Bhatia H…Ertürk A. DISCO-seq: 3D single-cell transcriptomics of intact systems Science, in review, biorXiv 2025
Integrates RNA-preserving tissue clearing with whole-organism 3D imaging and transcriptomics to deliver anatomically unbiased, single-cell–resolved gene expression readouts in intact systems.
Kadletz K…Ertürk A. LipiGo: A DNA-Lipid particle for Drug Delivery
Nature Nanotechnology, in review, biorXiv 2025
Using tissue clearing, introduces a programmable DNA–lipid nanoparticle hybrid that de-targets the liver and redirects functional mRNA delivery toward lymphoid organs, quantified by whole-body clearing and AI analysis.
Kaltenecker A…Ertürk A. Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity
Nature, in revision, biorXiv 2024
Presents MouseMapper, a foundation model-based deep-learning ensemble to segment and quantify whole-body nervous and immune system architecture in cleared mouse bodies, revealing systemic, tissue-specific remodeling in obesity.
Luo J.…Ertürk A. Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning
Nature Biotechnology. 2025 IF 41.7
ranked #1 by access in Nature Biotechnology
Introduces SCP-Nano, a tissue clearing + light-sheet + deep-learning pipeline that maps nanocarrier uptake across the entire mouse body at single-cell resolution, enabling quantitative, organism-wide delivery benchmarking.
Ertürk A. Deep 3D Histology powered by tissue clearing, omics and AI.
Nature Methods, 2024 IF 32.1
Perspective outlining how tissue clearing-based 3D histology, coupled with spatial omics and AI, can restore the missing 3D context in biology and enable comprehensive cellular maps of tissues and organs.
Rong Z.…Ertürk A. Persistence of spike protein at the skull-meninges-brain axis may contribute to the neurological sequelae of COVID-19
Cell Host & Microbe, 2024 IF 18.4
Tissue clearing reveals that spike protein can persist at the skull–meninges–brain axis and, even in isolation, induce neuroinflammation and related phenotypes, supporting a mechanistic link to post-COVID neurological sequelae.
Kaltenecker A…Ertürk A. Virtual reality-empowered deep-learning analysis of brain cells.
Nature Methods, 2024 (cover) IF 32.1
DELiVR uses virtual-reality–accelerated annotation to train deep networks for robust 3D detection of activity-linked c-Fos+ cells in cleared whole-brain datasets, outperforming prior segmentation approaches.
Kolabas I…Ertürk A. Distinct molecular profiles of skull bone marrow in health and neurological disorders
Cell 2023 IF 45.5
Tissue clearing shows the skull bone marrow as molecularly distinct and tightly coupled to brain inflammation, with disease-specific signatures that can be read out in humans (including via TSPO-PET), positioning it as a diagnostic/therapeutic target.
Mai H…Ertürk A. Whole-body cellular mapping in mouse using standard IgG antibodies.
Nature Biotechnology, 2023 (cover) IF 41.7
wildDISCO enables whole-body immunolabeling with off-the-shelf IgG antibodies (no transgenics), unlocking cellular-resolution mapping of endogenous proteins across intact cleared transparent mice.
Bhatia H….Ertürk A. Spatial proteomics in optically cleared pre-clinical & clinical specimens.
Cell, 2022 (cover) IF 45.5
DISCO-MS combines intact-specimen clearing/imaging with AI-guided, robotic ROI extraction and ultra-sensitive mass spectrometry to perform spatial proteomics directly in 3D volumes.
Todorov M…Ertürk A. Machine learning analysis of whole mouse brain vasculature.
Nature Methods, 2020 IF 33.1
VesSAP provides end-to-end staining, imaging, and deep-learning segmentation to quantify the entire brain vasculature after tissue clearing down to capillaries from terabyte-scale 3D datasets.
Zhao S…Ertürk A. Cellular and Molecular Probing of Intact Human Organs.
SHANEL introduces a permeabilization-based tissue clearing and labeling strategy that enables antibody-based 3D histology in centimeter-scale human organs (e.g., brain and kidney), paired with scalable computational analysis.
Pan C…Ertürk A. Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body
Cell, 2019 (cover) (video) IF 45.5
DeepMACT integrates whole-body clearing with deep learning to automatically detect micrometastases and quantify therapeutic antibody targeting across the entire organism in 3D.
Cai R…Ertürk A. Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections
Nature Neuroscience, 2019 (cover) IF 20.1
vDISCO boosts fluorescent protein signals for panoptic whole-body imaging, enabling mapping of long-range neuronal projections and revealing vascular connections between skull marrow and meninges in cleared transparent mice.
Pan C…Ertürk A. Shrinkage-mediated imaging of entire organs by uDISCO.
Nature Methods, 2016 (cover) IF 32.1
uDISCO pioneered shrinkage-assisted tissue clearing that preserves fluorescent proteins and renders intact organs and whole rodents transparent, enabling head-to-toe cellular imaging and unbiased whole-body screens.
