Got your own (mouse brain-) 3D data from clearing and light sheet imaging, but no idea how to tackle the analysis? We have just the solution for you in Munich: A two-day course on deep learning and VR-assisted segmentation, atlas registration, and so on! Take the course at @erturklab.bsky.social

Nature research paper: A deep-learning framework reveals whole-body perturbations at cell level go.nature.com/3Pjox61

A deep-learning framework reveals whole-body perturbations at cell level - Nature

An analysis of diet-induced obesity using MouseMapper—a suite of foundation-model-based deep-learning algorithms—identifies structural alterations of the infraorbital branch of the trigeminal ganglia.

go.nature.com

MouseMapper An imaging-omics workflow of whole-mouse analysis Up to single-cell resolution!👹 vDISCO WildDISCO whole-mouse optical clearing #SpatialProteomics Trigeminal ganglia VR annotation of major organs, peripheral nerve & Mφ @erturklab.bsky.social Nature 2026 www.nature.com/articles/s41...

Our recent work in @Nature, MouseMapper uses foundation-model AI, mapping perturbations in mouse body cell-by-cell, revealed unexpected facial nerve damage. Proud to see >75K accesses & >60 news stories in the first week. Paper->> www.nature.com/articles/s41... Next www.biorxiv.org/content/10.6...

Super happy to see our work published in @nature.com last week 🤩 By combining whole-body tissue clearing, light-sheet microscopy and AI, we mapped obesity-associated remodeling across the entire mouse body in 3D at cellular resolution. www.nature.com/articles/s41... @erturklab.bsky.social

Beautiful work published by my new Lab at @nature.com today! @dorie00.bsky.social et al. created MouseMapper, an AI-powered tool that identifies & maps cells/tissues throughout the whole mouse body. We can now use this for different diseases, such as #LongCovid. This is AI being used the right way!

A deep-learning framework reveals whole-body perturbations at cell level @nature.com @erturklab.bsky.social @dorie00.bsky.social www.nature.com/articles/s41...

🧠 Does brain aging always mean vessel loss? We found the opposite in some aged brains: maladaptive hypervascularization, linked to cognitive decline and blood-brain barrier damage. Check it out below! www.biorxiv.org/content/10.6...

RESEARCH @morignypauline.bsky.social @ondrej-kuda.bsky.social M Rohm (CAS, Helmholtz Munich) Multi-omics profiling of cancer cachexia models uncovers a multi-tissue coordinated response🧪

Multi-omics profiling of cachexia-targeted tissues reveals a spatio-temporally coordinated response to cancer - Nature Metabolism

Multi-omics profiling of diverse cancer cachexia models uncovers a multi-tissue metabolite-coordinated response associated with disease progression and links multi-tissue one-carbon metabolism to wasting.

dlvr.it

Such a great study, combining tissue clearing, imaging and scRNA-Seq 👏🏼

Ali Maximilian Erturk@erturklab.bsky.social · 8mo ago

Most transcriptomics studies sample ~0.001% of a mouse. Which region do we choose? Often: we guess. Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq. Preprint: www.biorxiv.org/content/10.6...

Congrats to the 2025 #EFSD/@novonordisk.bsky.social A/S Programme for #DiabetesResearch in 🇪🇺 #grant recipients!🏆👏 Driving innovation across 🇪🇺 to advance knowledge & treatments for #diabetes. Excited to see the impact of your research 👉 www.europeandiabetesfoundation.org/recipients/e... #Funding

We are introducing LipiGo 🤗 A programmable DNA–lipid nanocarrier 🧬 with built-in targeting logic. It de-targets the liver and redirects mRNA delivery into lymphoid organs, enhancing therapies requiring the immune system. Precision delivery at the cell level isn't far! www.biorxiv.org/content/10.1...

How are human brain regions connected? Are the connecting axons thicker and more myelinated the longer these connecting fibers are? In our recent paper we find that indeed, they are! Read the skeetorial below ⬇️⬇️⬇️ plos.io/4mq5tOy #neuroscience #neuroskyence #whitematter #deeplearning

Excited to share that our study on the role of the liver in #CancerCachexia is out in Cell! 😀 🧬 We found that the liver plays an active role in driving weight loss in cancer through disruption of the circadian regulator REV-ERBα and secretion of catabolic hepatokines www.cell.com/cell/fulltex...

🔬 New study: The #liver plays an active role in cancer #cachexia via silenced clock gene REV-ERBα. Key step toward new therapies. 👉 Read more: t1p.de/eh136 @tum.de @diabresearch-dzd.bsky.social @dorie00.bsky.social ky.social #CancerResearch #Cachexia #Liver

1/ Why do patients with late-stage cancer lose motivation & sink into apathy? 🔥 Our new Science paper shows chronic inflammation activates a cytokine-sensing brain circuit that lowers motivation. Huge team effort: Aelita Zhu, Sarah Starosta, Pignatelli & Janowitz labs! 🧵 🔗 doi.org/10.1126/scie...

A neuroimmune circuit mediates cancer cachexia-associated apathy

Cachexia, a severe wasting syndrome associated with inflammatory conditions, often leads to multiorgan failure and death. Patients with cachexia experience extreme fatigue, apathy, and clinical depres...

doi.org

See our recent @naturebiotech.bsky.social study SCP-Nano in flow! Mapping LNPs, AAVs, and DNA nanostructures to track targeting & unseen toxicity before clinical trials 🤩. Already >190K access, the most in recent years! 👇🏼 www.nature.com/articles/s41...

As of today, the main finding of my PhD is published in the European Journal for Neuroscience! 🥳🥳 Together with Gesine Müller, we looked at hemispheric asymmetries in the mouse auditory cortex. We find layer, sex, and hemispheric differences: doi.org/10.1111/ejn.... 🧵

Hemispheric Asymmetry of Intracortical Myelin Orientation in the Mouse Auditory Cortex

We find that the right and left auditory cortex in mice are both organised in cortical columns, with asymmetric myelination in the different layers and differences between the sexes. In addition, the...

doi.org

Twitter: LNP/mRNA therapeutics and AAV-based approaches require cell-level precision to achieve success without significant toxicity to other cells. To enable this, we developed SCP-Nano: an AI and tissue-clearing-based technology for precision nanotechnology. www.nature.com/articles/s41...

I am looking for a #PhD working on this exciting project! In case you are interested in how #immunometabolism and #macrophages affect #adipose tissue function, check the link below and apply! www.immunometabolism.at/job-openings/

How does obesity reshape peripheral nerves and immune cells at the whole-body level? 🌟 Our preprint explores this using an AI-driven pipeline to precisely identify, map, and quantify these changes. Thrilled to share it with you here on BlueSky! 🦋😀 www.biorxiv.org/content/10.1...

Ali Maximilian Erturk@erturklab.bsky.social · 2y ago

Imagine seeing a disease's impact on every cell in the body. Now, you can! We introduce MouseMapper, an AI tool to reveal system-wide disease perturbations. It reveals obesity-induced changes in facial nerves & body-wide inflammation 👉🧵https://biorxiv.org/content/10.1101/2024.08.18.608300v1.full.pdf

Our new study shows that SARS-CoV-2 spike protein accumulates & persists in the body for years after infection, especially in the skull-meninges-brain axis, potentially driving long COVID. mRNA vaccines help but cannot stop it🔬🧠🦠🧵Your weekend read👇 @cellpress.bsky.social cell.com/cell-host-mi...

The SARS-CoV-2 spike protein can persist in the brain—in the skull bone marrow and meninges—to induce neurologic damage www.cell.com/cell-host-mi... open-access

Thrilled to announce that our latest work has been published in Science and featured on the front cover! www.linkedin.com/posts/scienc...

Science Magazine on LinkedIn: This light-sheet microscopy three-dimensional rendering shows a…

This light-sheet microscopy three-dimensional rendering shows a first-of-its-kind mouse whole-brain mRNA analysis at single-cell resolution. Learn more in…

linkedin.com

Hey Bluesky! As Erturklab, we are also moving to alternative social media 😉. Stay in touch to follow our work on AI and tissue clearing driven cell-level imaging of intact mouse bodies and human organs, and how we use these methods to study diseases and develop therapeutics at the cellular level.

And our lab is here, too, now. @erturklab.bsky.social Stay tuned ...

bioRxiv goes big on Bluesky: accounts for all subject categories now available (Please Reskeet) connect.biorxiv.org/news/2023/09...

Hello Bluesky 🙋🏼‍♀️