Prediction of single cell gene expression

Fri, 21 Aug 2026 00:00:00 +0000

Learning the relationship between gene-regulatory regions from epigenome and transcriptome data measured for single-cell is hard. We have developed an automated Nextflow pipeline that addresses the noise and sparsity of single-cell data by aggregating individual cells into metacells. We show that analysis on metacell level often leads to superior models and we illustrate the use of these models on different datasets.

Linked publications

Laura Rumpf, Fatemeh Behjati Ardakani, Dennis Hecker, Marcel H. Schulz (2026). Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data. Bioinformatics.

DOI

A unified single-cell atlas of mouse tissue damage

Mon, 01 Jan 0001 00:00:00 +0000

Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular responses across tissues and disease states. As part of the collaborative efforts of the SFB 1531 consortium, with contributions from multiple research groups, we constructed an integrated atlas of approximately 390,000 mouse cells spanning multiple tissues (heart, carotid, lung, and brain) and disease models, including heart disease, stroke, and lung injury. To harmonize technical and biological variation across datasets, we applied scVI to integrate raw count data while effectively removing batch effects. Cell types were annotated using curated marker genes from the literature. This comprehensive atlas serves as a unique resource for a wide range of downstream analyses, including the identification of disease-specific and shared transcriptional programs, differential gene expression analysis, gene–disease association studies, dynamic transcription factor network inference, and the integration of spatial transcriptomics data.

Linked publications

Shamim Ashrafiyan, Iaroslav Kosaretskii, Marcel H. Schulz (2026). AtlasLens: Metadata-centric exploration and analysis of single-cell atlases. Preprint (BioRxiv).

URL DOI

SingleCell |

Prediction of single cell gene expression

Linked publications

A unified single-cell atlas of mouse tissue damage

Linked publications