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Two-dimensional HRS condensates drive the assembly of flat clathrin lattices on endosomes.
Hakala, Markku, Moparthi, Satish Babu, Ganeva, Iva, Gül, Mehmet ORCID: https://orcid.org/0000-0001-5513-1866, Bernat-Silvestre, César, Marcuello, Carlos, Espadas, Javier, Colom, Adai, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274, Kukulski, Wanda, Vassilopoulos, Stéphane, Kaksonen, Marko and Roux, Aurélien
Nature Communications 12 May 2026 (In Press)

Phospholipid-driven conformational switching of HCV NS5A links protein folding to replication membrane remodeling.
Bulankina, Anna V. ORCID: https://orcid.org/0009-0003-0992-7320, Richter, Rebecca M. ORCID: https://orcid.org/0000-0002-3831-7666, Nettles, James H. ORCID: https://orcid.org/0000-0002-5683-8481, Yamane, Daisuke ORCID: https://orcid.org/0000-0003-1592-9368, Grimm, Christian, Karami, Yasaman ORCID: https://orcid.org/0000-0001-8413-2665, Stanton, Richard A. ORCID: https://orcid.org/0000-0003-4810-7002, Introini, Bianca, Hermann, Jonas, Charif, Hanaa, König, Mia S. ORCID: https://orcid.org/0009-0009-5173-1798, Stroß, Claudia, Ortiz, Cristina, Kraus, Nico ORCID: https://orcid.org/0000-0002-5162-1048, Wood, Daniel, Galceran, Facundo ORCID: https://orcid.org/0000-0001-5023-0582, Abele, Rupert ORCID: https://orcid.org/0000-0001-6899-293X, Maigret, Bernard ORCID: https://orcid.org/0000-0002-1983-1950, Schinazi, Raymond F. ORCID: https://orcid.org/0000-0002-6688-3614, Zeuzem, Stefan, Biondi, Ricardo M. ORCID: https://orcid.org/0000-0002-8873-7167, Yi, MinKyung, Tampé, Robert ORCID: https://orcid.org/0000-0002-0403-2160, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274 and Welsch, Christoph ORCID: https://orcid.org/0000-0002-1823-4863
Science Advances 12 (14): eaeb8863. 3 April 2026

DeBCR: a sparsity-efficient framework for image enhancement through a deep-learning-based solution to inverse problems.
Li, Rui ORCID: https://orcid.org/0000-0002-3085-5267, Yushkevich, Artsemi ORCID: https://orcid.org/0000-0002-8729-9281, Chu, Xiaofeng ORCID: https://orcid.org/0000-0001-6801-3949, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, Artur ORCID: https://orcid.org/0000-0003-2458-4904
Communications Engineering 5 (1): 25. 10 February 2026

Dynamic nanoscale architecture of synaptic vesicle fusion in mouse hippocampal neurons.
Kroll, Jana ORCID: https://orcid.org/0000-0003-4243-4088, Kravčenko, Uljana ORCID: https://orcid.org/0009-0004-7176-8444, Sadeghi, Mohsen ORCID: https://orcid.org/0000-0002-7698-5630, Diebolder, Christoph A. ORCID: https://orcid.org/0000-0001-7694-7362, Ivanov, Lia, Lubas, Małgorzata, Sprink, Thiemo ORCID: https://orcid.org/0000-0002-0760-6828, Schacherl, Magdalena ORCID: https://orcid.org/0000-0002-5478-2509, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274 and Rosenmund, Christian ORCID: https://orcid.org/0000-0002-3905-2444
Nature Communications 16 (1): 11131. 15 December 2025

Insights into therapeutic discovery through the Kelch domain structure of Keap1 at ambient temperature.
Yilmaz, M. ORCID: https://orcid.org/0000-0003-3346-2781, Sever, B. ORCID: https://orcid.org/0000-0003-4847-9711, Kutlu, Y. ORCID: https://orcid.org/0000-0001-5917-2550, Gül, M. ORCID: https://orcid.org/0000-0001-5513-1866, Okuducu, C. ORCID: https://orcid.org/0009-0008-8976-0204, Tavli, S. ORCID: https://orcid.org/0000-0001-9362-8013, Otsuka, M. ORCID: https://orcid.org/0000-0002-2968-3939, Fujita, M. ORCID: https://orcid.org/0000-0001-6705-4052, Haliloğlu, T. ORCID: https://orcid.org/0000-0002-1279-5803, Çiftçi, H. ORCID: https://orcid.org/0000-0002-9796-7669 and Demirci, H. ORCID: https://orcid.org/0000-0002-9135-5397
Turkish Journal of Biology 49 (3): 247-260. 26 June 2025

Penta-ALFA-tagged substrates for self-labelling tags allow signal enhancement in microscopy.
Ghosh, S. ORCID: https://orcid.org/0000-0003-1224-5008, Birke, R., Natarajan, A.K. ORCID: https://orcid.org/0000-0001-7897-708X and Broichhagen, J. ORCID: https://orcid.org/0000-0003-3084-6595
Journal of Peptide Science 31 (5): e70015. May 2025

Microscopy image reconstruction with physics-informed denoising diffusion probabilistic model.
Li, R. ORCID: https://orcid.org/0000-0002-3085-5267, Della Maggiora, G., Andriasyan, V., Petkidis, A., Yushkevich, A. ORCID: https://orcid.org/0000-0002-8729-9281, Deshpande, N., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, A. ORCID: https://orcid.org/0000-0003-2458-4904
Communications Engineering 3 (1): 186. 29 December 2024

Architecture of the Sap S-layer of Bacillus anthracis revealed by integrative structural biology.
Sogues, A. ORCID: https://orcid.org/0000-0002-5752-6009, Leigh, K. ORCID: https://orcid.org/0000-0002-6467-3330, Halingstad, E.V., Van der Verren, S.E., Cecil, A.J., Fioravanti, A. ORCID: https://orcid.org/0000-0002-4065-0839, Pak, A.J. ORCID: https://orcid.org/0000-0003-2823-6480, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Remaut, H. ORCID: https://orcid.org/0000-0002-9775-4102
Proceedings of the National Academy of Sciences of the United States of America 121 (51): e2415351121. 17 December 2024

The big chill: growth of in situ structural biology with cryo-electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
QRB Discovery 5 : e10. 13 December 2024

Molecular architecture of synaptic vesicles.
Kravčenko, U. ORCID: https://orcid.org/0009-0004-7176-8444, Ruwolt, M., Kroll, J. ORCID: https://orcid.org/0000-0003-4243-4088, Yushkevich, A. ORCID: https://orcid.org/0000-0002-8729-9281, Zenkner, M., Ruta, J. ORCID: https://orcid.org/0009-0007-0524-6885, Lotfy, R., Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630, Rosenmund, C. ORCID: https://orcid.org/0000-0002-3905-2444, Liu, F. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Proceedings of the National Academy of Sciences of the United States of America 121 (49): e2407375121. 3 December 2024

Solving the inverse problem of microscopy deconvolution with a residual Beylkin-Coifman-Rokhlin neural network.
Li, R. ORCID: https://orcid.org/0000-0002-3085-5267, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, A.
Lecture Notes in Computer Science 15133 : 378-395. 1 November 2024

Structure of tetrameric forms of the serotonin-gated 5-HT3(A) receptor ion channel.
Introini, B. ORCID: https://orcid.org/0000-0001-8727-1070, Cui, W. ORCID: https://orcid.org/0000-0001-9913-3118, Chu, X. ORCID: https://orcid.org/0000-0001-6801-3949, Zhang, Y., Alves, A.C., Eckhardt-Strelau, L., Golusik, S., Tol, M., Vogel, H. ORCID: https://orcid.org/0000-0001-9695-8894, Yuan, S. ORCID: https://orcid.org/0000-0001-9858-4742 and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
EMBO Journal 4 September 2024

Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly.
Dick, A. ORCID: https://orcid.org/0000-0003-0580-1897, Mikirtumov, V. ORCID: https://orcid.org/0009-0004-6849-4825, Fuchs, J., Krupp, F. ORCID: https://orcid.org/0000-0002-0402-8647, Olal, D., Bendl, E., Sprink, T. ORCID: https://orcid.org/0000-0002-0760-6828, Diebolder, C. ORCID: https://orcid.org/0000-0001-7694-7362, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Kochs, G., Roske, Y. ORCID: https://orcid.org/0000-0001-6237-388X and Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414
Structure 32 (8): 1068-1078. 8 August 2024

Structural insights into the activation mechanism of antimicrobial GBP1.
Weismehl, M. ORCID: https://orcid.org/0000-0001-7583-9095, Chu, X. ORCID: https://orcid.org/0000-0001-6801-3949, Kutsch, M. ORCID: https://orcid.org/0000-0002-9346-2196, Lauterjung, P., Herrmann, C. ORCID: https://orcid.org/0000-0002-1824-3647, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414
EMBO Journal 43 (4): 615-636. 15 February 2024

Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.
Balyschew, N., Yushkevich, A. ORCID: https://orcid.org/0000-0002-8729-9281, Mikirtumov, V. ORCID: https://orcid.org/0009-0004-6849-4825, Sanchez, R.M., Sprink, T. ORCID: https://orcid.org/0000-0002-0760-6828 and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Nature Communications 14 (1): 6543. 17 October 2023

A weak-labelling and deep learning approach for in-focus object segmentation in 3D widefield microscopy.
Li, R. ORCID: https://orcid.org/0000-0002-3085-5267, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, A.
Scientific Reports 13 (1): 12275. 28 July 2023

Determining the structure of the bacterial voltage-gated sodium channel NaChBac embedded in liposomes by cryo electron tomography and subtomogram averaging.
Chang, S.Y.S. ORCID: https://orcid.org/0000-0002-5627-9106, Dijkman, P.M., Wiessing, S.A. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Scientific Reports 13 : 11523. 17 July 2023

An unusual aspartic acid cluster in the reovirus attachment fiber s1 mediates stability at low pH and preserves trimeric organization.
Glorani, G. ORCID: https://orcid.org/0000-0002-4191-1092, Ruwolt, M., Holton, N., Loll, B. ORCID: https://orcid.org/0000-0001-7928-4488 and Neu, U. ORCID: https://orcid.org/0000-0001-6852-0879
Journal of Virology 96 (8): e0033122. April 2022

KAHRP dynamically relocalizes to remodeled actin junctions and associates with knob spirals in Plasmodium falciparum-infected erythrocytes.
Sanchez, C.P. ORCID: https://orcid.org/0000-0002-3334-3726, Patra, P. ORCID: https://orcid.org/0000-0002-2275-3738, Chang, S.Y.S. ORCID: https://orcid.org/0000-0002-5627-9106, Karathanasis, C. ORCID: https://orcid.org/0000-0002-1333-2341, Hanebutte, L. ORCID: https://orcid.org/0000-0001-5911-0763, Kilian, N. ORCID: https://orcid.org/0000-0001-7489-9782, Cyrklaff, M., Heilemann, M. ORCID: https://orcid.org/0000-0002-9821-3578, Schwarz, U.S. ORCID: https://orcid.org/0000-0003-1483-640X, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Lanzer, M. ORCID: https://orcid.org/0000-0002-0220-6526
Molecular Microbiology 117 (2): 274-292. February 2022

Structure of the merozoite surface protein 1 from Plasmodium falciparum.
Dijkman, P.M., Marzluf, T., Zhang, Y., Chang, S.Y.S. ORCID: https://orcid.org/0000-0002-5627-9106, Helm, D., Lanzer, M., Bujard, H. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Science Advances 7 (23): eabg0465. June 2021

Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography.
Berger, C., Ravelli, R.B.G., López-Iglesias, C., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Diepold, A. and Peters, P.J.
Journal of Structural Biology 213 (1): 107701. March 2021

Asymmetric opening of the homopentameric 5-HT(3A) serotonin receptor in lipid bilayers.
Zhang, Y. ORCID: https://orcid.org/0000-0002-6478-476X, Dijkman, P.M. ORCID: https://orcid.org/0000-0001-6799-2399, Zou, R., Zandl-Lang, M., Sanchez, R.M., Eckhardt-Strelau, L., Köfeler, H. ORCID: https://orcid.org/0000-0002-2725-9616, Vogel, H., Yuan, S. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Nature Communications 12 (1): 1074. 16 February 2021

Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM.
Sanchez, R.M., Zhang, Y. ORCID: https://orcid.org/0000-0002-6478-476X, Chen, W., Dietrich, L. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Nature Communications 11 (1): 3709. 24 July 2020

Structure of RyR1 in native membranes.
Chen, W. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
EMBO Reports 21 (5): e49891. 6 May 2020

Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1.
Faelber, K., Dietrich, L., Noel, J.K. ORCID: https://orcid.org/0000-0003-3168-6036, Wollweber, F., Pfitzner, A.K., Mühleip, A., Sánchez, R., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Chiaruttini, N., Lilie, H., Schlegel, J., Rosenbaum, E., Hessenberger, M. ORCID: https://orcid.org/0000-0003-3021-1100, Matthaeus, C. ORCID: https://orcid.org/0000-0003-3242-1195, Kunz, S. ORCID: https://orcid.org/0000-0002-0131-3506, von der Malsburg, A., Noé, F., Roux, A., van der Laan, M., Kühlbrandt, W. and Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414
Nature 571 (7765): 429-433. 18 July 2019

Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy.
Bhaskara, R.M. ORCID: https://orcid.org/0000-0002-7742-0391, Grumati, P., Garcia-Pardo, J., Kalayil, S., Covarrubias-Pinto, A., Chen, W., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Dikic, I. ORCID: https://orcid.org/0000-0001-8156-9511 and Hummer, G. ORCID: https://orcid.org/0000-0001-7768-746X
Nature Communications 10 (1): 2370. 30 May 2019

Fast cross correlation for limited angle tomographic data.
Sánchez, R.M., Mester, R. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Lecture Notes in Computer Science 11482 : 415-426. 2019

Nuclear pore complex components in the malaria parasite Plasmodium berghei.
Kehrer, J., Kuss, C., Andres-Pons, A., Reustle, A. ORCID: https://orcid.org/0000-0002-6724-8065, Dahan, N., Devos, D., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Beck, M. ORCID: https://orcid.org/0000-0002-7397-1321, Mair, G.R. and Frischknecht, F.
Scientific Reports 8 (1): 11249. 26 July 2018

Cryo-EM structure of the extended type VI secretion system sheath-tube complex.
Wang, J. ORCID: https://orcid.org/0000-0001-8218-1981, Brackmann, M. ORCID: https://orcid.org/0000-0003-0079-1693, Castaño-Díez, D., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Goldie, K.N., Maier, T. ORCID: https://orcid.org/0000-0002-7459-1363, Stahlberg, H. ORCID: https://orcid.org/0000-0002-1185-4592 and Basler, M. ORCID: https://orcid.org/0000-0001-5414-2088
Nature Microbiology 2 (11): 1507-1512. November 2017

Membrane vesicle secretion and prophage induction in multidrug-resistant Stenotrophomonas maltophilia in response to ciprofloxacin stress.
Devos, S., Van Putte, W., Vitse, J., Van Driessche, G., Stremersch, S., Van Den Broek, W., Raemdonck, K., Braeckmans, K., Stahlberg, H., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Savvides, S.N. and Devreese, B.
Environmental Microbiology 19 (10): 3930-3937. October 2017

Dynamo Catalogue: geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms.
Castaño-Díez, D., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Stahlberg, H.
Journal of Structural Biology 197 (2): 135-144. February 2017

Recent progress in structure and dynamics of dual-membrane-spanning bacterial nanomachines.
Gold, V. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Current Opinion in Structural Biology 39 : 1-7. August 2016

The structure of the mouse serotonin 5-HT3 receptor in lipid vesicles.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Castaño-Díez, D., Deluz, C., Hassaine, G., Grasso, L., Graf-Meyer, A., Vogel, H. and Stahlberg, H.
Structure 24 (1): 165-170. 5 January 2016

Structure of a bacterial type III secretion system in contact with a host membrane in situ.
Nans, A., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Saibil, H.R. and Hayward, R.D.
Nature Communications 6 : 10114. 11 December 2015

De novo protein structure determination from near-atomic-resolution cryo-EM maps.
Wang, R.Y.R., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Li, X., Egelman, E.H., Basler, M., Cheng, Y., Baker, D. and DiMaio, F.
Nature Methods 12 (4): 335-338. April 2015

Yersinia enterocolitica type III secretion injectisomes form regularly spaced clusters, which incorporate new machines upon activation.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Diepold, A., Amstutz, M., Armitage, J.P., Stahlberg, H. and Cornelis, G.R.
Molecular Microbiology 95 (5): 875-884. March 2015

Structure of the type VI secretion system contractile sheath.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Wang, R.Y.R., Brackmann, M., Scherer, S., Maier, T., Baker, D., DiMaio, F., Stahlberg, H., Egelman, E.H. and Basler, M.
Cell 160 (5): 952-962. 26 February 2015

Composition, formation, and regulation of the cytosolic c-ring, a dynamic component of the type III secretion injectisome.
Diepold, A., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Delalez, N.J., Berry, R.M. and Armitage, J.P.
PLoS Biology 13 (1): e1002039. 15 January 2015

The ultrastructure of Chlorobaculum tepidum revealed by cryo-electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Aktoudianaki, A. ORCID: https://orcid.org/0000-0003-4571-4018, Dedoglou, D., Stahlberg, H. ORCID: https://orcid.org/0000-0002-1185-4592 and Tsiotis, G.
Biochimica et Biophysica Acta - Bioenergetics 1837 (10): 1635-1642. October 2014

Clostridium difficile toxin CDT hijacks microtubule organization and reroutes vesicle traffic to increase pathogen adherence.
Schwan, C., Kruppke, A.S., Nölke, T., Schumacher, L., Koch-Nolte, F., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Stahlberg, H. and Aktories, K.
Proceedings of the National Academy of Sciences of the United States of America 111 (6): 2313-2318. 11 February 2014

Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core.
Kowal, J., Chami, M., Ringler, P., Müller, S.A., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Castaño-Díez, D., Amstutz, M., Cornelis, G.R., Stahlberg, H. and Engel, A.
Structure 21 (12): 2152-2161. 3 December 2013

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.
Degiacomi, M.T., Iacovache, I., Pernot, L., Chami, M., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Stahlberg, H., van der Goot, F.G. and Dal Peraro, M.
Nature Chemical Biology 9 (10): 623-629. October 2013

Electron tomography of Plasmodium falciparum merozoites reveals core cellular events that underpin erythrocyte invasion.
Hanssen, E., Dekiwadia, C., Riglar, D.T., Rug, M., Lemgruber, L., Cowman, A.F., Cyrklaff, M., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Frischknecht, F., Baum, J. and Ralph, S.A.
Cellular Microbiology 15 (9): 1457-1472. September 2013

In situ structural analysis of the Yersinia enterocolitica injectisome.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Stenta, M., Schmelz, S., Amstutz, M., Wiesand, U., Castaño-Díez, D., Degiacomi, M.T., Münnich, S., Bleck, C.K., Kowal, J., Diepold, A., Heinz, D.W., Dal Peraro, M., Cornelis, G.R. and Stahlberg, H.
eLife 2 : e00792. 30 July 2013

Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast.
Lemgruber, L., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Dekiwadia, C., Riglar, D.T., Baum, J., Stahlberg, H., Ralph, S.A. and Frischknecht, F.
Malaria Journal 12 : 25. 19 January 2013

Structural basis for chirality and directional motility of Plasmodium sporozoites.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Münter, S., Lemgruber, L., Montagna, G., Stahlberg, H., Matuschewski, K., Meissner, M., Cyrklaff, M. and Frischknecht, F.
Cellular Microbiology 14 (11): 1757-1768. November 2012

Improving the quality of electron tomography image volumes using pre-reconstruction filtering.
Maiorca, M., Hanssen, E., Kazmierczak, E., Maco, B., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Hall, R., Quiney, H. and Tilley, L.
Journal of Structural Biology 180 (1): 132-142. October 2012

Assessing the benefits of focal pair cryo-electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Stahlberg, H. and Castaño-Díez, D.
Journal of Structural Biology 178 (2): 88-97. May 2012

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.
Castaño-Díez, D., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Arheit, M. and Stahlberg, H.
Journal of Structural Biology 178 (2): 139-151. May 2012

Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography.
Dudkina, N.V., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Stahlberg, H. and Boekema, E.J.
Proceedings of the National Academy of Sciences of the United States of America 108 (37): 15196-15200. 13 September 2011

Environmental constraints guide migration of malaria parasites during transmission.
Hellmann, J.K., Münter, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Schulz, S., Heiss, K., Müller, A.K., Matuschewski, K., Spatz, J.P., Schwarz, U.S. and Frischknecht, F.
PLoS Pathogens 7 (6): e1002080. 16 June 2011

Evidence of direct cell-cell fusion in Borrelia by cryogenic electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Cyrklaff, M., Alex, B., Lemgruber, L., Baumeister, W., Wallich, R. and Frischknecht, F.
Cellular Microbiology 13 (5): 731-741. May 2011

Key factors regulating Plasmodium berghei sporozoite survival and transformation revealed by an automated visual assay.
Hegge, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Barniol, L. and Frischknecht, F.
FASEB Journal 24 (12): 5003-5012. December 2010

Geometric constrains for detecting short actin filaments by cryogenic electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Lepper, S., Baumeister, W., Cyrklaff, M. and Frischknecht, F.
PMC Biophysics 3 (1): 6. 5 March 2010

Positioning of large organelles by a membrane-associated cytoskeleton in Plasmodium sporozoites.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Lepper, Simone, Stanway, Rebecca, Bohn, Stefan, Baumeister, Wolfgang, Cyrklaff, Marek and Frischknecht, Friedrich
Cellular Microbiology 12 (3): 362-371. March 2010

Distinct in situ structures of the Borrelia flagellar motor.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Cyrklaff, M., Wallich, R., Baumeister, W. and Frischknecht, F.
Journal of Structural Biology 169 (1): 54-61. January 2010

Plasmodium sporozoite motility is modulated by the turnover of discrete adhesion sites.
Münter, S., Sabass, B., Selhuber-Unkel, C., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Hegge, S., Engel, U., Spatz, J.P., Matuschewski, K., Schwarz, U.S. and Frischknecht, F.
Cell Host & Microbe 6 (6): 551-562. 17 December 2009

Automated classification of Plasmodium sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection.
Hegge, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Smith, A. and Frischknecht, F.
Biotechnology Journal 4 (6): 903-913. June 2009

Comparative cryo-electron tomography of pathogenic Lyme disease spirochetes.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Cyrklaff, M., Baumeister, W., Simon, M.M., Wallich, R. and Frischknecht, F.
Molecular Microbiology 71 (6): 1415-1434. March 2009

Cryoelectron tomography reveals periodic material at the inner side of subpellicular microtubules in apicomplexan parasites.
Cyrklaff, M., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Leis, A., Leonard, K., Baumeister, W., Menard, R., Meissner, M. and Frischknecht, F.
Journal of Experimental Medicine 204 (6): 1281-1287. 11 June 2007

Meeting report: Breaking barriers in microscopy.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Münter, S.
Biotechnology Journal 2 (1): 30-32. January 2007

Luminal particles within cellular microtubules.
Garvalov, B.K., Zuber, B., Bouchet-Marquis, C., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Gruska, M., Beck, M., Leis, A., Frischknecht, F., Bradke, F., Baumeister, W., Dubochet, J. and Cyrklaff, M.
Journal of Cell Biology 174 (6): 759-765. 11 September 2006

Book Section

Resolution in electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
In: Cellular Imaging. Biological and Medical Physics, Biomedical Engineering . Springer, Cham, Switzerland, 261–282. ISBN 978-3-319-68995-1 31 December 2017

Conference or Workshop Item

Fast alignment of limited angle tomograms by projected cross correlation.
Sanchez, R.M., Mester, R. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
In: 2019 27th European Signal Processing Conference (EUSIPCO), 2-6 Sep 2019, A Coruna, Spain. 18 November 2019

Review

Phosphoproteomics for studying signaling pathways evoked by hormones of the renin-angiotensin system: a source of untapped potential.
Souza-Silva, I.M. ORCID: https://orcid.org/0000-0002-6140-3503, Carregari, V.C. ORCID: https://orcid.org/0000-0001-6863-1333, Steckelings, U.M. ORCID: https://orcid.org/0000-0002-5430-4275 and Verano-Braga, T. ORCID: https://orcid.org/0000-0002-7083-2588
Acta Physiologica 241 (2): e14280. February 2025

Subtomogram averaging from cryo-electron tomograms.
Leigh, K.E., Navarro, P.P., Scaramuzza, S., Chen, W., Zhang, Y., Castaño-Díez, D. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Methods in Cell Biology 152 : 217-259. 2019

Functional insights into pathogen biology from 3D electron microscopy.
Cyrklaff, M., Frischknecht, F. and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
FEMS Microbiology Reviews 41 (6): 828-853. 1 November 2017

Limiting factors in single particle cryo electron tomography.
Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Castaño-Díez, D. and Stahlberg, H.
Computational and Structural Biotechnology Journal 1 (2): e201207002. July 2012

Special: biotech in Russia.
Rabinovich, M., Burghardt, N., Gorzka, G., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Leonov, A and Konov, A
Biotechnology Journal 2 (7): 775-789. July 2007

Editorial

Introducing Mikhail Kudryashev, Clorice R. Reinhardt, Alec H. Follmer, and Michael C. Thompson.
Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274, Reinhardt, Clorice R., Follmer, Alec H. and Thompson, Michael C.
Structure 34 (5): 681-684. 7 May 2026

Gentle ions for cryo-FIB milling.
Chu, X. ORCID: https://orcid.org/0000-0001-6801-3949 and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
Structure 31 (10): 1147-1148. 5 October 2023

Preprint

Cryo-SWAN: the Multi-Scale Wavelet-decomposition-inspired Autoencoder Network for molecular density representation of molecular volumes.
Li, Rui ORCID: https://orcid.org/0000-0002-3085-5267, Yushkevich, Artsemi ORCID: https://orcid.org/0000-0002-8729-9281, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, Artur
arXiv : 2603.03342. 18 February 2026

Cryo-EM structure of the naked mole-rat ribosome reveals a stabilized split 28S rRNA.
Gül, Mehmet ORCID: https://orcid.org/0000-0001-5513-1866, Rossi, Alice ORCID: https://orcid.org/0000-0002-8819-9813, Spahn, Christian M.T. ORCID: https://orcid.org/0000-0002-2939-9487, Lewin, Gary R. ORCID: https://orcid.org/0000-0002-2890-6352 and Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274
bioRxiv : 2025.10.26.684699. 27 October 2025

Integrative structural interactomics reveals protein organization and structure in a giant virus.
Mühlberg, L. ORCID: https://orcid.org/0009-0008-8046-007X, Ruta, J. ORCID: https://orcid.org/0009-0007-0524-6885, Mikirtumov, V. ORCID: https://orcid.org/0009-0004-6849-4825, Burton-Smith, R. ORCID: https://orcid.org/0000-0002-1535-6419, Murata, K. ORCID: https://orcid.org/0000-0001-9446-3652, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274, Okamoto, K. ORCID: https://orcid.org/0000-0002-4858-1196, Bogdanow, B. ORCID: https://orcid.org/0000-0002-9634-7353 and Liu, F. ORCID: https://orcid.org/0000-0002-2358-549X
bioRxiv : 2025.06.16.659922. 18 June 2025

Structures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization.
Vázquez-Sarandeses, E., Mikirtumov, V. ORCID: https://orcid.org/0009-0004-6849-4825, Noel, J.K. ORCID: https://orcid.org/0000-0003-3168-6036, Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414
bioRxiv : 2025.06.05.658037. 7 June 2025

Structural basis for membrane targeting and secretion of legionella SidE ubiquitin ligases.
Misra, Mohit ORCID: https://orcid.org/0000-0001-6309-8066, Mukherjee, Rukmini, Bhattacharya, Anshu, Weng, Tsai-Hsuan ORCID: https://orcid.org/0000-0002-3708-6384, Li, Chuang, Chen, Wenbo, van Ek, Larissa ORCID: https://orcid.org/0000-0002-8047-1560, Mohammed, Ahmed, Cristiani, Alberto, Liu, Yaobin, Pomirska, Julia, Vidov, Adela, Grewe, Diana, van der Heden van Noort, Gerbrand ORCID: https://orcid.org/0000-0001-5955-6431, Hummer, Gerhard ORCID: https://orcid.org/0000-0001-7768-746X, Gavin, Anne-Claude ORCID: https://orcid.org/0000-0003-4917-2340, Safarian, Schara, Luo, Zhao-Qing ORCID: https://orcid.org/0000-0001-8890-6621, Bhaskara, Ramachandra ORCID: https://orcid.org/0000-0002-7742-0391, Svergun, Dmitri, Kudryashev, Misha ORCID: https://orcid.org/0000-0003-3550-6274 and Dikic, Ivan ORCID: https://orcid.org/0000-0001-8156-9511
Research Square : rs.3.rs-6524297/v1. 12 May 2025

Inner-membrane GspF of the bacterial type II secretion system is a dimeric adaptor mediating pseudopilus biogenesis.
Van Putte, W. ORCID: https://orcid.org/0000-0001-8875-8198, De Vos, T., Van Den Broeck, W., Stahlberg, H., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Savvides, S.N.
bioRxiv : 435982. 5 October 2018

Dataset

DeBCR: trained model weights for fluorescence microscopy image enhancement.
Li, Rui ORCID: https://orcid.org/0000-0002-3085-5267, Yushkevich, Artsemi ORCID: https://orcid.org/0000-0002-8729-9281, Chu, Xiaofeng ORCID: https://orcid.org/0000-0001-6801-3949, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, Artur ORCID: https://orcid.org/0000-0003-2458-4904
[Dataset] 21 November 2025

Naked mole-rat 80S ribosome in post-translocation non-rotated state.
Gul, M. ORCID: https://orcid.org/0000-0001-5513-1866 and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
[Dataset] 14 October 2025 (Submitted)

Naked mole-rat 80S ribosome in pre-translocation rotated hybrid state.
Gul, M. ORCID: https://orcid.org/0000-0001-5513-1866 and Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274
[Dataset] 14 October 2025 (Submitted)

Cryo-EM structure of Legionella effector SdeC (3D flexible refinement).
Weng, T.H., Misra, M., Chen, W., Safarian, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Dikic, I.
[Dataset] 18 June 2025

Cryo-EM structure of Legionella effector SdeC (3D flexible refinement).
Weng, T.H., Misra, M., Chen, W., Safarian, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Dikic, I.
[Dataset] 4 June 2025

Cryo-EM structure of Legionella effector SdeC (PDE-mART domain).
Weng, T.H., Misra, M., Chen, W., Safarian, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Dikic, I.
[Dataset] 4 June 2025

Cryo-EM structure of Legionella effector SdeC (PDE-mART domain).
Weng, T.H., Misra, M., Chen, W., Safarian, S., Kudryashev, M. ORCID: https://orcid.org/0000-0003-3550-6274 and Dikic, I.
[Dataset] 4 June 2025

Data from: Denoising, deblurring, and optical deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR.
Li, Rui ORCID: https://orcid.org/0000-0002-3085-5267, Yushkevich, Artsemi ORCID: https://orcid.org/0000-0002-8729-9281, Chu, Xiaofeng ORCID: https://orcid.org/0000-0001-6801-3949, Kudryashev, Mikhail ORCID: https://orcid.org/0000-0003-3550-6274 and Yakimovich, Arturo ORCID: https://orcid.org/0000-0003-2458-4904
[Dataset] 4 July 2024