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2008

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...

2005

Ye, C., Wang, J., Li, S., Li, R., Wong, G.K.S., Ye, J., Yang, H., Han, Y., Yu, J.

We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer...

2000-09-01

Hughes, WR, Kibukawa, M, Wong, GKS, Kruglyak, L, Eberle, MA, Yang, ZY, Passey, DA, Yu, J

2005

Xia, Q., Chen, J., Dai, M., Ye, C., Wang, J., Li, S., Li, R., Zhou, Z., Ruan, J., Hu, Y., Yu, G., Yang, H., He, X., Yu, Jun, Xiang, Z., Yuan, H., Lu, C., Feng, T.

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ~6X draft genome sequence of the domestic silkworm (Bombyx mori ), SilkDB provides an integrated representation of the...

2008

Rosengarten, R.D., Sperling, E.A., Leys, S.P., Dellaporta, S.L., Moreno, M.A.

Background: Mitochondrial genomes (mtDNA) of numerous sponges have been sequenced as part of an ongoing effort to resolve the class-level phylogeny of the Porifera, as well as to place the various lower metazoan groups on the animal-kingdom tree. Most recently, the partial mtDNA of two glass...

2014

Rockwell, Geoffrey, Chartier, Ryan, Simpson, John, Dyrbye, Amy

What can we learn from the discourse around text tools? More than might be expected. The development of text analysis tools has been a feature of computing in the humanities since IBM supported Father Busa's production of the Index Thomisticus (Tasman 1957). Despite the importance of tools in the...

Fall 2016

Avis, Jillian LS

Background. Tools and resources (TRs) can help to prevent obesity in children, particularly in settings that are accessible to families and well-aligned with chronic disease prevention, such as primary care. To date, little is known about the TRs that primary care providers (PCPs) currently use...

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...

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...