Wouter Jozef L Saelens

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Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity(1). However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Liv ...

Background: Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify ...

Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw a ...

Although several mouse and human adipose SVF cellular subpopulations have by now been identified, we still lack an understanding of the cellular and functional variability of adipose stem and progenitor cell (ASPC) populations across human fat depots. To a ...

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed ti ...

The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITEseq, single-nuclei sequencing, spatial tran ...

Trajectory inference methods have emerged as a novel class of single-cell bioinformatics tools to study cellular dynamics at unprecedented resolution. Initial development focused on adapting methods based on clustering or graph traversal, but recent advanc ...

We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimul ...

DisCo is a deterministic droplet microfluidics tool for single-cell analysis on low cell input samples, which is demonstrated to profile individual intestinal organoids and in vivo-derived small tissues. ...

Wouter Jozef L Saelens

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Live-seq enables temporal transcriptomic recording of single cells

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Recent advances in trajectory inference from single-cell omics data

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition