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Computational methods for spatial and single-cell 'omics.
We are the research group of Naveed Ishaque, Professor of Cancer Bioinformatics at Center of Digital Health, BIH at Charité - Universitätsmedizin Berlin.
We study biological heterogeneity in disease using computational approaches applied to 'omics and imaging data. Our focus is oncology, with active interests in immunology, neurodegeneration and metabolic disease.
- Spatially resolved transcriptomics: segmentation-free analysis, cell-type mapping, spatially-aware clustering, quality control and benchmarking of imaging-based SRT.
- Single-cell and multi-omics integration: linking molecular layers to resolve tumour and microenvironment heterogeneity.
- AI for histology: predicting molecular readouts and immune states from H&E images using matched spatial transcriptomics.
- Community building and engagement: we are actively involved in ELIXIR, ELIXIR-Germany/de.NBI and coordinate the SpaceHack hackathon series.
We work closely with experimental and clinical collaborators who generate large-scale, high-dimensional datasets, and we build open-source tools so others can too.
This software is part of the approved de.NBI service Spatial Transcriptomics Toolbox. Please help us improve by taking our short user survey.
| Tool | Description | Code | Publication |
|---|---|---|---|
| SSAM | Segmentation-free cell-type mapping for imaging-based spatial transcriptomics |  |
Park et al. Nature Communications (2021) |
| SSAM-lite | Lightweight SSAM implementation that can run in the browser | |
Tiesmeyer et al. Frontiers in Genetics (2022) |
| Sainsc | Segmentation-free spatial analysis at scale for sequenincing and imaging-based spatial transcriptomics | |
Müller-Bötticher et al. Small Methods (2025) |
| SpatialLeiden | Spatially-aware clustering via multiplex modularity optimisation | |
Müller-Bötticher et al. Genome Biology (2025) |
| multiSPAETI | Dimensionality reduction approach that maximises the product of variance and Moran’s I | |
Müller-Bötticher et al. Genome Biology (2025) |
| ovrlpy | Detection of cell overlap and vertical signal integrity in imaging-based SRT | |
Tiesmeyer et al. Nature Biotechnology (2026) |
| clrmappy | A tool to automatically color high dimensional data using dimensionality reduction | |
|
| SACCELERATOR | A framework to run and compare spatial clustering tools | |
Sun et al. Nature Methods (2026) |
This software is part of the approved de.NBI service Spatial Transcriptomics Toolbox. Please help us improve by taking our short user survey.
We welcome Bachelor's and Master's students for internships and thesis projects in bioinformatics, computational biology and 'omics. Open positions are listed on the lab website.
Contact: naveed.ishaque@bih-charite.de
BIH Rahel Hirsch Center, Luisenstraße 65, 10115 Berlin, Germany (Charité Campus Mitte, 6th floor). Visitor information is on the lab website.
