We have created the Functional Element SNPs Database (FESD) that categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. In the FESD, the human genic regions were divided into 10 different functional elements, such as promoter regions, CpG islands, 5'-untranslated regions (5'-UTRs), translation start sites, sp...

Abstract Background Setaria italica is the second-most widely planted species of millets in world and an important model grain crop for research C4 photosynthesis abiotic stress tolerance. Through three genomes assembly annotation efforts, all were based on next generation sequencing technology, which limited genome continuity. Results Here we report a high-quality whole-genome new cultivar Hua...

The hypomethylated fraction of plant genomes is usually enriched in genes and can be selectively cloned using methylation filtration (MF). Therefore, MF has been used as a gene enrichment technology in sorghum and maize, where gene enrichment was proportional to genome size. Here we apply MF to a broad variety of plant species spanning a wide range of genome sizes. Differential methylation of g...

Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously bia...

An experimental plan for an exhaustive determination of genic variation at structural gene loci is presented. In the initial steps of this program, 146 isochromosomal lines from 12 geographic populations of D. pseudoobscura were examined for allelic variation of xanthine dehydrogenase by the serial use of 4 different electrophoretic conditions and a head stability test. The 5 criteria revealed ...

background : cryptosporidium parvum is a ubiquitous protozoan, which develops within the microvillous membrane of enterocytes in a wide variety of vertebrates, including man. cryptosporidiosis is an important parasite causing severe diseases in the immunodeficient people especially aids patients. cryptosporidiosis has been also reported as a com-mon serious primary cause of outbreaks of diarrhe...

This paper describes the system that we submitted to the “Learning Language in Logic” Challenge of extracting directed genic interactions from sentences in Medline abstracts. The system uses Markov Logic, a framework that combines log-linear models and First Order Logic, to create a set of weighted clauses which can classify pairs of gene named entities as genic interactions. These clauses are ...