Research
Our focus is bioinformatics in cancer research, at the intersection of spatial biology, single-cell genomics and cancer genomics. Cancer is not merely an intrinsic genetic disease of the cell but an ecosystem at the tissue level. The spatial arrangement of tumour, immune and stromal cells relative to one another carries information that conventional approaches cannot capture. We therefore try to understand the causal mechanisms that determine cell and tissue structure in the tumour microenvironment, with the goal of identifying robust routes to new therapies. While most of our work is in oncology, we have active interests in immunology, neurodegeneration and metabolic disease. Alongside this we develop software for the wider field of spatial analysis, including tools that identify data-quality problems in spatial transcriptomics.
Themes
Human disease biology
We investigate the complex cellular ecosystems that underlie cancer and metabolic disorders. Our aim is to uncover causal disease mechanisms and the therapeutic vulnerabilities they expose, rather than to describe tissue composition alone.
Single-cell and spatial 'omics
We apply and advance computational frameworks that resolve cellular heterogeneity, integrate atlas-scale datasets and map tissue architecture at single-cell resolution. Much of our methods work targets imaging-based spatial transcriptomics, where cell segmentation and data quality remain unsolved problems.
Clinical image analysis
We develop AI-driven multimodal learning pipelines for histological images that bridge high-dimensional spatial 'omics with scalable clinical applications, with extensions into 3D spatial biology.
Bioinformatics methods
We build robust open-source software, quality-control frameworks and scalable algorithms to process, integrate and analyse highly multiplexed biological data. Everything we release is documented, tested and free to use.
Translational medicine
We bridge computational biology and clinical practice by translating in silico discoveries and AI predictive models into viable clinical products and actionable diagnostic strategies.
Consortia and major projects
The MOSAIC Consortium is building one of the largest spatial multi-omics datasets in oncology. By combining large-scale spatial transcriptomics, single-cell 'omics and artificial intelligence, the project maps tumour microenvironments to uncover new disease biology, discover biomarkers and accelerate personalised medicine. It unites academic and industry partners globally; Charité is a founding partner alongside Owkin, Gustave Roussy, CHUV, Universitätsklinikum Erlangen and the University of Pittsburgh.
Our role
We direct the bioinformatics strategy across the consortium and manage the computational infrastructure, ensuring standardised processing, integration and quality control of spatial and single-cell datasets from multiple centres. We also lead the core computational research projects on spatial biology and cellular interactions in non-small cell lung cancer, bladder cancer, head and neck squamous cell carcinoma and glioblastoma.
The Berlin-Dresden NAFLD/MASLD Joint Research Initiative (CRC/TRR 412) investigates metabolic dysfunction-associated steatotic liver disease. The consortium aims to move beyond one-size-fits-all treatment by uncovering the diverse pathophysiological mechanisms that drive the disease, as a basis for tailored therapeutic strategies.
Our role
We are the central bioinformatics core for the initiative: we manage the computational infrastructure, standardise data integration and establish analytical workflows for the multi-omics datasets generated across all partner institutions. We lead the computational construction of single-cell and spatial transcriptomic atlases of the liver, integrating high-resolution spatial data to map tissue architecture and cellular states across disease progression. Our own research projects model early disease dynamics and intercellular signalling networks, applying spatial algorithms and systems biology approaches to decode the metabolic and immune interactions that drive the initial stages of steatosis and fibrotic remodelling.
NURTURE is a Berlin Institute of Health Digital Health Accelerator (BIH DHA) project that addresses the severe lack of preventative therapies for pregnancy complications. It targets the root causes of conditions such as pre-eclampsia in order to prevent long-term cardiovascular and metabolic consequences for mother and child.
Our role
We are building a predictive AI platform powered by a placental organoid multi-omics pipeline. Single-cell technologies and lab-grown organoid models profile cellular responses with high precision; by integrating in vitro organoid screening data with in vivo clinical profiles, the platform overcomes traditional limitations of maternal pre-clinical trials and identifies safe, effective compounds for pregnancy-related disease before animal testing. NURTURE is our first step in translating computational research and AI platforms directly into clinical products.
ELIXIR is a European intergovernmental organisation that coordinates life-science resources, including databases, software tools and training materials, across member states so that biological data are integrated and accessible. ELIXIR Germany is delivered through de.NBI, the German Network for Bioinformatics Infrastructure.
Our role
We co-lead the ELIXIR Single-Cell Omics Community, which we co-founded; the community establishes European computational standards, benchmarking protocols, data archival frameworks and training resources for single-cell biology. We contribute to the ELIXIR Spatial2Galaxy initiative, which builds a scalable, reproducible Galaxy platform for processing and standardising spatial transcriptomics data. Within de.NBI and ELIXIR Germany we organise and participate in the BioHackathon Germany infrastructure, driving open-source development and FAIR interoperability for spatial 'omics. We founded and coordinate SpaceHack, an international hackathon series that runs as an official de.NBI BioHackathon Germany event and brings computational biologists together to develop best practices and software infrastructure for spatial transcriptomics.
Naveed Ishaque: co-founder and co-lead, ELIXIR Single-Cell Omics Community; founder and lead coordinator, SpaceHack.