Jelle Jacobs

Lack of adoption of computational gene-panel-selection tools in targeted spatial transcriptomics

This study examines the low adoption of computational gene-panel-selection tools in targeted spatial transcriptomics, finding that most researchers still use manual or vendor panels.

LipoGrid: A High-Throughput Multi-omics Perturbation Screen Dissects the Genetic Architecture of Lipid Metabolism

LipoGrid quantifies lipidomic and transcriptomic changes across 143 gene knockouts, revealing gene-lipid relationships and compensatory feedback mechanisms.

FOCUS: end-to-end preprocessing, alignment and resolution-matched integration of spatial multi-omics data

FOCUS integrates spatial multi-omics data through preprocessing, alignment, and resolution-matching, producing a unified data object compatible with scverse tools.

Multi-omics integration and batch correction using a modality-agnostic deep learning framework

This paper introduces MIMA, a deep learning framework for multi-omics integration and batch correction, which effectively removes batch effects and preserves biological information across modalities.

Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila

This study identifies TF motifs that determine enhancer sensitivity or resistance to specific co-repressors in Drosophila, revealing regulatory rules for repression mechanisms.