Ali Max Erturk
@erturklab
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CEO of @DeepPiction, director at Helmholtz, LMU Prof. AI-based technologies for health. We’re🇩🇪🇹🇷🇭🇷🇨🇳🇮🇹🇮🇳🇸🇮🇴🇲🇨🇱🇭🇺🇧🇬🇺🇦🇷🇴🇦🇹🇹🇼🏳🌈
Munich, Germany
Joined March 2018
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🔬🧠🦠🧵👇@cellhostmicrobe
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I am excited to share preprint of our DeepMACT technology, based on vDISCO and deep learning. DeepMACT reveals cancer metastasis and antibody drug targeting at single cell level in whole mouse body in an unbiased and automated way.
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We are very excited to introduce SHANEL to map adult human organs. It employs a new tissue permeabilization chemistry for labeling and clearing. We generated the first transparent adult human brain. Developed by amazing scientists @shan_heather et al.
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😮~60% of us who had COVID still might have lingering viral spikes in our heads! Our new study reveals SARS-CoV-2 spike accumulation in the skull-meninges-brain axis & its implications in long COVID. By @zhouyi_rong @HongchengM @Sakethkapoor🔬🧠🦠🧵👇
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Many work with microglia. How many microglia are there in the brain?. We found the answer with our most advance technology:.
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Neuronal connectome of a whole adult mouse revealed by vDISCO technology
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Imagine you could stain whole adult mice with standard IgG antibodies. What you couldn't do! We present wildDISCO technology for this🤗, creating the first whole body vascular, lymphatic, and nerve atlases. By @HongchengM @jieluo692 🧵👇🏼(turn on the sound)
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I am excited to share our publication of vDISCO technology: a whole mouse body clearing & imaging method The thread below presents details of vDISCO and its biological findings. @NatureNeuro @nature. Happy New Year all! 1/12
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Discover the future of 3D-omics! Our perspective aritcle explores how tissue clearing and AI with single-cell omics could revolutionize understanding of entire organs & organisms. Read the full article:
What if we could map every cell in the body, revealing its location and molecular identity? In this @NatureMethods perspective, we discuss the new era of 3D-omics by tissue clearing and AI, called Deep 3D Histology: PDF: 🧵👇🏼
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What if we could map every cell in the body, revealing its location and molecular identity? In this @NatureMethods perspective, we discuss the new era of 3D-omics by tissue clearing and AI, called Deep 3D Histology: PDF: 🧵👇🏼
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Tissue clearing yields cool 3D images but not much molecular data. Not anymore🤗.Meet DISCO-MS enabling unbiased proteomics profiling of 3D-imaged organs. We co-developed with @labs_mann work by @HarsharanBhatia & @ADBxMPIB collab. with @fabian_theis🧵👇
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Spatial-omics goes 3D🤗! Out at Cell @CellCellPress 👉🏼 We developed DISCO-MS with @labs_mann, a spatial proteomics technology for specimens fully imaged in 3D. DISCO-MS is aided by robotics and enables the study of diseases at their early stages. �👇
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Our new study is now published at @NatureBiotech as open access. What is in it? Online Whole-Body Mouse Atlases, tertiary lymphatic structures (TLS) in the whole mouse along cancer, and more. Meet wildDISCO, thread 👇🏼.
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2/n Summary:.We found SARS-CoV-2 spike protein in the skull-meninges-brain axis in mouse models and human post-mortem tissues long after their COVID, which was associated with vascular and inflammatory changes in the brain along with neuronal damage.
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Want to use deep learning for image analysis but lack the coding skills? We introduce DELiVR, a game-changer in brain-wide cell analysis. No coding required, our Fiji Plug-in does the magic. Hats off to @Dorie00, @Rami96614090, @moritz_negwer! 🧵👇🏼 1/n
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We are very excited to share our SHANEL method making the intact human organs transparent, just published at Cell. by @shan_heather et al. See short tweetorial for details: .#clearing #imaging #3D #deeplearning #AI @CellCellPress
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2/n Summary: (Your weekend read:)).We found SARS-CoV-2 spike protein in the skull-meninges-brain axis in mouse models and human post-mortem tissues long after their COVID, which was associated with vascular, inflammatory changes in the brain along with neuronal damage.
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I am very happy to share the preprint of our VesSAP study:. A deep learning-based method to analyze whole mouse brain vasculature at the micro-capillary level. #AI #MachineLearning #brain #vessel
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I am very excited to share our paper on deep learning-based study of cancer metastasis and drug targeting, just out at Cell. Turn on the SOUND😀& hopefully enjoy the animation. More details are below 👇🏼.@CellPressNews @CellCellPress #AI #Cancer .
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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. MouseMapper showed obesity-induced changes in facial nerves & body-wide inflammation 👉🏼🧵
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Main Finding 7: Strikingly, we found spike accumulation in ~60% of people who had COVID-19 in the past long after their recovery. Thus, the identified spike in the human skull beyond the viral detection time might be a co-factor in developing long-term COVID-19 symptoms.
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I am glad that our new vDISCO article (nanobody labelling of whole mouse) made the cover of @NatureProtocols😃. Work by @MarikaRuiyao @ilginkolabas and @ChenchenPan1 et al.
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3/n Approach:.To discover all tissues that are targeted by SARS-CoV-2, we used unbiased DISCO clearing technology and mapped tissues hit by coronavirus spike vs. Influenza HA proteins (flu).
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Main Finding 1: Along with many organs, we discovered spike accumulations in the skull marrow niches and recently discovered skull-meninges connections (SMCs), revealing a new route of pathogens into the brain
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Main Finding 8: Compared to the control group, patients with Long COVID showed significantly elevated levels of neurodegenerative disease-related proteins, such as Tau protein and neurofilament light chain (NfL), in their cerebrospinal fluid.
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Very excited to share that our DELiVR method is now open access published @NatureMethods. We created a simple, brain-wide cell analysis deep learning tool, no coding needed! Fiji Plugin makes it accessible to all. by @Dorie00 @Rami96614090 @moritz_negwer
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Main Finding 3: Although COVID-19 patients' brain tissue was PCR-negative, spike protein was present in the brain, suggesting a longer half-life compared to viral particles.
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Yeni bilimsel çalışmamız online🤗. Tüm fareyi boyamak için antikorlar kullandık. Bu sayede ilk kez tüm vücut sinir ve damar bağlantı haritaları ortaya çıktı. Bu yöntem nörodejenerasyon ve kanser gibi hastalıkları daha iyi anlamamıza yardımcı olacak 💪🏻💪🏻💪🏻.
Imagine you could stain whole adult mice with standard IgG antibodies. What you couldn't do! We present wildDISCO technology for this🤗, creating the first whole body vascular, lymphatic, and nerve atlases. By @HongchengM @jieluo692 🧵👇🏼(turn on the sound)
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Main Finding 2: Critically, we found the spike protein also in the skull bone marrow niches, and meninges of people who died from COVID-19.
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Main Finding 11: The accumulation of spike protein in mice vaccinated with the BioNTech/Pfizer vaccine was significantly reduced, but not completely eliminated. This suggests that vaccination can significantly reduce the long-term effects of the virus on the nervous system,
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My pleasure to join the Ludwig Maximilian University of Munich @LMU_Muenchen as a W3 Full Professor🤓. We aim to bring our bioengineering and biotechnology solutions at @HelmholtzMunich into clinical studies at @LMU_Uniklinikum. Many thanks to the fantastic team @erturklab 🙏🏼.
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Clinical implications and future research directions.• Diagnosis: Neural injury markers in cerebrospinal fluid may be used as an important indicator for evaluating the sequelae of COVID-19. • Treatment: In the future, strategies for the removal or inhibition of spike proteins.
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Main Finding 4: Using unbiased proteomics, we found several dysregulated proteins involved in the neurodegeneration, coagulation cascades, neutrophil degranulation, and the PI3K-AKT signaling in the skull marrow, meninges, and brain of COVID-19 patients.
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Holograms 🤩 of organs we mapped are on exhibition during the celebration of 60th anniversary Helmholtz🎂@HelmholtzMunich
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Check out our VesSAP work in the current @naturemethods issue. This is a novel machine learning technology to segment complete mouse brain vasculature. It can readily be applied to any vascular data. #AI #deeplearning #machinelearning #vessel #3D
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İnsan organlarını şeffaf hale dönüştüren SHANEL teknolojisini geliştirdik. Bu çalışma hem kanser araştırmalarında hem de 3D biyoyazıcılarla böbrek, ciğer ve kalp gibi organ üretimine büyük katkılar yapabilir.
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Main Finding 10: In stroke and traumatic brain injury mouse models, the presence of spike protein exacerbates brain tissue damage, suggesting that it may enhance the susceptibility of the nervous system to further insults.
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Main Finding 6: Furthermore, injection of spike protein directly into skull marrow resulted in acute and long-term neuronal injury in mouse brain cortex tissue (observed as cell death and increased APP expression), while influenza HA did not lead to any changes.
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Main Finding 5: SARS-CoV-2 spike S1 protein i.v. injection alone was enough to trigger a wide range of proteomic changes in the skull marrow, meninges, and brain compared to the HA protein. These changes are similar to those observed in virus-infected human samples.
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Main Finding 9: The immune response triggered by the spike protein may activate the MAPK-JNK signaling pathway, leading to neuronal stress and inflammation.
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Exciting🥳 Our new study in Cell shows that our skull is a gateway for diagnosing & potentially treating brain diseases such as Alzheimer's & stroke. Imagine a future where a portable sensor on the skull can monitor brain health! @CellCellPress 🧵👇🏼with🔈
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Want to use tissue clearing but don't know where to start and have some problems? . Enjoy our Tissue Clearing Guidebook review, which is open access with step by step tips and troubleshooting info by @ilginkolabas & @MolbayM in @MolSystBiol @EMBOPress
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Very excited to see our work wildDISCO at the cover of Nature Biotechnology
The April issue is live Our cover shows an image of a whole mouse body with depth color-coding of a neuronal marker. Mai et al. present wildDISCO, a method for whole-body imaging compatible with standard IgG antibody labeling
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We are thrilled to present our new study unlocking precision in nanoparticles. Cell-level resolution imaging is key in targeted nanoparticle development. See our work on DNA Origami🧬: by @MolbayM, @shan_heather, Benni Kick et al, with @hendrik_dietz.🧵👇🏼
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1) We are super excited to present VesSAP with Bjoern Menze lab: a novel machine learning technology to segment complete mouse brain vasculature now online at @naturemethods .work by @jocpae & @MihailMuc .#AI #deeplearning #machinelearning #vessel #3D
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We are at the #SfN2022 Neuroscience meeting in San Diego with several posters and a talk😊👍🏼 .To learn more about deep learning and VR-aided cFOS mapping in whole brains, visit now (1-5 pm, Nov 12th) poster #XX4 by @Dorie00 @Rami96614090 @moritz_negwer #SFN
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Our current work as the cover of Cell. Looks a bit like 🎄doesn’t it? Happy holidays already all 🥳!.
On the cover: 90% of #cancer patients die due to #metastasis. Chenchen Pan, Ali Erturk and colleagues @erturklab develop a deep learning-based technology to detect metastasis + enable targeting by therapeutic #antibodies. #AI #deeplearning Paper @
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Our new paper describes the steps and applications of SHANEL tissue labelling, clearing, and imaging for 3D maps of human organs. In @NatureProtocols work by @HongchengM @zhouyi_rong @shan_heather. #SHANEL
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Kafatası beyin için fiziksel bir koruyucu olma göreviyle bilinir. Son çalışmmızda kafatasının çeşitli nöroinflamatuar hastalıklar sürecinde beyinle etkileşimini görmek ve izlemek için kullanılabileceğini gösteriyoruz. detaylar🧵👇1/n
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wow🤩🤩🤩, our wildDISCO @NatureBiotech paper presenting whole mouse body atlases has become its most downloaded article in 2023 (50K times) within a short time. Great follow-up studies are on the way, stay tuned 😉
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Artık ilaçları tam hedeflerine yönlendirip yan etkilerini azaltabiliriz. Takımımız bu küçük origamiyi kullanarak ilaçları doğru hedeflere, hastalıklı hücrelere göndermeyi planlıyor. Bu, hastalıklarla savaşmak için müthiş bir yol ! 🧪🧬 #Bilim #DNAOrigami.
We are thrilled to present our new study unlocking precision in nanoparticles. Cell-level resolution imaging is key in targeted nanoparticle development. See our work on DNA Origami🧬: by @MolbayM, @shan_heather, Benni Kick et al, with @hendrik_dietz.🧵👇🏼
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I am very glad to receive this honorable award from Nomis foundation to generate a human heart atlas.
👏 New grant for Ali Ertürk (@erturklab) 👏. Ertürk will collaborate with NOMIS to deliver a Human Heart Atlas: the project aims to generate vascular, cellular, and molecular maps of the human #heart by using novel technologies in #imaging and #AI. ‣
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A living transparent mouse has been a dream of many. Exciting steps have now been achieved, as reported in Science. See my and other experts' comments on this new study here:.Science: STAT: ZEIT: Study:
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Meet rDISCO (Raman 3D imaging of solvent-cleared organs) out in @NatureBiotech for multiplexed fluorescence labelling and imaging of thick tissues.
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🎉 Heyecan verici! Ekibimle birlikte DELiVR'i geliştirdik. Bu araç, beyin aktivitesini analiz etmek için yapay-zeka tabanlı bir yöntem. En güzel yanı: kullanmak için kodlama bilgisine gerek yok! Beyni keşfetmek artık daha kolay!.
Want to use deep learning for image analysis but lack the coding skills? We introduce DELiVR, a game-changer in brain-wide cell analysis. No coding required, our Fiji Plug-in does the magic. Hats off to @Dorie00, @Rami96614090, @moritz_negwer! 🧵👇🏼 1/n
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I'm very excited to receive €2 million ERC Consolidator from the EU to investigate the role of skull-meninges connections (SMCs) in brain pathologies that we described at @NatureNeuro with our vDISCO method work by @MarikaRuiyao & @ChenchenPan1 #ERCCoG
📢 Consolidator Grant results! 301 excellent researchers received #ERCCoG worth in total €600 million - to address frontier research questions, build up their teams and have far-reaching impact. .🇪🇺#EUfunded.@EUScienceInnov @EU_Commission @GabrielMariya
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Thanks to all contributors @PuellesVictor @janczogalla @.@ozumsehnaz @shan_heather.@mayarbali @ilginkolabas @SelinUlukaya @IzabelaHorvath.@NatalieKrahmer @AlionderCPC @Tobias_B_Huber @IngoBechmann @UlrikeProtzer @HarsharanBhatia @Farida80168644 Work done at the.
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@lisa_iannattone @zhouyi_rong @HongchengM @Sakethkapoor thanks very much Lisa- you are right, we did not notice in the video, but only in the tweet chain (therefore I had to remove that tweet from the chain).
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An unbiased study of whole biological systems is key to deciphering complexity. Our new paper describes the steps & applications of vDISCO whole mouse imaging in @NatureProtocols work by @MarikaRuiyao, @ilginkolabas et al. #vDISCO #clearing .🧵👇1/n
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We are pleased to see that our WildDISCO whole mouse nerve image, which was published at @NatureBiotech, has made it to one of the top images in @ScienceMagazine.
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DISCO clearing and 3D imaging reveals conserved cerebrospinal fluid drainage via meningeal lymphatic vasculature in mice and humans. Work by Jean-Leon Thomas and Anne Eichmann labs .
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At the Cover of Cell @CellCellPress.We studies aortic plaques in coronary artery disease using DISCO-MS spatial-proteomics and SHANEL clearing of human heart 🤍.@HarsharanBhatia @FurkOzturk .@shan_heather
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Our skull might be more than a physical barrier for the brain: .We found short vascular connections between skull marrow and brain surface which might carry cells and molecules into pathological brain. See our recent work for more info:
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You can read the news from our research center @HelmholtzMunich on our study:
#LongCOVID: SARS-CoV-2 Spike Protein Accumulation Linked to Long-Lasting Brain Effects. A new study by #HelmholtzMunich & @LMU_Muenchen has revealed a mechanism that may explain the neurological symptoms of Long #COVID. 👉 💡The researchers discovered
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LNP/mRNA therapeutics and AAV-based approaches require cell-level precision to achieve success without significant toxicity to other cells. To enable this, we now introduce SCP-Nano🤗 in @NatureBiotech: an AI-based technology for precision nanotechnology.
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Bilim, Türkiye’de virüsü taşıyanların şuan 1000ler seviyesinde olduğunu gösteriyor. Eğer herkes birkaç haftalık sıkı evde kalma politikası uygulamazsa, salgın aylar sürecek mecburi ev hapsine dönüşebilir ve vakalar yüz binlere varabilir. ŞİMDİ EVDE KALIN!!!.
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We are looking for an expert in light-sheet microscopy. We recently made intact human organs transparent. A grand challenge is now to make light-sheet microscope systems to image them. Please spread the word 🥳.#SHANEL #clearing #AI #imaging #humanorgans
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DISCO-MS allows molecular analysis via proteomics and AI after tissue clearing. Now we are in the game to discover the molecular underpinnings of diseases. To this end, we are expanding our proteomics team. Please apply at (distribute😊):
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If you missed👉wildDISCO enables whole mouse body labelling using standard antibodies, revealing diverse systems such as blood & lymph vessels, and nerves. We also mapped all tertiary lymphoid structures (TLS) in mice with cancer🤩:👉@NatureBiotech
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DeepMACT detects cancer metastasis and drug targeting at the cellular level, here in the lungs. Inflammation, pathogens, stem cells, and many others can also be studied using DeepMACT (vDISCO imaging + deep learning analysis): .#AI #deeplearning #cancer
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Here is a sneak preview of our vDISCO technology that will be presented at Chan Zuckerberg Biohub tomorrow (livestream). Core technology available at
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AI can 1000X multiply our work output. If you're not constantly learning and using it, you're falling behind very fast. Here are a few examples of how I use AI to gain the most valuable asset - time ⏳ in my scientific research. A thread👇 #AI #Research #TimeSaver.
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Our extensive review on tissue clearing is online now- enjoy!.
Everything you always wanted to know about tissue clearing and light sheet microscopy!.Happy new year to all co-authors 🍾.@hiroking1975 @erturklab @VivianGradinaru @AlainChedotal @PavelTomancak Philipp Keller @HHMIJanelia
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I am glad to announce that I started my new position at Helmholtz Munich today as the director of a new institute called iTERM: Institute of Tissue Engineering and Regenerative Medicine👇.
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We used DISCO clearing to reveal hypervascularization of hypothalamic nuclei in the brains of high-fat diet mice compared to chow. Collaboration with @CGarciaCaceres, @MatthiasTschop, work by @ChenchenPan1 .#DISCO #Motabolism #Vascular #VesSAP
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Heyecan verici!🥳 Yeni Cell yayınımız, kafatasımızın Alzheimer ve felç gibi beyin hastalıklarını teşhis ve tedavi etmek için bir kapı olabileceğini gösteriyor. Geleceği düşünün: Kafatasında taşınabilir bir sensör ile beyin sağlığınızı izleyebilirsiniz!
Exciting🥳 Our new study in Cell shows that our skull is a gateway for diagnosing & potentially treating brain diseases such as Alzheimer's & stroke. Imagine a future where a portable sensor on the skull can monitor brain health! @CellCellPress 🧵👇🏼with🔈
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Skull-meninges connections we recently described mediates immune cell trafficking between skull marrow and meninges opening new ways to diagnose and treat brain diseases ...@kipnislab @TheColonnaLab
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2/n Summary:.wildDISCO is a new tissue chemistry enabling uniform staining of whole bodies with conventional (150 kDa size) IgG antibodies. It reveals the first whole mouse body cellular & structural maps similar to Allen Brain Atlas only that main them at the whole mouse level.
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TBI is a major healthcare problem, permanently changing life of more than 10 million people annually, mostly the young and elderly. We recently found that TBI induces a widespread neurodegeneration and inflammation. 1/6
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During the COVID19 pandemic, we also learned that it is possible to publish research articles within weeks from start to end including in Cell & Nature Medicine. I am curious if we could learn and implement aspects of this speedy process to accelerate science in general?.
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We recently developed vDISCO to boost fluorescent protein signal and image subcellular details in intact organs and mice Want to learn vDISCO? Check below👇for demo and tips! .You have problems? Ask us, we are happy to help 😀
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All you need to know about 37 pdf pages of SHANEL paper in a 2 min animation (with sound). Have more questions- feel free to post here, we're happy to answer. #3D #imaging #AI #deeplearning @CellPressNews @CellCellPress
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New anatomical structure around the brain discovered- it may protect the brain from diverse diseases and might be targeted to alleviate neurodegeneration.Welcome 4th layer of meninges. Work by Maiken Nedergaard lab.
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Today is an exciting day for Turkey. The future of education, science, and technology will be defined. Turkey has great potential and deserves to move forward, not fall off a cliff. 🫶🏼.
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We developed scalable #AI-based imaging of human organs and mouse bodies at the cellular level. Now, we aim to aid #COVID19 research with these methods. I will present them at the Helmholtz Webinar on this Thursday, please join: @HelmholtzMunich 1/n
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Bu zamana kadar yaptığımız en iyi bilimsel çalışma ☺️.
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. MouseMapper showed obesity-induced changes in facial nerves & body-wide inflammation 👉🏼🧵
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Excited to see that our wildDISCO work made it to Science magazine news 😊.
🙋🏻♀️I am so proud to share that my news is now published in @ScienceMagazine. Prof Ali Ertürk and his team have carried out very different research.Thank you very much to @erturklab @HongchengM @jieluo692 @Muzz_Haniffa @AlainChedotal and my wonderful editors
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A news on our human organ clearing SHANEL technology and it’s potential to aid 3D-bioprinting of artificial human organs.
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Automated analysis of whole brain vasculature using machine learning. PDF: Our SFN Poster BB4 Saturday, Oct 19. work by @MihailMuc.#SFN2019 #SfN19 #AI #MachineLearning #DISCO #clearing #DeepLearning
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Great summary of our recent work on Long Covid by @EricTopol, along with other recent studies 👇🏼.
The Brain and #LongCovid.I reviewed and contextualized 2 new important German studies and their findings of persistent neuro-inflammation even after mild Covid.
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This is a game changer: Single cell proteomics by Mann lab.
We developed a scalable, quantitative and ultra-high sensitivity workflow for true single cell proteome analysis - one by one. Single cells have a stable proteome but not transcriptome. Great collaboration with @Bruker @EvosepBio @fabian_theis. Preprint:
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En son çalışmamız Türkiye’de Sözcü gazetesinde de yer buldu.
Almanya’daki gururumuz @erturklab’ün yeni çalışması #Cell dergisinde yayınlandı. Keşke #bilim insanlarımızın bu #insanlık tarihini değiştiren çalışmaları ülkelerinde yapabilmelerine olanak sağlayabilseydik😔 #gelecek #tıp #sağlık #inovasyon #kanser #SHANEL
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Neurons, microglia and vessels in the hippocampus by DISCO technology.
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Noble prize Committee missed their chances to aid the Corona pandemic by not giving the Nobel prize to developers of vaccine. That would help hundreds of millions to accept and get the vaccine.
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