Genome sequencing efforts will soon generate hundreds of millions of bases of human genomic DNA containing thousands of novel genes. In the past year, the accuracy of computational gene-finding methods has improved significantly, to the point where a reasonable approximation of the gene structures within an extended genomic region can often be predicted in advance of more detailed experimental ...

Genome sequencing efforts will soon generate hundreds of millions of bases of human genomic DNA containing thousands of novel genes. In the past year, the accuracy of computational gene-finding methods has improved significantly, to the point where a reasonable approximation of the gene structures within an extended genomic region can often be predicted in advance of more detailed experimental ...

Many economically important traits in plant breeding have low heritability or are difficult to measure. For these traits, genomic selection has attractive features and may boost genetic gains. Our goal was to evaluate alternative scenarios to implement genomic selection for yield components in soybean (Glycine max L. merr). We used a nested association panel with cross validation to evaluate th...

A genomic island (GI) is a genomic segment in a host genome, and it was transferred from donor genomes. Since genomic islands (GIs) usually contain important genes such as pathogenicity genes, the detection of GIs becomes extremely critical to medical research and industrial applications. Previous computational GI detection tools used one or a few GI-associate features, and thus they suffered t...

DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain largely unexplored. We used publicly available genome-scale DNA methylation and histone modification profiles to study their relationships among different genomic regions in human embryonic stem cells (H1), H1-derived neu...

OBJECTIVE Intramuscular fat is one of the meat quality traits that is considered in the selection strategies for Hanwoo (Korean cattle). Different methods are used to estimate the breeding value of selection candidates. In the present work we focused on accuracy of different genotype relationship matrices as described by forni and pedigree based relationship matrix. METHODS The data set inclu...

The aim of this study was to investigate the effect of different strategies for handling lowquality or missing data on prediction accuracy for direct genomic values of protein yield, mastitis and fertility using a Bayesian variable model and a GBLUP model in the Danish Jersey population. The data contained 1 071 Jersey bulls that were genotyped with the Illumina Bovine 50K chip. After prelimina...

Most ab initio gene predictors use a probabilistic sequence model, typically a hidden Markov model, to combine separately trained models of genomic signals and content. By combining separate models of relevant genomic features, such gene predictors can exploit small training sets and incomplete annotations, and can be trained fairly efficiently. However, that type of piecewise training does not...

We established a genomic model of quantitative trait with genomic additive and dominance relationships that parallels the traditional quantitative genetics model, which partitions a genotypic value as breeding value plus dominance deviation and calculates additive and dominance relationships using pedigree information. Based on this genomic model, two sets of computationally complementary but m...

Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each o...