Emma K. Farley

The paper benchmarks a high-efficiency prime editing platform for multiplexed dropout screening of genetic variants, identifying negative growth phenotypes for nonsense mutations and splice-disrupting synonymous mutations.

The paper identifies conserved notochord-specific enhancers of Brachyury/T/TBXT in vertebrates and shows their role in notochord expression and development.

The paper identifies notochord enhancers in Ciona robusta and shows that Zic and ETS sites, along with other factors, regulate enhancer activity through conserved grammar.

EUGENe is a FAIR Python toolkit for deep learning analysis of regulatory sequences, offering modular tools for data handling, model training, and evaluation.

The paper shows that optimizing low-affinity ETS binding sites in the ZRS enhancer causes limb development defects, with severity increasing with higher affinity gains.

The paper identifies ETS affinity-optimizing SNVs in heart enhancers that disrupt development and contribute to cardiac traits in Ciona and human iPSC-CMs.