Ertürk, Ali

Chayama Y, Rao NR, Perla D, Zhang Z, Reid M, Nelson S, Wen X, Ding B, Blumenfeld J, Apolonio A, Doddipalli S, Zhou H, Turhan SG, Shih PY, Brendel M, Fu YH, Ertürk A, Kolabas ZI, Huang Y, Yang AC. Physiological brain clearance architecture revealed by neuronal protein tracing. Cell. 2026 May 29:S0092-8674(26)00515-5. doi: 10.1016/j.cell.2026.04.048. Epub ahead of print. PMID: 42214342.
Kaltenecker D, Horvath I, Al-Maskari R, Chen Y, Kolabas ZI, Hoeher L, Todorov M, Minde DP, Kapoor S, Turhan SG, Kuemmerle LB, Steinke H, Wohlgemuth T, Ali M, Kofler F, Morigny P, Geppert J, Jeridi D, Wittmann B, Luo J, Shit S, Cigankova C, Kolenic VM, Gür N, Aydeniz E, Yücecan A, Ertürk M, Simons LHA, Pan C, Piraud M, Rueckert D, Rohm M, Hellal F, Elsner M, Bhatia HS, Bechmann I, Menze BH, Herzig S, Paetzold JC, Diaz MB, Ertürk A. A deep-learning framework reveals whole-body perturbations at cell level. Nature. 2026 May 20. doi: 10.1038/s41586-026-10535-2. Epub ahead of print. PMID: 42162424.

González-Gallego J, Todorov-Völgyi K, Müller SA, Antesberger S, Todorov MI, Malik R, Grimalt-Mirada R, Gonçalves CC, Schifferer M, Kislinger G, Weisheit I, Lindner B, Crusius D, Kroeger J, Borri M, Erturk A, Nelson M, Misgeld T, Lichtenthaler SF, Dichgans M, Paquet D. A fully iPS-cell-derived 3D model of the human blood-brain barrier for exploring neurovascular disease mechanisms and therapeutic interventions. Nat Neurosci. 2025 Dec 15. doi: 10.1038/s41593-025-02123-w. Epub ahead of print. PMID: 41398476.
Luo J, Molbay M, Chen Y, Horvath I, Kadletz K, Kick B, Zhao S, Al-Maskari R, Singh I, Ali M, Bhatia HS, Minde DP, Negwer M, Hoeher L, Calandra GM, Groschup B, Su J, Kimna C, Rong Z, Galensowske N, Todorov MI, Jeridi D, Ohn TL, Roth S, Simats A, Singh V, Khalin I, Pan C, Arús BA, Bruns OT, Zeidler R, Liesz A, Protzer U, Plesnila N, Ussar S, Hellal F, Paetzold J, Elsner M, Dietz H, Erturk A. Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning. Nat Biotechnol. 2025 Jan 14. doi: 10.1038/s41587-024-02528-1. Epub ahead of print. PMID: 39809933.
Molenaar A, Mallet N, Bralo M, Hoeher LJ, Schriever SC, Pathak E, Bernecker M, Müller TD, Ertürk A, Cebrian-Serrano A, Pfluger PT. A novel tamoxifen-inducible Mct8-CreERT2 mouse model for targeted studies of Mct8-expressing cells and thyroid hormone transport and function. Transgenic Res. 2025 Nov 28;34(1):50. doi: 10.1007/s11248-025-00471-8. PMID: 41310287; PMCID: PMC12660349.
Rong Z, Ertürk A, Tang Y, Mai H. Tissue Clearing and Its Application in Nanoparticle Development. Small. 2025 Feb 3:e2410032. doi: 10.1002/smll.202410032. Epub ahead of print. PMID: 39901464.
Todorov-Völgyi K, González-Gallego J, Müller SA, Todorov MI, Seker FB, Frerich S, Cernilogar FM, Schröger L, Malik R, Cao J, Llovera G, Roth S, Schillinger U, Schifferer M, Reyahi A, Crusius D, Pedro LD, Simons M, Carlsson P, Ertürk A, Liesz A, Schotta G, Plesnila N, Lichtenthaler SF, Paquet D, Dichgans M. The stroke risk gene Foxf2 maintains brain endothelial cell function via Tie2 signaling. Nat Neurosci. 2025 Dec 15. doi: 10.1038/s41593-025-02136-5. Epub ahead of print. PMID: 41398477.

Kaltenecker D, Al-Maskari R, Negwer M, Hoeher L, Kofler F, Zhao S, Todorov M, Rong Z, Paetzold JC, Wiestler B, Piraud M, Rueckert D, Geppert J, Morigny P, Rohm M, Menze BH, Herzig S, Berriel Diaz M, Ertürk A. Virtual reality-empowered deep-learning analysis of brain cells. Nat Methods. 2024 Apr 22. doi: 10.1038/s41592-024-02245-2. Epub ahead of print. PMID: 38649742.
Kuemmerle LB, Luecken MD, Firsova AB, Barros de Andrade E Sousa L, Straßer L, Mekki II, Campi F, Heumos L, Shulman M, Beliaeva V, Hediyeh-Zadeh S, Schaar AC, Mahbubani KT, Sountoulidis A, Balassa T, Kovacs F, Horvath P, Piraud M, Ertürk A, Samakovlis C, Theis FJ. Probe set selection for targeted spatial transcriptomics. Nat Methods. 2024 Nov 18. doi: 10.1038/s41592-024-02496-z. Epub ahead of print. PMID: 39558096.
Rong Z, Mai H, Ebert G, Kapoor S, Puelles VG, Czogalla J, Hu S, Su J, Prtvar D, Singh I, Schädler J, Delbridge C, Steinke H, Frenzel H, Schmidt K, Braun C, Bruch G, Ruf V, Ali M, Sühs KW, Nemati M, Hopfner F, Ulukaya S, Jeridi D, Mistretta D, Caliskan ÖS, Wettengel JM, Cherif F, Kolabas ZI, Molbay M, Horvath I, Zhao S, Krahmer N, Yildirim AÖ, Ussar S, Herms J, Huber TB, Tahirovic S, Schwarzmaier SM, Plesnila N, Höglinger G, Ondruschka B, Bechmann I, Protzer U, Elsner M, Bhatia HS, Hellal F, 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 Nov 26:S1931-3128(24)00438-4. doi: 10.1016/j.chom.2024.11.007. Epub ahead of print. PMID: 39615487.
Todorov-Völgyi K, González-Gallego J, Müller SA, Beaufort N, Malik R, Schifferer M, Todorov MI, Crusius D, Robinson S, Schmidt A, Körbelin J, Bareyre F, Ertürk A, Haass C, Simons M, Paquet D, Lichtenthaler SF, Dichgans M. Proteomics of mouse brain endothelium uncovers dysregulation of vesicular transport pathways during aging. Nat Aging. 2024 Mar 22. doi: 10.1038/s43587-024-00598-z. Epub ahead of print. PMID: 38519806.

Bartos LM, Kirchleitner SV, Kolabas ZI, Quach S, Beck A, Lorenz J, Blobner J, Mueller SA, Ulukaya S, Hoeher L, Horvath I, Wind-Mark K, Holzgreve A, Ruf VC, Gold L, Kunze LH, Kunte ST, Beumers P, Park HE, Antons M, Zatcepin A, Briel N, Hoermann L, Schaefer R, Messerer D, Bartenstein P, Riemenschneider MJ, Lindner S, Ziegler S, Herms J, Lichtenthaler SF, Ertürk A, Tonn JC, von Baumgarten L, Albert NL, Brendel M (2023). Deciphering sources of PET signals in the tumor microenvironment of glioblastoma at cellular resolution. Sci Adv. 2023 Oct 27;9(43):eadi8986. doi: 10.1126/sciadv.adi8986. Epub 2023 Oct 27. PMID: 37889970; PMCID: PMC10610915.
Cai R, Kolabas ZI, Pan C, Mai H, Zhao S, Kaltenecker D, Voigt FF, Molbay M, Ohn TL, Vincke C, Todorov MI, Helmchen F, Van Ginderachter JA, Ertürk A (2023). Whole-mouse clearing and imaging at the cellular level with vDISCO. Nat Protoc. 2023 Jan 25. doi: 10.1038/s41596-022-00788-2. Epub ahead of print. PMID: 36697871.
Kolabas ZI, Kuemmerle LB, Perneczky R, Förstera B, Ulukaya S, Ali M, Kapoor S, Bartos LM, Büttner M, Caliskan OS, Rong Z, Mai H, Höher L, Jeridi D, Molbay M, Khalin I, Deligiannis IK, Negwer M, Roberts K, Simats A, Carofiglio O, Todorov MI, Horvath I, Ozturk F, Hummel S, Biechele G, Zatcepin A, Unterrainer M, Gnörich J, Roodselaar J, Shrouder J, Khosravani P, Tast B, Richter L, Díaz-Marugán L, Kaltenecker D, Lux L, Chen Y, Zhao S, Rauchmann BS, Sterr M, Kunze I, Stanic K, Kan VWY, Besson-Girard S, Katzdobler S, Palleis C, Schädler J, Paetzold JC, Liebscher S, Hauser AE, Gokce O, Lickert H, Steinke H, Benakis C, Braun C, Martinez-Jimenez CP, Buerger K, Albert NL, Höglinger G, Levin J, Haass C, Kopczak A, Dichgans M, Havla J, Kümpfel T, Kerschensteiner M, Schifferer M, Simons M, Liesz A, Krahmer N, Bayraktar OA, Franzmeier N, Plesnila N, Erener S, Puelles VG, Delbridge C, Bhatia HS, Hellal F, Elsner M, Bechmann I, Ondruschka B, Brendel M, Theis FJ, Erturk A (2023). Distinct molecular profiles of skull bone marrow in health and neurological disorders. Cell. 2023 Aug 3:S0092-8674(23)00742-0. doi: 10.1016/j.cell.2023.07.009. Epub ahead of print. PMID: 37562402
Mai H, Luo J, Hoeher L, Al-Maskari R, Horvath I, Chen Y, Kofler F, Piraud M, Paetzold JC, Modamio J, Todorov M, Elsner M, Hellal F, Ertürk A. Whole-body cellular mapping in mouse using standard IgG antibodies. Nat Biotechnol. 2023 Jul 10. doi: 10.1038/s41587-023-01846-0. Epub ahead of print. PMID: 37430076.
Ziegler KA, Ahles A, Dueck A, Esfandyari D, Pichler P, Weber K, Kotschi S, Bartelt A, Sinicina I, Graw M, Leonhardt H, Weckbach LT, Massberg S, Schifferer M, Simons M, Hoeher L, Luo J, Ertürk A, Schiattarella GG, Sassi Y, Misgeld T Engelhardt S (2023). Immune-mediated denervation of the pineal gland underlies sleep disturbance in cardiac disease. Science. 2023 Jul 21;381(6655):285-290. doi: 10.1126/science.abn6366. Epub 2023 Jul 20. PMID: 37471539.

Bhatia HS, Brunner AD, Öztürk F, Kapoor S, Rong Z, Mai H, Thielert M, Ali M, Al-Maskari R, Paetzold JC, Kofler F, Todorov MI, Molbay M, Kolabas ZI, Negwer M, Hoeher L, Steinke H, Dima A, Gupta B, Kaltenecker D, Caliskan ÖS, Brandt D, Krahmer N, Müller S, Lichtenthaler SF, Hellal F, Bechmann I, Menze B, Theis F, Mann M, Ertürk A (2022). Spatial proteomics in three-dimensional intact specimens. Cell. 2022 Dec 22;185(26):5040-5058.e19. doi: 10.1016/j.cell.2022.11.021. PMID: 36563667.
Empl L, Chovsepian A, Chahin M, Kan WYV, Fourneau J, Van Steenbergen V, Weidinger S, Marcantoni M, Ghanem A, Bradley P, Conzelmann KK, Cai R, Ghasemigharagoz A, Ertürk A, Wagner I, Kreutzfeldt M, Merkler D, Liebscher S, Bareyre FM (2022). Selective plasticity of callosal neurons in the adult contralesional cortex following murine traumatic brain injury. Nat Commun. 2022 May 12;13(1):2659. doi: 10.1038/s41467-022-29992-0. PMID: 35551446; PMCID: PMC9098892.
Mai H, Rong Z, Zhao S, Cai R, Steinke H, Bechmann I, Ertürk A. Scalable tissue labeling and clearing of intact human organs. Nat Protoc. 2022 Oct;17(10):2188-2215. doi: 10.1038/s41596-022-00712-8. Epub 2022 Jul 20. PMID: 35859136.
Mohanta SK, Peng L, Li Y, Lu S, Sun T, Carnevale L, Perrotta M, Ma Z, Förstera B, Stanic K, Zhang C, Zhang X, Szczepaniak P, Bianchini M, Saeed BR, Carnevale R, Hu D, Nosalski R, Pallante F, Beer M, Santovito D, Ertürk A, Mettenleiter TC, Klupp BG, Megens RTA, Steffens S, Pelisek J, Eckstein HH, Kleemann R, Habenicht L, Mallat Z, Michel JB, Bernhagen J, Dichgans M, D'Agostino G, Guzik TJ, Olofsson PS, Yin C, Weber C, Lembo G, Carnevale D, Habenicht AJR (2022). Neuroimmune cardiovascular interfaces control atherosclerosis. Nature. 2022 May;605(7908):152-159. doi: 10.1038/s41586-022-04673-6. Epub 2022 Apr 27. PMID: 35477759.
Ramos-Vega M, Kjellman P, Todorov MI, Kylkilahti TM, Bäckström BT, Ertürk A, Madsen CD, Lundgaard I. Mapping of neuroinflammation-induced hypoxia in the spinal cord using optoacoustic imaging. Acta Neuropathol Commun. 2022 Apr 11;10(1):51. doi: 10.1186/s40478-022-01337-4. PMID: 35410629; PMCID: PMC8996517.
Schwarzmaier SM, Knarr MRO, Hu S, Ertürk A, Hellal F, Plesnila N (2022). Perfusion pressure determines vascular integrity and histomorphological quality following perfusion fixation of the brain. J Neurosci Methods. 2022 Feb 10;372:109493. doi: 10.1016/j.jneumeth.2022.109493. Epub ahead of print. PMID: 35151669.
Sun T, Li Y, Förstera B, Stanic K, Lu S, Steffens S, Yin C, Ertürk A, Megens RTA, Weber C, Habenicht A, Mohanta SK (2022). Tissue Clearing Approaches in Atherosclerosis. Methods Mol Biol. 2022;2419:747-763. doi: 10.1007/978-1-0716-1924-7_45. PMID: 35237999.

Gruber T, Pan C, Contreras RE, Wiedemann T, Morgan DA, Skowronski AA, Lefort S, De Bernardis Murat C, Le Thuc O, Legutko B, Ruiz-Ojeda FJ, Fuente-Fernández M, García-Villalón AL, González-Hedström D, Huber M, Szigeti-Buck K, Müller TD, Ussar S, Pfluger P, Woods SC, Ertürk A, LeDuc CA, Rahmouni K, Granado M, Horvath TL, Tschöp MH, García-Cáceres C (2021). Obesity-associated hyperleptinemia alters the gliovascular interface of the hypothalamus to promote hypertension. Cell Metab. 2021 Apr 30:S1550-4131(21)00173-X. doi: 10.1016/j.cmet.2021.04.007. Epub ahead of print. PMID: 33951475.
Molbay M, Kolabas ZI, Todorov MI, Ohn TL, Ertürk A. A guidebook for DISCO tissue clearing. Mol Syst Biol. 2021 Mar;17(3):e9807. doi: 10.15252/msb.20209807. PMID: 33769689; PMCID: PMC7995442.
Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. Nat Rev Methods Primers. 2021;1(1):84. doi: 10.1038/s43586-021-00080-9. Epub 2021 Dec 16. PMID: 35128463; PMCID: PMC8815095.

Schoppe O, Pan C, Coronel J, Mai H, Rong Z, Todorov MI, Müskes A, Navarro F, Li H, Ertürk A, Menze BH (2020). Deep learning-enabled multi-organ segmentation in whole-body mouse scans. Nat Commun. 2020 Nov 6;11(1):5626. doi: 10.1038/s41467-020-19449-7. PMID: 33159057; PMCID: PMC7648799.
Todorov MI, Paetzold JC, Schoppe O, Tetteh G, Shit S, Efremov V, Todorov-Völgyi K, Düring M, Dichgans M, Piraud M, Menze B, Ertürk A (2020). Machine learning analysis of whole mouse brain vasculature. Nat Methods. 2020 Mar 11. doi: 10.1038/s41592-020-0792-1. [Epub ahead of print]
Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ (2020). Tissue clearing and its applications in neuroscience. Nat Rev Neurosci. 2020 Jan 2. doi: 10.1038/s41583-019-0250-1. [Epub ahead of print]
Zhao S, Todorov MI, Cai R, Maskari RA, Steinke H, Kemter E, Mai H, Rong Z, Warmer M, Stanic K, Schoppe O, Paetzold JC, Gesierich B, Wong MN, Huber TB, Duering M, Bruns OT, Menze B, Lipfert J, Puelles VG, Wolf E, Bechmann I, Ertürk A (2020). Cellular and Molecular Probing of Intact Human Organs. Cell. 2020 Feb 20;180(4):796-812.e19. doi: 10.1016/j.cell.2020.01.030. Epub 2020 Feb 13.
Zhou H, Cai R, Quan T, Liu S, Li S, Huang Q, Ertürk A, Zeng S (2020). 3D high resolution generative deep-learning network for fluorescence microscopy imaging. Opt Lett. 2020 Apr 1;45(7):1695-1698. doi: 10.1364/OL.387486.

Pan C, Schoppe O, Parra-Damas A, Cai R, Todorov MI, Gondi G, von Neubeck B, Böğürcü-Seidel N, Seidel S, Sleiman K, Veltkamp C, Förstera B, Mai H, Rong Z, Trompak O, Ghasemigharagoz A, Reimer MA, Cuesta AM, Coronel J, Jeremias I, Saur D, Acker-Palmer A, Acker T, Garvalov BK, Menze B, Zeidler R, Ertürk A (2019). Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body. Cell. 2019 Dec 12;179(7):1661-1676.e19. doi: 10.1016/j.cell.2019.11.013.
Parhizkar S, Arzberger T, Brendel M, Kleinberger G, Deussing M, Focke C, Nuscher B, Xiong M, Ghasemigharagoz A, Katzmarski N, Krasemann S, Lichtenthaler SF, Müller SA, Colombo A, Monasor LS, Tahirovic S, Herms J, Willem M, Pettkus N, Butovsky O, Bartenstein P, Edbauer D, Rominger A, Ertürk A, Grathwohl SA, Neher JJ, Holtzman DM, Meyer-Luehmann M, Haass C (2019). Loss of TREM2 function increases amyloid seeding but reduces plaque-associated ApoE. Nat Neurosci. 2019 Jan 7. doi: 10.1038/s41593-018-0296-9. [Epub ahead of print]

Cai R, Pan C, Ghasemigharagoz A, Todorov MI, Förstera B, Zhao S, Bhatia HS, Parra-Damas A, Mrowka L, Theodorou D, Rempfler M, Xavier ALR, Kress BT, Benakis C, Steinke H, Liebscher S, Bechmann I, Liesz A , Menze B, Kerschensteiner M, Nedergaard M, Ertürk A (2018). Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections. Nat Neurosci. 2018 Dec 31. doi: 10.1038/s41593-018-0301-3. [Epub ahead of print]
Mano T, Albanese A, Dodt HU, Ertürk A, Gradinaru V, Treweek JB, Miyawaki A, Chung K, Ueda HR (2018). Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy. J Neurosci. 2018 Oct 31;38(44):9330-9337. doi: 10.1523/JNEUROSCI.1677-18.2018.
Mattugini N, Merl-Pham J, Petrozziello E, Schindler L, Bernhagen J, Hauck SM, Götz M (2018). Influence of white matter injury on gray matter reactive gliosis upon stab

Garvalov BK, Ertürk A (2017). Seeing whole-tumour heterogeneity. Nat Biomed Eng. 2017 Oct;1(10):772-774. doi: 10.1038/s41551-017-0150-5.
Llovera G, Benakis C, Enzmann G, Cai R, Arzberger T, Ghasemigharagoz A, Mao X, Malik R, Lazarevic I, Liebscher S, Ertürk A, Meissner L, Vivien D, Haffner C, Plesnila N, Montaner J, Engelhardt B, Liesz A (2017). The choroid plexus is a key cerebral invasion route for T cells after stroke. Acta Neuropathol. 2017 Jul 31. doi: 10.1007/s00401-017-1758-y. [Epub ahead of print]

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Ertürk, Ali

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