Publications

2025

Simpkin, A., Elliot, L., et al. (2025) “Slice’N’Dice: maximizing the value of predicted models for structural biologists”. Acta Cryst. D81(3), 105-121. https://doi.org/10.1107/S2059798325001251

Mirecka, J., et al. (2025). “Affinity-VAE: incorporating prior knowledge in representation learning from scientific images”. https://arxiv.org/abs/2209.04517

Ning, J., et al. (2025) “Uncovering synaptic and cellular nanoarchitecture of brain tissue via seamless in situ trimming and milling for cryo-electron tomography”. https://www.biorxiv.org/content/10.1101/2025.03.09.642162v1

Costa-Gomes, B, et al. (2025). “PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modelling and machine learning”. https://arxiv.org/abs/2503.13329

2024

Kleywegt, G.J., Winn, M.D., et al. (2024) “Community recommendations on cryoEM data archiving and validation”  IUCrJ 11, 140-151 https://doi.org/10.1107/S2052252524001246

Winn, M.D. (2024) “Communities in structural biologyNature Structural & Molecular Biology, 31, 6-7 https://doi.org/10.1038/s41594-023-01197-z

Lawson, C.L., et al. (2024) “Outcomes of the EMDataResource CryoEM Ligand Modeling ChallengeNature Methods 21(7):1340–1348. https://doi.org/10.1038/s41592-024-02321-7

Joosten, M., Greer, J., Parkhurst, J., Burnley, T., & Jakobi, A. J. (2024) “Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions.IUCrJ, 11(6):951-965 https://doi.org/10.1107/S2052252524009321

Burt, A. et al. (2024) “An image processing pipeline for electron cryo‐tomography in RELION‐5” FEBS Open Bio 14 (11), 1788-1804. https://doi.org/10.1002/2211-5463.13873

Schwab, J. et al. (2024) “DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images” Nature Methods 21 (10), 1855-1862. https://doi.org/10.1038/s41592-024-02377-5

2023

Lucy M. Collinson, Carles Bosch, Anwen Bullen, Jemima J. Burden, Raffaella Carzaniga, Cheng Cheng, Michele Darrow, Georgina Fletcher, Errin Johnson, Gerard J. Kleywegt, Christopher J. Peddie, Kedar Narayan, Ardan Patwardhan, Martyn Winn, Charles Wood, Paul Verkade (2023) “Volume EM: A quiet revolution takes shapeNature Methods 20, 777–782 https://doi.org/10.1038/s41592-023-01861-8

Malhotra, S., Mulvaney, T., Cragnolini, T., Sidhu, H., Joseph, A. P., Beton, J. G., & Topf, M. (2023) “RIBFIND2: identifying rigid bodies in protein and nucleic acid structures.” Nucleic Acids Research, 51(18), 9567-9575. https://doi.org/10.1093/nar/gkad721

J.. M. Short, C. M. Palmer,T. Burnley, M. D. Winn, Q. Zhang, B. V. Venkataram Prasad, S. Chen, R. A. Crowther, P. N. T. Unwin, R. Henderson (2023) “MRC2020: improvements to Ximdisp and the MRC image-processing programs” IUCrJ 10, 579–583. https://doi.org/10.1107/S2052252523006309

2022

Joseph, A. P., Olek, M., Malhotra, S., Zhang, P., Cowtan, K., Burnley, T., & Winn, M. D. (2022) “Atomic model validation using the CCP-EM software suite.Acta Cryst. D78(2), 152-161. https://doi.org/10.1107/S205979832101278X

Joseph, A. P., Malhotra, S., Burnley, T., & Winn, M. D. (2022) “Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday Discussions, 240, 196-209. https://doi.org/10.1039/D2FD00103A

Mirecka, J., Famili, M., Kotańska, A., Juraschko, N., Costa-Gomes, B., Palmer, C. M., Thiyagalingam, J., Burnley, T., Basham, M., & Lowe, A. R. (2022) “Affinity-VAE for disentanglement, clustering and classification of objects in multidimensional image data.” arXiv preprint https://doi.org/10.48550/arXiv.2209.04517

Ivanova, M. E., Lukoyanova, N., Malhotra, S., Topf, M., Trapani, J. A., Voskoboinik, I., & Saibil, H. R. (2022) “The pore conformation of lymphocyte perforin.Science advances, 8(6), eabk3147. https://doi.org/10.1126/sciadv.abk3147

Palmer, C. M. and Aylett, C.H.S. (2022) “Real space in cryo-EM: the future is localActa Cryst D78(2), 136-143. https://doi.org/10.1107/S2059798321012286

2021

Mateusz Olek and Agnel Praveen Joseph (2021) “CryoEM map based model validation using the False Discovery Rate approach”, Front. Mol. Biosci. https://doi.org/10.3389/fmolb.2021.652530

T Croll, K Diederichs, F Fischer, C Fyfe, Y Gao, S Horrell, AP Joseph, L Kandler, O Kippes, F Kirsten et al. (2021) “Making the invisible enemy visible” Nature Structural & Molecular Biology, 28, 404–408. https://www.nature.com/articles/s41594-021-00593-7

S Malhotra, AP Joseph, J Thiyagalingam, M Topf. (2021) “Assessment of protein-protein interfaces in cryoEM derived assembliesNat. Comm. 12, 3399. https://doi.org/10.1038/s41467-021-23692-x

CL Lawson, A Kryshtafovych, T Burnley, AP Joseph, C Palmer, MD Winn et al. (2021) “CryoEM model validation recommendations based on outcomes of the 2019 EMDataResource challengeNature Methods  18, 156-164 https://doi.org/10.1038/s41592-020-01051-w

Keitaro Yamashita, Colin M Palmer, Tom Burnley, Garib N Murshudov (2021) “Cryo-EM single-particle structure refinement and map calculation using ServalcatActa Cryst D77(10):1282-1291. https://doi.org/10.1107/S2059798321009475

2020

Hoh SW, Burnley T, Cowtan K. (2020) “Current approaches for automated model building into cryoEM maps using Buccaneer with CCP-EMActa Cryst. D76 (Pt 6), pp. 531-541 https://doi.org/10.1107/S2059798320005513

Maximilian Beckers, Colin M. Palmer and Carsten Sachse (2020) “Confidence maps: statistical inference of cryoEM maps” Acta Cryst D76 (4), 332-339. https://doi.org/10.1107/S2059798320002995

Kailash Ramlaul, Colin M. Palmer, Christopher H.S. Aylett (2020) “Mitigating Local Over-fitting During Single Particle Reconstruction with SIDESPLITTERJ. Struct Biol. 211, 107545 https://doi.org/10.1016/j.jsb.2020.107545

Joseph, Agnel Praveen; Lagerstedt, Ingvar; Jakobi, Arjen; Burnley, Tom; Patwardhan, Ardan; Topf, Maya; Winn, Martyn (2020) “Comparing CryoEM Reconstructions and Validating Atomic Model Fit using Difference MapsJ. Chem. Inf. Mod. https://doi.org/10.1021/acs.jcim.9b01103

2019

Andriy Kryshtafovych, Sony Malhotra, Bohdan Monastyrskyy, Tristan Cragnolini, Agnel‐Praveen Joseph, Wah Chiu, Maya Topf (2019) “Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results”  Proteins 87 (12), 1128-1140  https://doi.org/10.1002/prot.25817

Patrick Schwarb, Anwen Bullen, Dean Flanders, Maria Marosvölgyi, Martyn Winn, Urs Gomez, Roland A Fleck (2019) “Image and Resource Management in Microscopy in the Digital AgeBiological Field Emission Scanning Electron Microscopy, 2, 611-623 https://doi.org/10.1002/9781118663233.ch29

Kailash Ramlaul, Colin M. Palmer, Christopher H.S. Aylett (2019) “A Local Agreement Filtering Algorithm for Transmission EM ReconstructionsJ. Struct. Biol. 205, 30-40. https://doi.org/10.1016/j.jsb.2018.11.011

2018

Anaïs Menny, Marina Serna, Courtney M. Boyd, Scott Gardner, Agnel Praveen Joseph, B. Paul Morgan, Maya Topf, Nicholas J. Brooks & Doryen Bubeck (2018) “CryoEM reveals how the complement membrane attack complex ruptures lipid bilayersNature Comm, 9, Article number: 5316  https://www.nature.com/articles/s41467-018-07653-5

Tom Burnley and Paula da Fonseca (2018) “Proceedings of the third CCP-EM Spring SymposiumActa Cryst. D74, 490-491. https://doi.org/10.1107/S2059798318008239

McNicholas, S., Croll, T., Burnley, T., Palmer, CM., Hoh, SW., Jenkins, HT., Dodson, E., Cowtan, K. and Agirre, J. (2018) “Automating tasks in protein structure determination with the clipper python module”  Protein Science, 27, 207-216 https://doi.org/10.1002/pro.3299

2017

Tom Burnley, Colin M Palmer, Martyn Winn (2017) “Recent developments in the CCP‐EM software suiteActa Cryst., D9, 469-477. https://doi.org/10.1107/S2059798317007859

Tom Burnley and Paula da Fonseca (2017) “Introducing the Proceedings of the CCP-EM Spring SymposiumActa Cryst. D74, 467-468. https://doi.org/10.1107/S2059798317008002