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 …

Sequencing technologies have placed a wide range of genomic analyses within the
capabilities of many laboratories. However, sequencing costs often set limits to the amount …

Annotating the molecular basis of human disease remains an unsolved challenge, as 93%
of disease loci are non-coding and gene-regulatory annotations are highly incomplete …

Abstract The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory
information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays …

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 …

Abstract The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN. itps. ncku. edu.
tw/) is an effective resource for predicting regulatory elements and reconstructing …

Chromatin is dynamically reorganized when DNA replication forks are challenged. However,
the process of epigenetic reorganization and its implication for fork stability is poorly …

Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1,
NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually …

YAP/TAZ are nuclear effectors of the Hippo pathway regulating organ growth and
tumorigenesis. Yet, their function as transcriptional regulators remains underinvestigated. By …

Gene regulatory elements are central drivers of phenotypic variation and thus of critical
importance towards understanding the genetics of complex traits. The Functional Annotation …