The field of 3D genome organization produces large amounts of sequencing data from Hi-C
and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive …

Zebrafish, a popular organism for studying embryonic development and for modeling human
diseases, has so far lacked a systematic functional annotation program akin to those in other …

The first activation of gene expression during development (zygotic genome activation, ZGA)
is accompanied by massive changes in chromosome organization. The connection between …

Precise control of gene expression is crucial to ensure proper development and biological
functioning of an organism. Enhancers are non-coding DNA elements which play an …

Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in
single-cell genomics, mapping these patterns across whole embryos with comprehensive …

A file of nucleic acid sequences itself is not descriptive. Accompanying information
describing data, known as metadata, is important for fueling artificial intelligence and …

A large-scale collaborative effort now provides a comprehensive annotation of functional
non-coding elements in the zebrafish genome. This work serves as an essential foundation …

To enable large-scale analyses of transcription regulation in model species, we developed
DeepArk, a set of deep learning models of the cis-regulatory activities for four widely studied …

Hematopoiesis is an optimal system for studying stem cell maintenance and lineage
differentiation under physiological and pathological conditions. In vertebrate organisms …

Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation
across species, prompting concern in the field. This study delves into functional signatures of …