Noncoding DNA regions have central roles in human biology, evolution, and disease.
ChromHMM helps to annotate the noncoding genome using epigenomic information across …

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect
protein/DNA-binding and histone-modification sites across an entire genome. Recent …

Transcription is regulated by transcription factor (TF) binding at promoters and distal
regulatory elements and histone modifications that control the accessibility of these …

Advanced sequencing technologies have generated a plethora of data for many chromatin
marks in multiple tissues and cell types, yet there is lack of a generalized tool for optimal …

We describe a method based on a latent Dirichlet allocation model for predicting functional
effects of noncoding genetic variants in a cell-type-and/or tissue-specific way (FUN-LDA) …

Chromatin is an essential contributor to the regulation of transcription. The two histone post-
translational modifications H3K4me3 and H3K27me3 act as an activator and repressor of …

Background Genome-wide maps of chromatin marks such as histone modifications and
open chromatin sites provide valuable information for annotating the non-coding genome …

The genomic neighborhood of a gene influences its activity, a behavior that is attributable in
part to domain-scale regulation. Previous genomic studies have identified many types of …

With the goal of map** genomic activity, international projects have recently measured
epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations …

Semi-automated genome annotation methods such as Segway take as input a set of
genome-wide measurements such as of histone modification or DNA accessibility and …