Ryan Friedman

Program: Computational and Systems Biology

Current advisor: Barak A. Cohen, PhD

Undergraduate university: Washington University, 2017

Enrollment year: 2017

Research summary
Design Principles of Enhancers During Rod Photoreceptor Development

Enhancers are non-coding sequences that modulate spatiotemporal gene expression, which ultimately determines cellular identity. Although enhancers play an important role in orchestrating development and are frequently implicated in disease, we lack a fundamental understanding of the properties (design principles) that define a functional enhancer. Using rod photoreceptors as a model system, I couple Massively Parallel Reporter Assays with computational models to guide the design of future experiments. These experiments learn how cis-regulatory sequence features and interactions with trans-acting transcription factors influence enhancer activity. With an understanding of enhancer design principles, we can elucidate developmental processes, interpret non-coding disease-associated variants, and engineer useful synthetic sequences for gene therapy or bioengineering.

Graduate publications
Friedman RZ, Granas DM, Myers CA, Corbo JC, Cohen BA, White MA. 2021 Information content differentiates enhancers from silencers in mouse photoreceptors. Elife, 10():e67403. PMCID: PMC8492058

Choudhary MN, Friedman RZ, Wang JT, Jang HS, Zhuo X, Wang T. 2020 Co-opted Transposons Help Perpetuate Conserved Higher-Order Chromosomal Structures. Genome Biol, 21(1):. PMCID: PMC6979391