Publications  2025


 
 
 
 

1. Ainatzi S, Kaufmann SV, Silbern I, Georgiev SV, Lorenz S, Rizzoli SO, Urlaub H.

Ca2+-triggered (de)ubiquitination events in synapses

Mol Cell Proteomics. 2025 Mar 13:100946. doi: 10.1016/j.mcpro.2025.100946. Online ahead of print.

 
 
 

2. Becker M, Safari N, Tetzlaff C.

The Brownian dynamics simulator PyRID for reacting
and interacting particles written in Python

Cell Rep Methods. 2025 Oct 20;5(10):101182. doi: 10.1016/j.crmeth.2025.101182. Epub 2025 Sep 18.

 
 
 

3. Bergmann C, Mousaei K, Rizzoli SO, Tchumatchenko T.

How energy determines spatial localisation
and copy number of molecules in neurons

Nat Commun. 2025 Feb 7;16(1):1424. doi: 10.1038/s41467-025-56640-0.

 
 
 

4. Bogaciu CA, Rizzoli SO.

Membrane trafficking of synaptic adhesion molecules

J Physiol. 2025 Oct;603(20):5921-5934. doi: 10.1113/JP286401. Epub 2024 Sep 25.

 
 
 

5. Caterino C, Ugolini M, Durso W, Jevdokimenko K, Groth M, Riege K, Görlach M, Fornasiero E,
Ori A, Hoffmann S, Cellerino A.

Translational Remodeling of the Synaptic Proteome During Aging

Aging Cell. 2025 Dec;24(12):e70262. doi: 10.1111/acel.70262. Epub 2025 Oct 16.

 
 
 

6. Chhabra A, Hoffmann C, Aguilar Pérez G, Korobeinikov AA, Rentsch J, Hümpfer N, Kokwaro L,
Gnidovec L, Petrović A, Wallace JN, Tromm JV, Román-Vendrell C, Johnson EC, Ranković B, Perego E,
Volpi T, Fernández-Busnadiego R, Köster S, Rizzoli SO, Ewers H, Morgan JR, Milovanović D.

Condensates of synaptic vesicles and synapsin-1 mediate actin sequestering and polymerization

EMBO J. 2025 Sep;44(18):5112-5148. doi: 10.1038/s44318-025-00516-y. Epub 2025 Aug 14.

 
 
 

7. Chouaib AA, Chang HF, Khamis OM, Alawar N, Echeverry S, Demeersseman L, Elizarova S,
Daniel JA, Tian Q, Lipp P, Fornasiero EF, Valitutti S, Barg S, Pape C, Shaib AH, Becherer U.

Highly adaptable deep-learning platform for automated detection
and analysis of vesicle exocytosis

Nat Commun. 2025 Jul 12;16(1):6450. doi: 10.1038/s41467-025-61579-3.

 
 
 

8. Chowdhury R, Krah D, Ntolkeras A, Heimbrodt A, Shaib AH.

High Precision Antibody-Free Microtubule Labeling
for Expansion Microscopy

Bio Protoc. 2025 Dec 20;15(24):e5539. doi: 10.21769/BioProtoc.5539.

 
 
 

9. Chowdhury R, Mimoso T, Chouaib AA, Mougios N, Krah D, Opazo F,
Köster S, Rizzoli SO, Shaib AH.

Microtubules as a versatile reference standard
for expansion microscopy

Commun Biol. 2025 Mar 26;8(1):499. doi: 10.1038/s42003-025-07967-3.

 
 
 

10. Dannenberg S, Reshetniak S, Mohammadinejad S, Rizzoli SO, Klumpp, S.

Geometry effects on protein mobility in a synapse

Biophys J. 2025 Aug 8:S0006-3495(25)00500-4. doi: 10.1016/j.bpj.2025.08.007. Online ahead of print.

 
 
 

11. Di Fraia D, Marino A, Lee JH, Kelmer Sacramento E, Baumgart M, Bagnoli S, Balla T,
Schalk F, Kamrad S, Guan R, Caterino C, Giannuzzi C, Tomaz da Silva P, Sahu AK, Gut H,
Siano G, Tiessen M, Terzibasi-Tozzini E, Fornasiero EF, Gagneur J, Englert C, Patil KR,
Correia-Melo C, Nedialkova DD, Frydman J, Cellerino A, Ori A.

Altered translation elongation contributes to key hallmarks
of aging in the killifish brain

Science. 2025 Jul 31;389(6759):eadk3079. doi: 10.1126/science.adk3079. Epub 2025 Jul 31.

 
 
 

12. Fries LM, Montrazi ET, Allouche-Arnon H, Opazo F, Bar-Shir A, Frydman L, Glöggler S.

Deuterated Nanopolymers for Renal and Lymphatic Imaging
via Quantitative Deuterium MRI

Nano Lett. 2025 Feb 5;25(5):1758-1764. doi: 10.1021/acs.nanolett.4c03036. Epub 2025 Jan 22.

 
 
 

13. Gallimore AR, Hepburn I, Georgiev SV, Rizzoli SO, De Schutter E.

Dynamic regulation of vesicle pools in a detailed spatial model
of the complete synaptic vesicle cycle

Sci Adv. 2025 May 30;11(22):eadq6477. doi: 10.1126/sciadv.adq6477. Epub 2025 May 28.

 
 
 

14. Georgiev SV, Rizzoli SO.


 
 
 

15. Kowald M, Bachollet, Benseler F, Steinecker M, Boll M, Kaushik,
Soykan T, Sun S, Birke R, Ilic D, Brose N, Hörnberg H, Lehmann M,
Rizzoli SO, Broichhagen J, Lipstein N.

Endogenous SNAP-Tagging of Munc13‑1 for
Monitoring Synapse Nanoarchitecture

JACS Au. 2025 May 23;5(6):2475-2490. doi: 10.1021/jacsau.4c00946.
eCollection 2025 Jun 23.

 
 
 

16. Hemandhar-Kumar N, Kluever V, Kaufmann SV, Bergmann C, Mousaei K, Tomas M,
Marrero MC, Chopra A, Hirose M, Pallas M, Sanfeliu C, Ibrahim SM, Fischer A, Outeiro TF,
Urlaub H, Tchumatchenko T, Lopez Otin C, Fornasiero EF.


 
 
 

17. Hofmann M, Becker MFP, Tetzlaff C, Mäder P.

Concept transfer of synaptic diversity from biological
to artificial neural networks

Nat Commun. 2025 Jun 2;16(1):5112. doi: 10.1038/s41467-025-60078-9.

 
 
 

18. Li W, Dasgupta A, Yang K, Wang S, Hemandhar-Kumar N, Chepyala SR,
Yarbro JM, Hu Z, Salovska B, Fornasiero EF, Peng J, Liu Y.

Turnover atlas of proteome and phosphoproteome
across mouse tissues and brain regions

Cell. 2025 Apr 17;188(8):2267-2287.e21. doi: 10.1016/j.cell.2025.02.021. Epub 2025 Mar 20.

 
 
 

19. Markusson S, Raasakka A, Schröder M, Sograte-Idrissi S, Mohammad Rahimi A,
Asadpour O, Körner H, Lodygin D, Eichel-Vogel MA, Chowdhury R, Sutinen A,
Muruganandam G, Iyer M, Cooper MH, Weigel MK, Ambiel N, Werner HB, Zuchero JB,
Opazo F, Kursula P.

Nanobodies against the myelin enzyme CNPase as tools
for structural and functional studies

J Neurochem. 2025 Jan;169(1):e16274. doi: 10.1111/jnc.16274.

 
 
 

20. Mikulasch FA, Georgiev SV, Rudelt L, Rizzoli SO, Priesemann V.

Power-law adaptation in the presynaptic vesicle cycle

Commun Biol. 2025 Apr 2;8(1):542. doi: 10.1038/s42003-025-07956-6.

 
 
 

21. Mimoso T, Korobeinikov A, Stein A, Milovanovic D, Rizzoli SO, Köster S, Reshetniak S.

Brain-derived synaptic vesicles have an intrinsic ability
to sequester tubulin

BMC Biol. 2025 Nov 14;23(1):340. doi: 10.1186/s12915-025-02464-9.

 
 
 

22. Mohar B, Michel G, Wang YZ, Hernandez V, Grimm JB, Park JY, Patel R, Clarke M,
Brown TA, Bergmann C, Gebis KK, Wilen AP, Liu B, Johnson R, Graves A, Tchumatchenko T,
Savas JN, Fornasiero EF, Huganir RL, Tillberg PW, Lavis LD, Svoboda K, Spruston N.

DELTA: a method for brain-wide measurement of synaptic
protein turnover reveals localized plasticity during learning

Nat Neurosci. 2025 May;28(5):1089-1098. doi: 10.1038/s41593-025-01923-4. Epub 2025 Mar 31.

 
 
 

23. Muth S, Moschref F, Freckmann L, Mutschall S, Hojas-Garcia-Plaza I, Bahr JN, Petrovic A,
Do TT, Schwarze V, Archit A, Weyand K, Michanski S, Maus L, Imig C, Hintze A, Brose N,
Wichmann C, Fernandez-Busnadiego R, Moser T, Rizzoli SO, Cooper BH, Pape C.

SynapseNet: Deep Learning for Automatic Synapse Reconstruction

Mol Biol Cell. 2025 Aug 28:mbcE24110519. doi: 10.1091/mbc.E24-11-0519. Online ahead of print.

 
 
 

24. Pronto JRD, Mason FE, Rog-Zielinska EA, Fakuade FE, Bülow D, Tóth M, Machwart K, Brandes P,
Wiedmann F, Kohlhaas M, Nickel A, Wolf M, Mustroph J, Vu KC, Brandenburg S, Do TQ, Siedler PJ,
Ritzenhoff K, Xue Z, Zhou X, Kestel S, Dschun O, Kyshynska O, Kensah G, Rebbeck RT, El-Essawi A,
Jebran AF, Danner BC, Baraki H, Schredelseker J, Bogeski I, Brundel BJJM, Lehnart SE, Bening C,
Kutschka I, Bremmer F, Kallenberger SM, Rizzoli SO, Knollmann BC, Neef S, Streckfuss-Bömeke K,
Schmidt C, Maack C, Voigt N.

Impaired Atrial Mitochondrial Calcium Handling in Patients With Atrial Fibrillation

Circ Res. 2025 Nov 7;137(11):1333-1352. doi: 10.1161/CIRCRESAHA.124.325658. Epub 2025 Oct 15.

 
 
 

25. Reshetniak S, Bogaciu CA, Bonn S, Brose N, Cooper BH, D’Este E, Fauth M, Fernández-Busnadiego R,
Fiosins M, Fischer A, Georgiev SV, Jakobs S, Klumpp S, Köster S, Lange F, Lipstein N, Macarrón-Palacios V, Milovanovic D, Moser T, Müller M, Opazo F, Outeiro TF, Pape C, Priesemann V, Rehling P, Salditt T, Schlüter O, Simeth N, Steinem C, Tchumatchenko T, Tetzlaff C, Tirard M, Urlaub H, Wichmann C, Wolf F, Rizzoli SO.

The synaptic vesicle cluster as a controller of pre- and postsynaptic
structure and function

J Physiol. 2025 Oct;603(20):5935-5964. doi: 10.1113/JP286400. Epub 2024 Oct 5.

 
 
 

26. Sakthivelu V, Schmitt A, Odenthal F, Ndoci K, Touet M, Shaib AH, Chihab A, Wani GA, Nieper P,
Hartmann GG, Pintelon I, Kisis I, Boecker M, Eckert NM, Iannicelli Caiaffa M, Ibruli O, Weber J,
Maresch R, Bebber CM, Chitsaz A, Lütz A, Kim Alves Carpinteiro M, Morris KM, Franchino CA,
Benz J, Pérez-Revuelta L, Soriano-Campos JA, Huetzen MA, Goergens J, Jevtic M, Jahn-Kelleter HM,
Zempel H, Placzek A, Hennrich AA, Conzelmann KK, Tumbrink HL, Hunold P, Isensee J, Werr L,
Gaedke F, Schauss A, Minère M, Müller M, Fenselau H, Liu Y, Heimsoeth A, Gülcüler Balta GS,
Walczak H, Frezza C, Jachimowicz RD, George J, Schmiel M, Brägelmann J, Hucho T, von Karstedt S,
Peifer M, Annibaldi A, Hänsel-Hertsch R, Persigehl T, Grüll H, Sos ML, Reifenberger G, Fischer M,
Adriaensen D, Büttner R, Sage J, Brouns I, Rad R, Thomas RK, Anstötz M, Rizzoli SO, Bergami M,
Motori E, Reinhardt HC, Beleggia F.

Functional synapses between neurons and small cell lung cancer

Nature. 2025 Oct;646(8086):E17. doi: 10.1038/s41586-025-09638-z.

 
 
 

27. Santos PI, García-Plaza IH, Shaib A, Rhee JS, Chouaib AA, Brose N, Rizzoli SO, Daniel J, Outeiro TF.

Glutamatergic synaptic resilience to overexpressed human alpha-synuclein

NPJ Parkinsons Dis. 2025 Aug 12;11(1):238. doi: 10.1038/s41531-025-01085-x.

 
 
 

28. Shaib AH, Chouaib AA, Chowdhury R, Altendorf J, Mihaylov D, Zhang C, Krah D, Imani V, Spencer RKW,
Georgiev SV, Mougios N, Monga M, Reshetniak S, Mimoso T, Chen H, Fatehbasharzad P, Crzan D, Saal KA,
Alawieh MM, Alawar N, Eilts J, Kang J, Soleimani A, Müller M, Pape C, Alvarez L, Trenkwalder C, Mollenhauer B, Outeiro TF, Köster S, Preobraschenski J, Becherer U, Moser T, Boyden ES, Aricescu AR, Sauer M,
Opazo F, Rizzoli SO

One-step nanoscale expansion microscopy reveals individual protein shapes

Nat Biotechnol. 2025 Sep;43(9):1539-1547. doi: 10.1038/s41587-024-02431-9. Epub 2024 Oct 9.

 
 
 

29. Torres J, Vural Z, Fiosins M, Schwarze V, Hojas-García-Plaza I, Benseler F, Bonn S, Rizzoli SO, Cooper BH,
Rhee J, Brose N, Tirard M.

Neddylation regulates the development and function of glutamatergic neurons

Commun Biol. 2025 Sep 9;8(1):1338. doi: 10.1038/s42003-025-08680-x.

 
 
 

30. Unterauer EM, Schentarra EM, Pachmayr I, Tashrin T, Kwon J, Strauss S, Jevdokimenko K,
Kowalewski R, Opazo F, Fornasiero EF, Masullo LA, Jungmann R.

Left-handed DNA for efficient highly multiplexed imaging
at single-protein resolution

Nat Commun. 2025 Oct 2;16(1):8773. doi: 10.1038/s41467-025-64228-x.

 
 
 

31. Unterauer EM, Schentarra EM, Jevdokimenko K, Boushehri SS, Marr C, Opazo F,
Fornasiero EF, Jungmann R.

Protocol for SUM-PAINT spatial proteomic imaging generating
neuronal architecture maps in rat hippocampal neurons

STAR Protoc. 2025 Mar 21;6(1):103637. doi: 10.1016/j.xpro.2025.103637. Epub 2025 Mar 5.

 
 
 

32. Woeste H, van Agen L, Müller M.

Mapping of neuronal redox conditions in a mouse model of Rett syndrome

NeuroImage: Reports. 2025 Dec; doi: 10.1016/j.ynirp.2025.100297.

 
 
 

33. Yilmaz E, Rahimi A, Münchhalfen M, Alevra M, Golmohammadi A, Tetzlaff C, Opazo F, Engels N.

Immunoglobulin divalence promotes B-cell antigen receptor cluster
scale-dependent functions

Cell Mol Immunol. 2025 Sep;22(9):1093-1108. doi: 10.1038/s41423-025-01327-1. Epub 2025 Aug 6.