Browse by Research Team

Article

Solving the inverse problem of microscopy deconvolution with a residual Beylkin-Coifman-Rokhlin neural network.
Li, R., Kudryashev, M. 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., Cui, W., Chu, X., Zhang, Y., Alves, A.C., Eckhardt-Strelau, L., Golusik, S., Tol, M., Vogel, H., Yuan, S. and Kudryashev, M.
EMBO Journal 4 September 2024

Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly.
Dick, A., Mikirtumov, V., Fuchs, J., Krupp, F., Olal, D., Bendl, E., Sprink, T., Diebolder, C., Kudryashev, M., Kochs, G., Roske, Y. and Daumke, O.
Structure 32 (8): 1068-1078. 8 August 2024

Structural insights into the activation mechanism of antimicrobial GBP1.
Weismehl, M., Chu, X., Kutsch, M., Lauterjung, P., Herrmann, C., Kudryashev, M. and Daumke, O.
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., Mikirtumov, V., Sanchez, R.M., Sprink, T. and Kudryashev, M.
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., Kudryashev, M. 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., Dijkman, P.M., Wiessing, S.A. and Kudryashev, M.
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., Ruwolt, M., Holton, N., Loll, B. and Neu, U.
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., Patra, P., Chang, S.Y.S., Karathanasis, C., Hanebutte, L., Kilian, N., Cyrklaff, M., Heilemann, M., Schwarz, U.S., Kudryashev, M. and Lanzer, M.
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., Helm, D., Lanzer, M., Bujard, H. and Kudryashev, M.
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., 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., Dijkman, P.M., Zou, R., Zandl-Lang, M., Sanchez, R.M., Eckhardt-Strelau, L., Köfeler, H., Vogel, H., Yuan, S. and Kudryashev, M.
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., Chen, W., Dietrich, L. and Kudryashev, M.
Nature Communications 11 (1): 3709. 24 July 2020

Structure of RyR1 in native membranes.
Chen, W. and Kudryashev, M.
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., Wollweber, F., Pfitzner, A.K., Mühleip, A., Sánchez, R., Kudryashev, M., Chiaruttini, N., Lilie, H., Schlegel, J., Rosenbaum, E., Hessenberger, M., Matthaeus, C., Kunz, S., von der Malsburg, A., Noé, F., Roux, A., van der Laan, M., Kühlbrandt, W. and Daumke, O.
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., Grumati, P., Garcia-Pardo, J., Kalayil, S., Covarrubias-Pinto, A., Chen, W., Kudryashev, M., Dikic, I. and Hummer, G.
Nature Communications 10 (1): 2370. 30 May 2019

Fast cross correlation for limited angle tomographic data.
Sánchez, R.M., Mester, R. and Kudryashev, M.
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., Dahan, N., Devos, D., Kudryashev, M., Beck, M., 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., Brackmann, M., Castaño-Díez, D., Kudryashev, M., Goldie, K.N., Maier, T., Stahlberg, H. and Basler, M.
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., 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. 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.
Current Opinion in Structural Biology 39 : 1-7. August 2016

The structure of the mouse serotonin 5-HT3 receptor in lipid vesicles.
Kudryashev, M., 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., 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., 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., 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., 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., 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., Aktoudianaki, A., Dedoglou, D., Stahlberg, H. 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., Smith, A. and Frischknecht, F.
Biotechnology Journal 4 (6): 903-913. June 2009

Comparative cryo-electron tomography of pathogenic Lyme disease spirochetes.
Kudryashev, M., 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., 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. 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., 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.
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.
In: 2019 27th European Signal Processing Conference (EUSIPCO), 2-6 Sep 2019, A Coruna, Spain. 18 November 2019

Review

Subtomogram averaging from cryo-electron tomograms.
Leigh, K.E., Navarro, P.P., Scaramuzza, S., Chen, W., Zhang, Y., Castaño-Díez, D. and Kudryashev, M.
Methods in Cell Biology 152 : 217-259. 2019

Functional insights into pathogen biology from 3D electron microscopy.
Cyrklaff, M., Frischknecht, F. and Kudryashev, M.
FEMS Microbiology Reviews 41 (6): 828-853. 1 November 2017

Limiting factors in single particle cryo electron tomography.
Kudryashev, M., 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., Leonov, A and Konov, A
Biotechnology Journal 2 (7): 775-789. July 2007

Editorial

Gentle ions for cryo-FIB milling.
Chu, X. and Kudryashev, M.
Structure 31 (10): 1147-1148. 5 October 2023

Preprint

Insights into therapeutic discovery through the Kelch domain structure of Keap1 at ambient temperature.
Yilmaz, M., Sever, B., Kutlu, Y., Gul, M., Okuducu, C., Tavli, S., Otsuka, M., Fujita, M., Haliloglu, T., Ciftci, H. and DeMirci, H.
bioRxiv : 2024.07.30.605796. 2 August 2024

Denoising, deblurring, and optical deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR.
Li, R., Yushkevich, A., Chu, X., Kudryashev, M. and Yakimovich, A.
bioRxiv : 2024.07.12.603278. 16 July 2024