Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …
Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation
Precise spatio–temporal control of gene activity is essential for organismal development,
growth, and survival in a changing environment. Decisive steps in gene regulation involve …
growth, and survival in a changing environment. Decisive steps in gene regulation involve …
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
Abstract JASPAR (http://jaspar. genereg. net/) is an open-access database containing
manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six …
manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six …
JASPAR 2020: update of the open-access database of transcription factor binding profiles
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 …
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
Efficient low-cost chromatin profiling with CUT&Tag
Abstract We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …
Base-resolution models of transcription-factor binding reveal soft motif syntax
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …
An efficient targeted nuclease strategy for high-resolution map** of DNA binding sites
We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a
chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal …
chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal …
GTRD: an integrated view of transcription regulation
Abstract The Gene Transcription Regulation Database (GTRD; http://gtrd. biouml. org/)
contains uniformly annotated and processed NGS data related to gene transcription …
contains uniformly annotated and processed NGS data related to gene transcription …
Defining genome architecture at base-pair resolution
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 …
(bp) away from the promoter. Enhancers contain transcription-factor-binding sites (which are …
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 …