From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
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 …
used in studying chromatin biology, but a comprehensive review of the analysis tools has …
Chromatin-state discovery and genome annotation with ChromHMM
Noncoding DNA regions have central roles in human biology, evolution, and disease.
ChromHMM helps to annotate the noncoding genome using epigenomic information across …
ChromHMM helps to annotate the noncoding genome using epigenomic information across …
Global reference map** of human transcription factor footprints
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 all organisms. Genetic variation in regulatory regions has been connected with diseases …
Identification of transcription factor binding sites using ATAC-seq
Abstract Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a
simple protocol for detection of open chromatin. Computational footprinting, the search for …
simple protocol for detection of open chromatin. Computational footprinting, the search for …
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq),
based on direct in vitro transposition of sequencing adaptors into native chromatin, as a …
based on direct in vitro transposition of sequencing adaptors into native chromatin, as a …
[HTML][HTML] An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium - Nature, 2012 - ncbi.nlm.nih.gov
The human genome encodes the blueprint of life, but the function of the vast majority of its
nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) …
nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) …
Annotation of functional variation in personal genomes using RegulomeDB
As the sequencing of healthy and disease genomes becomes more commonplace, detailed
annotation provides interpretation for individual variation responsible for normal and …
annotation provides interpretation for individual variation responsible for normal and …
Transcription factor–DNA binding: beyond binding site motifs
S Inukai, KH Kock, ML Bulyk - Current opinion in genetics & development, 2017 - Elsevier
Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
Chromatin accessibility: a window into the genome
M Tsompana, MJ Buck - Epigenetics & chromatin, 2014 - Springer
Transcriptional activation throughout the eukaryotic lineage has been tightly linked with
disruption of nucleosome organization at promoters, enhancers, silencers, insulators and …
disruption of nucleosome organization at promoters, enhancers, silencers, insulators and …
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Abstract We developed Lisa (http://lisa. cistrome. org/) to predict the transcriptional
regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input …
regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input …