MOTIVATION: As next generation sequencing gains a foothold in clinical genetics, there is a need for annotation tools to characterize increasing amounts of patient variant data for identifying clinically relevant mutations. While existing …
Exome sequencing in cancer is a powerful tool for identifying mutational events across the coding region of human genes. Here, we describe computational methods that use exome sequencing reads from cancer samples to identify somatic single nucleotide …
A common goal of tumor sequencing projects is finding genes whose mutations are selected for during tumor development. This is accomplished by choosing genes that have more non-synonymous mutations than expected from an estimated background mutation …
BACKGROUND: Several studies report association of alpha-4 nicotinic acetylcholine receptors (encoded by CHRNA4) with nicotine dependence (ND). A meta-analysis of genomewide linkage studies for ND implicated a single chromosomal region, which includes …
MOTIVATION: Next-generation sequencing technologies enable the identification of sequence variation in the genome and transcriptome. Differences between the reference genome and transcript libraries complicate the determination of the effect of …
PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature. They are derived by calculating the word similarity between two articles, relating articles with overlapping word content. …
The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data …
BACKGROUND: Cardiovascular development is vital for embryonic survival and growth. Early gestation embryo loss or malformation has been linked to yolk sac vasculopathy and congenital heart defects (CHDs). However, the molecular pathways that underlie …
In biomedical publications, figures and images concisely summarize a paper's experimental findings and results. Recent studies have therefore explored the use of images to assist in information retrieval (IR) in biomedicine, mostly based on mining …
DNA methylation is an important component of epigenetic modifications that influences the transcriptional machinery and is aberrant in many human diseases. Several methods have been developed to map DNA methylation for either limited regions or …