Evan M. Cofer

The paper maps eQTLs in Drosophila melanogaster using an outbred panel, identifying cis and trans regulatory loci for most expressed genes and revealing non-modular gene co-expression networks.

DeepArk uses deep learning to model cis-regulatory codes in four model species, accurately predicting regulatory features and variant impacts.

AMBIENT is a NAS framework that creates accurate CNN architectures for genomic sequences with reduced computing costs.

Selene is a PyTorch-based deep learning library for biological sequences, enabling model development, training, and application for various biological data.

Deep learning rivals or beats baselines across imaging, health records, genomics and drug discovery but is not yet transformative; scarce labels, privacy and opacity remain hurdles.

Aether uses linear programming to optimally deploy cloud resources for genomics tasks, achieving cost savings and efficiency in metagenomic assembly.