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A user with 2,462 edits. Account created on 30 March 2009.
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22 May 2026

  • 06:3206:32, 22 May 2026 diff hist +2,278 N 2026Silva CryoJax Created page with "== Citation == Silva-Sánchez, D., Berezuk, A.M., Zhu, X., Thiede, E.H., Lederman, R.R. and Cossio, P. 2026. Cryo-Electron Microscopy Structural Ensemble Optimization Using Individual Particles. J. of Chemical Theory and Computation. (2026). == Abstract == Biomolecules are inherently dynamic, transitioning between various conformational states to execute their biological functions; consequently, characterizing their ensemble distributions (the population of these conf..." current
  • 06:3006:30, 22 May 2026 diff hist +111 Main Page →3D Heterogeneity current

16 May 2026

13 May 2026

  • 06:5206:52, 13 May 2026 diff hist +1,980 N 2026Premaraj DualJet Created page with "== Citation == Premaraj, N., Huysmans, P., Ploum, M., Schijns, L., Peters, P.J., López-Iglesias, C., Ravelli, R.B. and Knoops, K. 2026. An experimental platform for exploring dual-jet vitrification mechanisms in cryo-EM sample preparation. Methods in Microscopy. 0 (2026). == Abstract == Jet vitrification harnesses the exceptionally high cooling potential of rapidly moving liquid cryogens to achieve ultrafast sample freezing with superior cooling efficiency. Building..." current
  • 06:5206:52, 13 May 2026 diff hist +64 Main Page →Sample preparation
  • 05:4505:45, 13 May 2026 diff hist +1 Main Page →Data Processing
  • 05:4505:45, 13 May 2026 diff hist +1,730 N 2026Thibodeaux MR Created page with "== Citation == Thibodeaux, A., Bu, G., Edwards, L.C. and Rova Danelius, E. 2026. High-throughput automated molecular replacement for small-molecule MicroED data. IUCrJ. 13, 3 (2026). == Abstract == Interest in electron diffraction (ED) for structural characterization of both proteins and small molecules has grown significantly over the last decade. While ab initio phasing methods remain the gold standard for ED data from smallmolecule samples, radiation beam damage du..." current
  • 05:4405:44, 13 May 2026 diff hist +87 Main Page →Data Processing

4 May 2026

  • 08:3608:36, 4 May 2026 diff hist +2,220 N 2025Hu Denoising Created page with "== Citation == Hu, B., Zhang, D.-X., Liu, S.-Q., Xie, X.-L., Zhou, X.-H., Li, H.-J., Zheng, Q.-B., Zhang, F., Hou, Z.-G. and Xia, N.-S. 2025. Particle Restoration: A Novel Image Processing Framework for Improving Real Cryo-EM Image Quality in Single Particle Analysis. IEEE Trans. on Computational Biology and Bioinformatics. (2025). == Abstract == Cryo-electron microscopy single particle analysis (cryo-EM SPA) is the most powerful technique for biomacromolecule structu..." current
  • 08:3508:35, 4 May 2026 diff hist +78 Main Page →2D Preprocessing

30 April 2026

  • 06:5106:51, 30 April 2026 diff hist +2,456 N 2025Costa PERC Created page with "== Citation == Costa-Gomes, B., Greer, J., Juraschko, N., Parkhurst, J., Mirecka, J., Famili, M., Rangel-Smith, C., Strickson, O., Lowe, A., Basham, M. and others 2025. PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning. Structural Biology and Crystallization Communications. 81, 10 (2025). == Abstract == Ease of access to data, tools and models expedites scientific research. In structural biolo..." current
  • 06:5006:50, 30 April 2026 diff hist +86 Main Page →Software
  • 06:4206:42, 30 April 2026 diff hist +1,604 N 2025Giri Sharpening Created page with "== Citation == Giri, N., Chen, X., Wang, L. and Cheng, J. 2025. A labeled dataset for AI-based cryo-EM map enhancement. Computational and Structural Biotechnology Journal. 27, (2025), 2843–2850. == Abstract == Cryogenic electron microscopy (cryo-EM) has transformed structural biology by enabling near atomic resolution imaging of macromolecular complexes. However, cryo-EM density maps suffer from intrinsic noise arising from structural sources, shot noise, and digita..." current
  • 06:4106:41, 30 April 2026 diff hist +79 Main Page →Databases
  • 05:5105:51, 30 April 2026 diff hist +1,124 N 2026Lin HDX Created page with "== Citation == Lin, X. and Cheng, Y. 2026. Making sense of invisible densities in single-particle cryo-EM. IUCrJ. 13, 3 (2026). == Abstract == In the era of single-particle cryogenic electron microscopy (cryo-EM) and AIdriven protein structure prediction, obtaining high-resolution protein structures, either experimentally or computationally, has become increasingly routine. Yet studying and understanding protein dynamics remains challenging. In singleparticle cryo-EM,..." current
  • 05:5005:50, 30 April 2026 diff hist +109 Main Page →Books and reviews

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

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
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