Koen Theunis

Modeling cis-regulatory variation in human brain enhancers across a large Parkinson's Disease cohort

The paper identifies cis-acting genetic variants affecting enhancer function in Parkinson's Disease using multi-omics data and develops models to predict their regulatory impact.

HyDrop v2: Scalable atlas construction for training sequence-to-function models

The paper introduces HyDrop v2, a microfluidic system for generating large scATAC-seq atlases, and shows its data is comparable to commercial platforms for training sequence-to-function models.

Single-cell Genome-and-Transcriptome sequencing without upfront whole-genome amplification reveals cell state plasticity of melanoma subclones

This paper introduces Gtag&T-seq, a low-cost single-cell multi-omics method that reveals cell state plasticity and treatment response in melanoma subclones.

Cell type directed design of synthetic enhancers

This study uses deep learning to design synthetic enhancers that target specific cell types in fruit flies and humans, revealing the enhancer code as optimal TF activator motifs and absence of repressor motifs.

HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

HyDrop is a droplet microfluidic platform for scATAC-seq and scRNA-seq that improves throughput and sensitivity while reducing cost.