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A user with 2,445 edits. Account created on 30 March 2009.
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28 April 2026

  • 06:4106:41, 28 April 2026 diff hist +1,574 N 2026Chen MPM Created page with "== Citation == Chen, J., Leung, V.C., Wang, R., Bubeck, D. and Dragotti, P.L. 2026. Masked Projection Modelling for Sparse-view cryo-EM Reconstruction. ICASSP 2026-2026 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (2026), 11567–11571. == Abstract == Resolving conformational heterogeneity in cryo-electron microscopy (cryo-EM) remains challenging, especially for rare states. Standard reconstruction methods, reliant on abundant simi..." current
  • 06:4106:41, 28 April 2026 diff hist +84 Main Page →3D Reconstruction current

23 April 2026

  • 08:5208:52, 23 April 2026 diff hist +1,678 N 2026Gauvin 200kV Created page with "== Citation == Gauvin, C.C., Findlay, J.L., Hophan-Nichols, C. and Lawrence, C.M. 2026. A cost-effective 200 kV cryo-EM core facility for high resolution single particle analysis. Methods in Microscopy. (2026). == Abstract == We sought to establish a sustainable 200 kV cryo- EM core facility for the Northern Rocky Mountain region with high resolution single particle capabilities. With modest funding, relative to 300 kV instruemnts, from the NSF, theMurdock Charitable..." current
  • 08:5108:51, 23 April 2026 diff hist +99 Main Page →Books and reviews
  • 07:0707:07, 23 April 2026 diff hist +1,540 N 2026Eluru MISO Created page with "== Citation == Eluru, G., De Gieter, S., Schenck, S., Stroobants, A., Shrestha, B., Erbel, P., Brunner, J.D. and Efremov, R.G. 2025. MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony. Nature methods. (2025), 1–11. == Abstract == Single-particle cryogenic electron microscopy (cryo-EM) enables reconstruction of atomic-resolution 3D maps of proteins by visualizing thousands to millions of purified pro..." current
  • 07:0607:06, 23 April 2026 diff hist +98 Main Page →Sample preparation

15 April 2026

  • 12:3012:30, 15 April 2026 diff hist +1,677 N 2022Calcraft SPATilts Created page with "== Citation == Calcraft, T. and Rosenthal, P.B. 2022. Cryogenic electron microscopy approaches that combine images and tilt series. Microscopy. 71, Supplement_1 (Feb. 2022), i15–i22. == Abstract == Cryogenic electron microscopy can be widely applied to biological specimens from the molecular to the cellular scale. In single-particle analysis, 3D structures may be obtained in high resolution by averaging 2D images of single particles in random orientations. For pleo..." current
  • 12:2812:28, 15 April 2026 diff hist +67 Main Page →Collection geometry

13 April 2026

  • 12:4612:46, 13 April 2026 diff hist +1,482 N 2026Wazny Damage Created page with "== Citation == Ważny, G., Jaciuk, M., Indyka, P., Glatt, S., Biela, A. and Rawski, M. 2026. Influence of total electron dose on the quality of nucleic acids potential maps in Cryo-EM. Ultramicroscopy. (2026), 114358. == Abstract == The standardization of protocols in science lies at the basis of every experiment. During this process, some crucial questions need to be answered. The quality of results in single particle cryo-Electron Microscopy (cryo-EM) requires optim..." current
  • 12:4512:45, 13 April 2026 diff hist +67 Main Page →Automated data collection
  • 12:3312:33, 13 April 2026 diff hist +685 N 2026Evans Counting Created page with "== Citation == Evans, L., Dingeldein, L., Covino, R., Gilles, M.A., Thiede, E. and Cossio, P. 2026. Counting particles in cryo-electron microscopy may result in incorrect population estimates. Communications Biology. 9, 1 (2026), 421. == Abstract == Counting particles is a common practice in estimating populations from cryo-electron microscopy data. Here, it is shown that counting particles is not robust to noise, whereas statistically rigorous population-estimation m..." current
  • 12:3212:32, 13 April 2026 diff hist +133 Main Page →3D Heterogeneity
  • 12:2012:20, 13 April 2026 diff hist +1,590 N 2026He prismPYP Created page with "== Citation == He, L. and Bartesaghi, A. 2026. prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation. Structure. 34, (2026), 1–12. == Abstract == High-throughput data collection in single-particle cryo-electron microscopy (EM) necessitates fast, accurate, and generalizable methods to assess micrograph quality. Manual micrograph curation scales poorly to large datasets and often misclassifies images due to sample-specific variab..." current
  • 12:1912:19, 13 April 2026 diff hist +130 Main Page →Automatic particle picking

9 April 2026

  • 12:5212:52, 9 April 2026 diff hist +1,664 N 2026Chen 3DDF-VAE Created page with "== Citation == Chen, Y., Li, F., Dong, H., Wang, X., Zhang, F., Hu, B. and Wan, X. 2026. 3DDF-VAE: Dual-frequency variational autoencoder with pose-consistency validation for rare cryo-EM conformation discovery. J. Structural Biology. (2026), 108311. == Abstract == Revealing the 3D conformational variability of biomolecules is crucial for understanding their function, while cryo-EM reconstruction of rare states remains difficult due to data imbalance and structural de..." current
  • 12:5212:52, 9 April 2026 diff hist +93 Main Page →3D Heterogeneity

7 April 2026

6 April 2026

  • 16:2016:20, 6 April 2026 diff hist +2,215 N 2026Xu MMSE Created page with "== Citation == Xu, S., Balanov, A., Singer, A. and Bendory, T. 2026. Bayesian perspective for orientation determination in cryo-EM with application to structural heterogeneity analysis. Biological Crystallography. 82, 4 (2026). == Abstract == Accurate orientation estimation is a crucial component of 3D molecular structure reconstruction, both in single-particle cryo-electron microscopy (cryo-EM) and in the increasingly popular field of cryo-electron tomography (cryo-E..." current
  • 16:2016:20, 6 April 2026 diff hist +98 Main Page →3D Alignment

24 March 2026

  • 10:4410:44, 24 March 2026 diff hist +1,221 N 2022Vilas Emerging Created page with "== Citation == Vilas, J.L., Carazo, J.M. and Sorzano, C.O.S. 2022. Emerging themes in CryoEM─ Single particle analysis image processing. Chemical Reviews. 122, 17 (2022), 13915–13951. == Abstract == Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars hav..." current
  • 10:4310:43, 24 March 2026 diff hist +145 Main Page →Books and reviews

20 February 2026

  • 06:3506:35, 20 February 2026 diff hist +2,316 N 2025Balanov Confirmation Created page with "== Citation == Balanov, A., Bendory, T. and Huleihel, W. 2025. Confirmation bias in Gaussian mixture models. IEEE Trans. on Information Theory. (2025). == Abstract == Confirmation bias, the tendency to interpret information in a way that aligns with one’s preconceptions, can profoundly impact scientific research, leading to conclusions that reflect the researcher’s hypotheses even when the observational data do not support them. This issue is especially critical i..." current
  • 06:3406:34, 20 February 2026 diff hist +72 Main Page →2D Alignment

18 February 2026

  • 07:2607:26, 18 February 2026 diff hist +1,122 N 2026Li Atomic Created page with "== Citation == Li, T. and Huang, S.-Y. 2026. Deep learning–based postprocessing and model building for cryo-electron microscopy maps. Current Opinion in Structural Biology. 96, (2026), 103196. == Abstract == Cryo-electron microscopy (cryo-EM) has emerged as one of the most powerful techniques for determining the structures of biological macromolecules. The ultimate goal of cryo-EM is to determine the atomic structure of target molecules, where map postprocessing and..." current
  • 07:2407:24, 18 February 2026 diff hist +109 Main Page →Books and reviews

17 February 2026

  • 04:5104:51, 17 February 2026 diff hist +1,489 N 2026Chen CryoEvoBuild Created page with "== Citation == Chen, J., Li, T., He, J. and Huang, S.-Y. 2026. Protein model building for intermediate-resolution cryo-EM maps by integrating evolutionary and experimental information. Structure. 34, (2026), 375–384. == Abstract == Accurate model building in intermediate-resolution cryo-EM maps normally requires flexible fitting of reliable initial structures. However, while deep learning-based methods such as AlphaFold2 can predict highly accurate structures, the p..." current
  • 04:5004:50, 17 February 2026 diff hist +109 Main Page →Fitting and docking
  • 04:3804:38, 17 February 2026 diff hist +1,148 N 2026Urzhumtsev ProjDir Created page with "== Citation == Urzhumtsev, A.G. 2026. Quantifying distributions of cryo-EM projections. Biological Crystallography. 82, 2 (2026). == Abstract == In cryo-electron microscopy, a set of two-dimensional projections collected from different viewing directions may complicate image processing and subsequent model building if the distribution of these views is non-uniform. View distributions are traditionally represented as color-coded two-dimensional diagrams. However, such..." current
  • 04:3804:38, 17 February 2026 diff hist +115 Main Page →Validation
  • 04:3004:30, 17 February 2026 diff hist +1,627 N 2026Barchet NonUniform Created page with "== Citation == Barchet, C., von Loeffelholz, O., Bahena-Ceron, R., Klaholz, B.P. and Urzhumtsev, A.G. 2026. Explicit correction of severely non-uniform distributions of cryo-EM views. Biological Crystallography. 82, 2 (2026). == Abstract == The quality of three-dimensional macromolecular image reconstruction by cryo electron microscopy (cryo-EM) strongly depends on the number and the quality of the respective two-dimensional projections and on their angular distributi..." current
  • 04:2904:29, 17 February 2026 diff hist +109 Main Page →3D Reconstruction

13 February 2026

  • 09:0409:04, 13 February 2026 diff hist +1,480 N 2025Zhang CryoPROS Created page with "== Citation == Zhang, H., Zheng, D., Wu, Q., Yan, N., Peng, H., Hu, Q., Peng, Y., Yan, Z., Shi, Z., Bao, C. and others 2025. CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles. Nature Communications. 16, 1 (2025), 4565. == Abstract == The preferred orientation phenomenon is a common issue in cryo-EM, posing a persistent challenge to conventional reconstruction methods. In this study, we introduce cryoPROS, a comput..." current
  • 09:0309:03, 13 February 2026 diff hist +106 Main Page →3D Reconstruction
  • 07:5807:58, 13 February 2026 diff hist +677 N 2026Zhou Atomic Created page with "== Citation == Zhou, X., Xu, X. and Zhang, G. 2026. When cryo-EM modeling meets structure prediction: Structural biology technologies. Nature Structural & Molecular Biology. (2026), 1–3. == Abstract == Accurately interpreting density maps into atomic models is a central yet challenging goal of cryo-EM. Two studies now reveal distinct ways in which protein structure prediction can be incorporated into cryo-EM model building to enable more accurate and robust automate..." current
  • 07:5807:58, 13 February 2026 diff hist 0 Main Page →Books and reviews
  • 07:5707:57, 13 February 2026 diff hist +90 Main Page →Books and reviews

12 February 2026

  • 08:5908:59, 12 February 2026 diff hist +2,467 N 2025Mondal EMSequenceFinder Created page with "== Citation == Mondal, D., Kumar, V., Satler, T., Ramachandran, R., Saltzberg, D., Chemmama, I., Pilla, K.B., Echeverria, I., Webb, B.M., Gupta, M. and others 2025. Recognizing amino acid sidechains in a medium-resolution cryo-electron density map. Protein Science. 34, 8 (2025), e70217. == Abstract == Building an accurate atomic structure model of a protein into a cryo-electron microscopy (cryo-EM) map at worse than 3 Å resolution is difficult. To facilitate this t..." current
  • 08:5808:58, 12 February 2026 diff hist +128 Main Page →Fitting and docking
  • 08:2508:25, 12 February 2026 diff hist +2,201 N 2025Hansel Ligand Created page with "== Citation == Hansel-Harris, A.T., Tillack, A.F., Santos-Martins, D., Holcomb, M. and Forli, S. 2025. Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance. Protein Science. 34, 3 (2025), e70082. == Abstract == Recent advances in structural biology have led to the publication of a wealth of high-resolution x-ray crystallography (XRC) and cryo-EM macromolecule structures, including many complexe..." current
  • 08:2408:24, 12 February 2026 diff hist +92 Main Page →Fitting and docking

16 January 2026

  • 15:4915:49, 16 January 2026 diff hist +1,266 N 2025Yan Foundation Created page with "== Citation == Yan, Y., Fan, S., Yuan, F. and Shen, H. 2025. A comprehensive foundation model for cryo-EM image processing. Nature Methods. 23, (2025), 88–95. == Abstract == Cryogenic electron microscopy (cryo-EM) has become a premier technique for determining high-resolution structures of biological macromolecules. However, its broad application is constrained by the demand for specialized expertise. Here, to address this limitation, we introduce the Cryo-EM Image..." current
  • 15:4815:48, 16 January 2026 diff hist +118 Main Page →2D Preprocessing
  • 15:3715:37, 16 January 2026 diff hist +2,138 N 2025Ma DeepTracer Created page with "== Citation == Ma, X. and Si, D. 2025. Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps. Computational Biology and Chemistry. 119, (2025), 108494. == Abstract == Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and grap..." current
  • 15:3615:36, 16 January 2026 diff hist +100 Main Page →Fitting and docking

9 January 2026

  • 10:1610:16, 9 January 2026 diff hist +1,472 N 2025Matinyan TRPX Created page with "== Citation == Matinyan, S., Filipcik, P., Waterman, D., Owen, C. and Abrahams, J. 2025. TRPXv2. 0: superfast, parallel compression of diffraction patterns and images, with native Python and HDF5 support. Ultramicroscopy. (2025), 114298. == Abstract == Scientific data in structural biology are being produced faster and in larger volumes than can be comfortably stored, processed, or shared. To address this challenge, we introduced the next generation TERSE/PROLIX (TRPX..." current
  • 10:1610:16, 9 January 2026 diff hist +78 Main Page →Software
  • 08:3108:31, 9 January 2026 diff hist +2,019 N 2026Heymann Ewald Created page with "== Citation == Heymann, J.B. 2026. The relationship between the Ewald sphere and exit wave explored using focal series electron micrographs. IUCrJ. 13, 1 (2026). == Abstract == CryoEM reconstructions must be performed along the Ewald spheres to achieve resolutions beyond the projection approximation limit. The linear theory of image formation models the scattering from the specimen and focusing by the objective lens as two conjugate Ewald spheres that correspond to th..." current
  • 08:3008:30, 9 January 2026 diff hist +144 Main Page →Image formation

7 January 2026

  • 08:1408:14, 7 January 2026 diff hist +1,873 N 2026Mulvaney CASP16 Created page with "== Citation == Mulvaney, T., Kryshtafovych, A. and Topf, M. 2026. Cryo-EM Analysis in CASP16. Proteins: Structure, Function, and Bioinformatics. (2026). == Abstract == Since CASP13, experimentalists have been encouraged to provide their cryo-EM data along with the derived atomic models to the CASP organizers to aid assessment. In CASP16, 38 cryo-EM datasets were provided for assessment, which represented most cryo-EM targets. The corresponding targets typically compri..." current
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