Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …

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

While footprinting analysis of ATAC-seq data can theoretically enable investigation of
transcription factor (TF) binding, the lack of a computational tool able to conduct different …

With the goal of charting plant transcriptional regulatory maps (ie transcription factors (TFs),
cis-elements and interactions between them), we have upgraded the TF-centred database …

Abstract JASPAR (http://jaspar. genereg. net) is an open-access database of curated, non-
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …

With the goal of providing a comprehensive, high-quality resource for both plant transcription
factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF …

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation
in all organisms. Genetic variation in regulatory regions has been connected with diseases …

In higher eukaryotes, many genes are regulated by enhancers that are 104–106 base pairs
(bp) away from the promoter. Enhancers contain transcription-factor-binding sites (which are …

Abstract Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a
simple protocol for detection of open chromatin. Computational footprinting, the search for …

Identifying functional effects of noncoding variants is a major challenge in human genetics.
To predict the noncoding-variant effects de novo from sequence, we developed a deep …