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Thermodynamic framework accurately predicts the sign of epistasis and its environment dependence for a canonical cis-regulatory element.

The seemingly simple, constitutive response of the patched/Ptch1 gene to Hedgehog signaling is in fact regulated by large batteries of context-specific Hedgehog-responsive enhancers in both fly and mouse, allowing tissue-specific tuning of the Hedgehog pathway in animal development and evolution.

Long intergenic noncoding RNA molecules (lincRNAs) are shown to have critical roles in mammalian development and physiology in vivo.

Mathematical modeling of mutagenesis data for a suite of enhancers uncovers new relationships between the binding sites of transcription factors that help in genome-wide prediction of enhancers.

Genome-wide analysis of DNA methylation and accessible chromatin shows that retinal rods and cones have distinct epigenomic features that reflect differences in their development and function.

The evolution of a butterfly mimetic phenotype is driven by modular cis-regulstory switches controlling a ‘hotspot’ gene.

Embryonic gene expression is strongly influenced by maternal genetic variation and by embryonic variation that acts in cis but not in trans.

The FGF-induced Etv transcription factors operate outside the confines of upstream signaling in lens development.

Terminal selectors reorganize postmitotic neuronal chromatin to select cis-regulatory elements during 5-HT neuron maturation.

Non-coding mutations in microsatellite-instable (MSI) colorectal tumors are prevalent and activate cancer-specific enhancers, thereby disrupting gene expression control.