David M. Granas

Autoregulation of three yeast ribosomal protein genes by splicing inhibition

The paper shows that splicing inhibition autoregulates three yeast ribosomal protein genes by inserting introns into GFP and observing repression.

Autoregulation of RPL7B by inhibition of a structural splicing enhancer

The paper shows that RPL7B autoregulation occurs through inhibition of splicing by Rpl7 protein binding to a conserved structure in the first intron.

Active learning of enhancer and silencer regulatory grammar in a developing neural tissue

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.

Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

The paper performs a deep mutational scan of CRX variants to classify clinical variants and reveals biochemical properties of the transcriptional effector domain.

Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

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.

A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity

The paper introduces scMPRA, a single-cell assay to measure cis-regulatory activity across cell types, showing it detects cell-type specific effects of genetic variants in retinas.

Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors

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

Autoregulation of Many Yeast Ribosomal Proteins Discovered by Efficient Search for Feedback Regulation

The paper identifies autoregulation in yeast ribosomal proteins by overexpressing genes and observing repression of GFP-fused versions, finding 21 genes with at least three-fold repression.

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells

The paper uses MPRA libraries to analyze cis-regulatory grammar in mouse ESCs, finding that synthetic and genomic elements share binding site quality as a key factor, but genomic activity is better explained by binding site affinity and spacing.