Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

Linking regulatory DNA elements to their target genes, which may be located hundreds of
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …

A major challenge in understanding gene regulation is the unequivocal identification of
enhancer elements and uncovering their connections to genes. We present GeneHancer, a …

Chromatin topology is intricately linked to gene expression, yet its functional requirement
remains unclear. Here, we comprehensively assessed the interplay between genome …

Long-range interactions between regulatory elements and gene promoters play key roles in
transcriptional regulation. The vast majority of interactions are uncharted, constituting a …

Genome-wide association studies (GWASs) are a valuable tool for understanding the
biology of complex human traits and diseases, but associated variants rarely point directly to …

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C
(CHi-C) experiments, which are techniques used to investigate three-dimensional genomic …

Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects …

Genetic studies promise to provide insight into the molecular mechanisms underlying type 2
diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer …