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STEVEN REILLY, Ph.D.

SteveR

Steven Reilly was a postdoctoral fellow in the Sabeti lab. His overarching interests lie in understanding the genetic basis of human evolution and recent adaptation. He is specifically interested in furthering our understanding of non-coding variation, the main cache of human genetic diversity. To this end, he uses a two-pronged approach, creating novel machine-learning methods to predict the subset of human variants under selection that are functional, and experimental methods to characterize variants in a massively parallel fashion. His ongoing research employs CRISPR screening and synthetic DNA technologies coupled with genomic readouts to directly assess the cellular phenotypes of adaptive alleles.

Steven completed degrees in Biological Sciences and Chemistry, with an emphasis in Molecular Biology at Carnegie Mellon University. There he studied under Javier Lopez, dissecting the mechanisms of recursive splicing and its roles in proper expression of homeobox genes in Drosophila. He received his Ph.D. in 2015 from the Department of Genetics at Yale University under James Noonan. His dissertation work comparing enhancers and promoters in the developing brains of mammals uncovered thousands of putative regulatory regions with increased activity on human-lineage. His undergraduate work was supported as a Beckman School in 2007. He was awarded at NSF graduate research fellowship in 2010 and the Carolyn Slayman Thesis Prize from Yale School of Medicine in 2015. He is currently supported by an F32 fellowship from the NHGRI.

“The Reilly Lab is broadly interested in how variation in human genomes leads to the diverse array of phenotypes observed across evolution, diseases, and traits. We’re a multi-disciplinary team with a variety of backgrounds including genomics, math, biochemistry, machine-learning, and population genetics working to build new high-throughput tools for genome interpretation. To achieve such large-scale science, we’re part of many international consortia, including ENCODE, IGVF, and Zoonomia, in addition to working closely with the Sabeti Lab. Our foundational goal is answer one of the remaining fundamental questions in biology: ‘how do genetic changes lead to functional changes at the molecular, cellular, and phenotypic level?'”

SELECTED PUBLICATIONS

Evolution of gene regulation in humans.

Annual review of genomics and human genetics. 2016.
Reilly SK, Noonan JP.

Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay.

Cell. 2016.
Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Origin and evolution of developmental enhancers in the mammalian neocortex

PNAS USA. 2016.
Emera D, Yin J, Reilly SK, Gockley J, Noonan JP.

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.

Nature Communications. 2015.
Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP.

Evolutionary changes in promoter and enhancer activity during human corticogenesis.

Science. 2015.
Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP.

Origin and evolution of developmental enhancers in the mammalian neocortex.

In Review.
Emera D, Yin J, Reilly SK, Noonan JP.

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.

Nat. Communications. 2014.
Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP.

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.

Cell. 2013.
Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan- Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP,Roeder K, Devlin B, Sestan N, State MW.

The evolution of lineage-specific regulatory activities in the human embryonic limb.

Cell. 2013.
Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP.

The genomic landscape of cohesin-associated chromatin interactions.

Genome Res. 2013.
DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Genome Res. 2012.
Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP.

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