hua
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2004
Wishart, David S., Dong, Xaoli, Forsythe, Ian J., Stothard, Paul
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
Cheng, Dean, Stothard, Paul, Damaraju, Sambasivarao, Wishart, David S., Knox, Craig, Young, Nelson
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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Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life
Download2014
Liang, Guanxiang, Bao, Hua, Guan, Leluo, Griebel, Philip J., Stothard, Paul, McFadden, Thomas B., Malmuthuge, Nilusha
This study aimed to investigate the potential regulatory role of miRNAs in the development of gastrointestinal tract (GIT) during the early life of dairy calves. Rumen and small intestinal (mid-jejunum and ileum) tissue samples were collected from newborn (30 min after birth; n = 3), 7-day-old...
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The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences
Download2000
JavaScript is an object-based scripting language that can be interpreted by most commonly used Web browsers, including Netscape® Navigator® and Internet Explorer®. In conjunction with HTML form elements, JavaScript can be used to make flexible and easy-to-use applications that can be accessed by...
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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 sequence analysis of an alachlor and endosulfan degrading Pseudomonas strain W15Feb9B isolated from Ochlockonee River, Florida
Download2016
Ewida, Ayman Y. I., Stothard, Paul, Chauhan, Ashvini, Griffiths, Zabrenna, Pathak, Ashish
We recently isolated a Pseudomonas sp. strain W15Feb9B from Ochlockonee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides - Alachlor [(2-chloro-2′,6′-diethylphenyl-N (methoxymethyl)acetanilide)] and Endosulfan...
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2015
Stothard, Paul, Wang, Yining, Lin, Guohui, Wylie, Tim
Background Despite ongoing reductions in the cost of sequencing technologies, whole genome SNP genotype imputation is often used as an alternative for obtaining abundant SNP genotypes for genome wide association studies. Several existing genotype imputation methods can be efficient for this...
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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...
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Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity
Download2013
Lee, Kyung-Tai, Ahn, Sungmin, Choy, Yun H., Lee, Sang-Heon, Jang, Gul-Won, Liao, Xiaoping, Lee, Seunghwan, Lee, Sung-Yeoun, Chung, Won-Hyong, Stothard, Paul, Choi, Jung-Woo, Kim, Tae-Hun, Kim, Bumsoo, Kim, Jiwoong, Lim, Dajeong, Moore, Stephen S., Kim, Namshin
Background Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred...