Prof. Dr. Ali Maximilian Ertürk

Primary research focus: Cellular & Systems Neuroscience

Second research focus: Digital Biology (In Silico Neuroscience) & AI-driven Discovery Platforms

Third research focus: Translational Biomedical Neuroscience (Neurodegeneration, Cancer, Infection)

Keywords: Whole-organ/whole-body tissue clearing (DISCO, SHANEL), light-sheet microscopy, cell-level 3D imaging, spatial multi-omics, AI/ML, digital twins, neurodegeneration, immunology, delivery, gene editors

Bullet-point focus (what we do)

• Neuroscience at scale: brain-wide and body-wide mapping of cells, circuits, vasculature, immune interfaces, and disease spread—without sectioning. 
• Cell-level 3D imaging of intact systems: tissue clearing + light-sheet pipelines enabling comprehensive, atlas-registered quantification across organs and whole organisms. 
• Single-cell molecular readouts in 3D: integrating spatial proteomics and next-generation 3D single-cell transcriptomics with imaging to connect phenotype ↔ mechanism across intact tissues. 
• AI-native biology: deep learning to segment, classify, and interpret hundreds of millions of cells—turning cleared-tissue datasets into reusable, queryable “biological maps.” 
• Digital biology / in silico experimentation: building predictive models that let us test hypotheses computationally first, prioritize experiments, and reduce animal use by maximizing information per specimen. 
• Precision targeting & intervention: quantitative whole-body readouts for cell-level targeting nanocarriers and gene editors, linking biodistribution to efficacy and safety in a systems context. 

Brief research description

At the Ertürk Lab, we build digital biology platforms by fusing cell-level 3D imaging of intact organs and whole organisms with spatial multi-omics and AI. Our tissue clearing technologies (including the DISCO ecosystem and SHANEL) and light-sheet imaging pipelines generate comprehensive, atlas-registered maps of cells, circuits, vasculature, and disease processes—capturing biology in its native 3D context rather than in thin sections. We then integrate 3D spatial proteomics and emerging 3D single-cell transcriptomic approaches with scalable deep learning, transforming massive datasets into computational models that support in silico experimentation: testing ideas digitally, prioritizing the most informative experiments, and helping reduce animal use by extracting maximal insight per study. Finally, we translate these capabilities into discovery and preclinical applications, including quantitative, whole-body evaluation of cell-targeting nanocarriers and gene editors—linking delivery, mechanism, and outcome across the entire organism. Scientists who are excited about building the next era of AI-native, systems-level neuroscience and digital biomedicine are warmly encouraged to connect and collaborate. 

GSN Students and Alumni: Eva Küsters, Dr. Mayar Ali, Dr. Chenchen Pan, Dr. Ruiyao Cai, Dr. Mihail Todorov, Dr. Ilgin Kolabas

Selected publications: 

• Luo J.…Ertürk A. Deep Learning for Nanocarriers at single cell level. Nature Biotech. 2025 (ranked #1 by access in NBT)

• Ertürk A. Deep 3D Histology powered by tissue clearing, omics and AI. Nature Methods, 2024

•Rong Z.…Ertürk A. SARS-CoV-2 Spike Protein drives long COVID… Cell Host & Microbe, 2024 (3^rd in 360K papers)

• Kaltenecker A…Ertürk A. Virtual reality and deep learning for brain…, Nature Methods, 2024 (cover)

• Kolobas I…Ertürk A. Multi-omics and 3D-imaging reveal bone heterogeneity… Cell 2023 (GSN Student)

• Mai H…Ertürk A. Whole mouse body histology using IgGs. (biorxiv in top 0.05%) Nature Biotech, 2023 (cover)

• Bhatia...Ertürk A. Spatial proteomics in optically cleared pre-clinical & clinical specimens, Cell, 2022 (cover)

• Todorov M…Ertürk A. Machine learning analysis of whole mouse brain vasculature. Nature Methods, 2020 (GSN Student)

• Zhao S…Ertürk A. Cellular and Molecular Probing of Intact Human Organs. Cell, 2020 (video)

• Pan C…Ertürk A. Deep learning reveals cancer metastasis & therapeutic antibody… Cell, 2019 (cover) (video) (GSN Student)

• Cai R…Ertürk A. Panoptic imaging of transparent mice reveals… Nature Neuroscience, 2019 (cover) (GSN Student)

• Pan C…Ertürk A. Shrinkage-mediated imaging of entire organs by uDISCO. Nature Methods, 2016 (cover)  (GSN Student)