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 …

Gene regulation arises out of dynamic competition between nucleosomes, transcription
factors, and other chromatin proteins for the opportunity to bind genomic DNA. The …

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 …

The human epigenome has been experimentally characterized by thousands of
measurements for every basepair in the human genome. We propose a deep neural …

We describe a method based on a latent Dirichlet allocation model for predicting functional
effects of noncoding genetic variants in a cell-type-and/or tissue-specific way (FUN-LDA) …

Transcriptional enhancers are critical for development and phenotype evolution and are
often mutated in disease contexts; however, even in well-studied cell types, the sequence …

With the goal of mapping genomic activity, international projects have recently measured
epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations …

Whole-genome sequencing is accelerating identification of noncoding variants that disrupt
gene expression, although reports of such regulatory variants implicated in disease remain …

Experimental approaches to study tissue specificity enable insight into the nature and
organization of the cell types and tissues that constitute complex multicellular organisms …

Non-coding variants have long been recognized as important contributors to common
disease risks, but with the expansion of clinical whole genome sequencing, examples of …