Wouter Saelens

ChromatinHD uses raw ATAC-seq data to predict gene expression and detect differential accessibility, outperforming existing methods by capturing functional accessibility changes.

SPArrOW is a pipeline for spatial transcriptomics analysis that improves data quality, provides visual quality checks, and enables interactive exploration and optimization of processing parameters.

The paper evaluates CM mapping tools, shows cell type-specific CRE interactions, and demonstrates how non-coding variants affect CM activity in a cell type-specific manner.

The paper provides single nucleus and single cell RNA-seq data from Drosophila testes to study spermatogenesis, identifying rare cell types and developmental transitions.

The paper creates a single-cell transcriptomic atlas of the adult fruit fly, identifying over 250 cell types and analyzing gene signatures and sexual dimorphism across tissues.

dyngen is a multi-modal simulation tool that enables the development and testing of new computational methods for single-cell omics analyses.

The paper introduces a generalized additive model framework for trajectory-based differential expression analysis in single-cell RNA-seq data, enabling flexible inference of within and between lineage gene expression differences.

This paper benchmarks 29 trajectory inference methods on real and synthetic datasets, identifies top-performing tools, and provides guidelines for users.

Unsupervised trajectory inference by SCORPIUS outperformed Wanderlust, Monocle and Waterfall across ten scRNA-seq datasets and predicted falling protein synthesis during dendritic cell development, validated in vivo.