Journal Articles (Agricultural, Food and Nutritional Science)

2008

Santana, Andre M., Tonhati, Humberto, Greco, Anthony J., Mishra, Bina, Cai, Zhipeng, Kumar, S. T. Bharani, Tantia, Madhu S., Jones, Brittany C., Saradhi, G. Pardha, Miziara, Melissa N., Kumar, M. Aravind, Kochan, Kelli J., Goldammer, Tom, Brunner, Ronald M., Caetano, Alexandre R., Weikard, Rosemarie, Womack, James E., Mathew, Boby, Kumar, Satish, Pelai, Vanderlei A., Filho, Edson A. R., Jeong, Jooha, Prasad, Aparna, Vijh, Ramesh K., Lin, Guohui, Moore, Stephen, Galvao, Stephan R., Mariani, Paola, Grant, Jason R., Stafuzza, Nedenia B., Fornitano, Larissa C., Riggs, Penny K., Stothard, Paul, Amaral, M. Elisabete

Background The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the...

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...

2012

Wishart, David S., Cruz, Joseph, Tang, Peter, Stothard, Paul, Zhou, Jianjun, Berjanskii, Mark, Liang, Yongjie, Lu, Paul, Zhou, You, Lin, Gouhui, MacDonell, Cam

Originally released in 2005, BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains fully labeled, zoomable and searchable chromosome maps for essentially all sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level...

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...

2009

Grant, Jason, Stothard, Paul, Moore, Stephen S., Guan, Leluo, Jin, Weiwu

Background MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules which regulate gene expression by fully or partially binding to their complementary sequences in mRNAs or promoters. A large number of miRNAs and their expression patterns have been reported in human, mouse and rat....

2014

Dobrinsky, John, Zhou, Chi, Dixon, Walter T., Dyck, Michael K., Stothard, Paul, Foxcroft, George R., Tsoi, Stephen, Verstegen, John

The in vitro production of early porcine embryos is of particular scientific and economic interest. In general, embryos produced from in vitro Assisted Reproductive Technologies (ART) manipulations, such as somatic cell chromatin transfer (CT) and parthenogenetic activation (PA), are less...

2012

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),...

2012

Stothard, Paul, Arantes, Adriano S., Grant, Jason R.

Background Continued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the...

2016

Ladinig, Andrea, Stothard, Paul, Wilkinson, Jamie M., Kommadath, Arun, Plastow, Graham S., Harding, John C. S., Bao, Hua, Lunney, Joan K.

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant females causes fetal death and increased piglet mortality, but there is substantial variation in the extent of reproductive pathology between individual dams. This study used RNA-sequencing to characterize the whole...

2006

Chang, Zhan, Hassanali, Murtaza, Wishart, David S., Stothard, Paul, Woolsey, Jennifer, Guo, AnChi, Shrivistava, Savita, Knox, Craig

DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200...