Ryan Z. Friedman

This study identifies functional non-coding variants associated with orofacial cleft by combining GWAS, reporter assays, and stem cell modeling.

This paper introduces two tools to infer genetic requirements from single-cell sequencing data of perturbed embryos, revealing new roles for transcription factors in zebrafish development.

The paper uses active learning to improve models of enhancer and silencer activities in mouse retina, achieving better discrimination between functionally distinct TF binding sites.

The paper examines how different pathogenic variants in the CRX gene affect cis-regulatory elements in photoreceptors, showing overlapping enhancer effects and distinct silencer impacts.

The paper shows CRX binding sites can act as enhancers or silencers based on sequence context, with negative homotypic interactions causing silencing and positive interactions or other TFBSs overcoming this.

The paper develops a method to assess the functional effects of non-coding elements in specific cell types in vivo using a Cre-dependent MPRA approach.

The paper identifies sequence features that distinguish enhancers from silencers in mouse photoreceptors by analyzing TF motifs and information content.

Co-opted transposable elements maintain conserved 3D genome structures via CTCF binding site turnover in human and mouse.