The transcriptome describes the expression of all genes in a sample. Most studies have
investigated the differential patterns or discrimination powers of transcript expression levels …

Chromatin accessibility maps are important for the functional interpretation of the genome.
Here, we systematically analysed assay specific differences between DNase I-seq, ATAC …

Background Enhancers play a fundamental role in orchestrating cell state and development.
Although several methods have been developed to identify enhancers, linking them to their …

Motivation Identifying regulatory regions in the genome is of great interest for understanding
the epigenomic landscape in cells. One fundamental challenge in this context is to find the …

Understanding how epigenetic variation in non-coding regions is involved in distal gene-
expression regulation is an important problem. Regulatory regions can be associated to …

Background Single-cell RNA sequencing is a powerful technology to discover new cell types
and study biological processes in complex biological samples. A current challenge is to …

Background Inferring the mechanisms that drive transcriptional regulation is of great interest
to biologists. Generally, methods that predict physical interactions between transcription …

Abstract Background Elucidating the Transcription Factors (TFs) that drive the gene
expression changes in a given experiment is a common question asked by researchers. The …

Understanding the factors that underlie the epigenetic regulation of genes is crucial to
understand the gene regulatory machinery as a whole. Several experimental and …

Identifying regulatory regions in the genome is of great interest for understanding the
epigenomic landscape in cells. One fundamental challenge in this context is to find the …