We present a major update of the HOCOMOCO collection that consists of patterns describing
DNA binding specificities for human and mouse transcription factors. In this release, we …

Abstract Models of transcription factor (TF) binding sites provide a basis for a wide spectrum
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …

ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of
thousands of DNA segments with base-specific coverage values. We present a new version of …

Transcription factor (TF) binding site (TFBS) models are crucial for computational reconstruction
of transcription regulatory networks. In existing repositories, a TF often has several …

We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make this …

Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by
changes in the DNA sequence per se . Rather, covalent modifications of DNA and histones …

Background DNA methylation in promoters is closely linked to downstream gene repression.
However, whether DNA methylation is a cause or a consequence of gene repression …

The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/ ) contains
uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, …

The human genome contains millions of candidate cis-regulatory elements (cCREs) with cell-type-specific
activities that shape both health and many disease states 1 . However, we …

A systematic evaluation of how model architectures and training strategies impact genomics
model performance is needed. To address this gap, we held a DREAM Challenge where …