Jasper Wouters

Routine FFPE sections support clinically compatible single-nucleus transcriptomics across six human cancer types

This paper develops a workflow for single-nucleus transcriptomics from FFPE tumor samples, showing reproducible cellular composition analysis across six cancer types.

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

SCENIC+ infers enhancer-driven gene regulatory networks from single-cell multi-omics data, improving TF identification and enabling analysis of regulatory dynamics and perturbations.

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.

Analysis of long and short enhancers in melanoma cell states

The paper identifies and characterizes enhancer activity in melanoma cell states using MPRA and DeepMEL2, showing AP-1 drives MES enhancers and SOX/MITF influence MEL enhancers.

Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning

The paper uses a deep learning model on melanoma genomes to prioritize enhancer mutations by analyzing allelic imbalance in chromatin accessibility and gene expression.

Cross-species analysis of melanoma enhancer logic using deep learning

The paper uses deep learning to analyze enhancer logic across species in melanoma, identifying conserved regulatory complexes and their roles.

Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching

The paper identifies an intermediate cell state in melanoma through single-cell RNA-seq and ATAC-seq, revealing a gene regulatory network that governs phenotype switching and potential therapeutic targets.

Cis-topic modelling of single cell epigenomes

The paper introduces cisTopic, a probabilistic framework for discovering cis-regulatory topics and cell states from single-cell epigenomics data, and validates its findings using RNA-seq co-expression networks and perturbation experiments.

SCENIC: Single-Cell Regulatory Network Inference And Clustering

Building gene regulatory networks from scRNA-seq and clustering cells on them identifies stable states robustly to batch effects, applied to mouse and human brain and to melanoma.