Statistics

Abstract A major challenge in biological research today is extraction of useful information from large amount of raw biological data. We developed three tools-Cis-Find, CisGibbs and CisTree-to analyze genomic data based on conserved patterns. CisFind is used for finding common conserved patterns in multiple DNA sequences. CisGibbs and CisTree, which use CisFind as a core, are tools for cis-regulatory element discovery of the co-expressed genes and phylogenetic tree construction respectively.

Abstract Heterosis refers to the superior performance of hybrid progeny relative to their inbred parents, but the mechanisms responsible are unknown. Hybrids between the maize inbred lines B73 and Mo17 exhibit heterosis regardless of cross direction. These reciprocal hybrids differ from each other phenotypically, and 30 to 50% of their genes are differentially expressed. We identified~ 4000 expression quantitative trait loci (eQTL) that allowed us to identify markers linked to variation in expression.

Abstract The Mu transposon system of maize is highly active, with each of the, 50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar, 215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology.

The Mu transposon system of maize is highly active, with each of the~ 50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar~ 215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology.

Following the domestication of maize over the past~ 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated.

Abstract Salmonella enterica serovar enteritidis is an enteric bacterium that can contaminate chicken eggs and meat, resulting in production losses and consumer illness. To provide insight into the systemic metabolic effects of S. enteritidis infection, liver samples were harvested 10-days postinfection from broiler hens. Hepatic global gene expression levels were assessed using a chicken 44K Agilent microarray. Forty-four genes were differentially expressed at a significance level of q value< 0.05.