A. Kundaje

Flexible use of conserved motifs constrains genome access in cell type evolution.

Massively parallel characterization and predictive modelling of neuronal regulatory variation

A large-scale lentiMPRA in human excitatory neurons is performed, quantifying the impact of >46,000 naturally occurring variants across >27,000 candidate CREs near 524 disease-associated genes, establishing a large-scale functional variant catalog and providing a complementary benchmark and resource for developing and evaluating models of noncoding regulatory variation.

Architectural chromatin interactions provide a framework for context-dependent gene regulation

A biologically informed framework for classifying and interpreting chromatin interactions is developed and dual-state regulatory elements connected to these dual-state regulatory elements are enriched for developmental and signaling pathways and exhibit increased expression specificity across cell types, consistent with specialized roles in context-dependent gene regulation.

Mapping enhancer–gene regulatory interactions from single-cell data

A family of classification models, scE2G, is introduced that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues and will enable accurate mapping of enhancer–gene regulatory interactions across thousands of human cell types.

An encyclopedia of human enhancer–gene regulatory interactions

An encyclopedia of enhancer–gene regulatory interactions in the human genome is built, revealing global properties of enhancer networks, identifying differences in regulatory complexity across genes, and improving analyses linking noncoding variants to target genes and cell types for common, complex diseases.