Lukas Mahieu

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.

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species

CREsted is a software package for modeling and designing cell type-specific enhancers using deep learning, validated across tissues and species.

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.

Decoding cnidarian cell type gene regulation

The paper identifies regulatory elements and reconstructs gene regulatory networks in cnidarian cell types using chromatin accessibility data.

GAME: Genomic API for Model Evaluation

GAME provides a standardized framework for benchmarking genomics models across tasks, enabling consistent evaluation and community contributions.