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Research

Cancer Bioinformatics

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Cancer Bioinformatics Overview

Berlin

Cancer is an ecosystem. We map it.

Bioinformatics for cancer research at the intersection of spatial biology, single-cell genomics and cancer genomics.

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. 

Topics

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. 

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. 
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Naveed Ishaque obtained a M.Sc. in Bioinformatics and Systems Biology at Imperial College London and undertook his Ph.D. under Jonathan Jones at Sainsbury Laboratory in Norwich, focusing on NGS applications determining host-pathogen interactions. He joined Roland Eils’s lab at DKFZ in Heidelberg in 2013. In 2018, he moved with Roland Eils to Berlin where he leaded the Computational Oncology research group. Since September 2026, Naveed Ishaque has held the professorship in Cancer Bioinformatics at the Berlin Institute of Health at Charité (BIH). 

Prof. Naveed Ishaque, Ph.D.

Group leader Cancer Bioinformatics

BIH at Charité - Center of Digital Health
Luisenstr. 65
10117 Berlin
 

Research Group

Sophy Denker
Digital Clinician Scientist
sophy.denker@charite.de
Peiru Du
PhD Student
peiru.du@bih-charite.de
Georgios Gavriilidis
PostDoc
georgios.gavriilidis@charite.de
Kaixin Huang
PhD Student
kaixin.huang@bih-charite.de
Yiheng Jiang
PhD Student
yiheng.jiang@bih-charite.de
Timon Last
medical doctoral student
timon.last@charite.de
Alexander Malt
PhD Student
alexander.malt@bih-charite.de
Andreas Ian Lackner
Research Assistant
andreas-ian.lackner@charite.de
Fei Wang
PhD Student
fei.wang@bih-charite.de
Haoxin Wang
PhD Student
Haoxin.Wang@bih-charite.de
Yizhen Xiang
PhD Student
yizhen.xiang@bih-charite.de
Jianpeng Zhang
Medical doctoral Student
jianpeng.zhang@bih-charite.de
Oleg Berns
Medical doctoral Student
oleg.berns@charite.de

Projects

de.NBI/ELIXIR

PATH2XNET

SAGE

CRC/TR 412 MASLD

 

 

Publications

Latest News

de.KCD Industry Forum

As part of the de.KCD/de.NBI network the Center of Digital Health organizes this year’s de.KCD Industry Forum on June 18, 2026 at the Einstein Center Digital Future in Berlin. de.KCD creates a forum

SBHD 2026

Our colleagues from Northestern University in Boston are organising the 18th INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY OF HUMAN DISEASE – SBHD 2026 in Boston from June 08-10. This years Conference

Development of the European Cancer Information Portal Launched

The Berlin Institute of Health at Charité (BIH) coordinates the pan-European research initiative "EU-CiP" (European Cancer Information Portal). Supported by 12 million euros from the EU’s Horizon

SBHD 2025

The Digital Health Center once again organises the INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY OF HUMAN DISEASE – SBHD 2025 in Berlin from June 16-18. Don’t miss this opportunity to participate in a