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 biology” Nature 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 Challenge” Nature 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 shape” Nature 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 local” Acta 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 assemblies” Nat. 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 challenge” Nature 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 Servalcat” Acta 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-EM” Acta 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 SIDESPLITTER” J. 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 Maps” J. 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 Age” Biological 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 Reconstructions” J. 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 bilayers” Nature 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 Symposium” Acta 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 suite” Acta 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 Symposium” Acta Cryst. D74, 467-468. https://doi.org/10.1107/S2059798317008002