Daniel Seung Kim

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper identifies dynamic cis-regulatory elements in epidermal differentiation using multi-omic data and deep learning, revealing combinatorial motif rules linked to gene expression and polygenic skin disease.

The paper predicts genome-wide chromatin accessibility across cell types by integrating DNA sequence and gene expression data using neural networks.

Kipoi provides a framework for standardized, reusable machine learning models in genomics, enabling tasks like variant effect prediction and model benchmarking.