Main public logs

Combined display of all available logs of 3DEM-Methods. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 17:28, 17 January 2025 WikiSysop talk contribs created page 2025Elferich CTFFind5 (Created page with "== Citation == J. Elferich, L. Kong, X. Zottig, and N. Grigorieff, “CTFFIND5 provides improved insight into quality, tilt, and thickness of TEM samples,” eLife, vol. 13, p. RP97227, 2024. == Abstract == Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of...")
• 17:20, 17 January 2025 WikiSysop talk contribs created page 2024Zhang Kam (Created page with "== Citation == A. Zhang et al., “Moment-based metrics for molecules computable from cryogenic electron microscopy images,” Biological Imaging, vol. 4, p. e3, 2024. == Abstract == Single-particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution three-dimensional (3D) structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3D reconstruction, known...")
• 09:47, 14 January 2025 WikiSysop talk contribs created page 2024Sanchez Cesped (Created page with "== Citation == R. Sanchez-Garcia, M. Saur, J. Vargas, C. Poelking, and C. M. Deane, “CESPED: A benchmark for supervised particle pose estimation in cryo-EM,” Physical Review Research, vol. 6, no. 2, p. 23245, 2024. == Abstract == Cryo-EM is a powerful tool for understanding macromolecular structures, yet current methods for structure reconstruction are slow and computationally demanding. To accelerate research on pose estimation, we present CESPED, a data set spec...")
• 08:02, 3 January 2025 WikiSysop talk contribs created page 2023Lucas Baited (Created page with "== Citation == B. A. Lucas, B. A. Himes, and N. Grigorieff, “Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias,” Elife, vol. 12, p. RP90486, 2023. == Abstract == Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and c...")
• 07:55, 3 January 2025 WikiSysop talk contribs created page 2024Bhattacharjee TimeResolved (Created page with "== Citation == S. Bhattacharjee et al., “Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling,” Cell, vol. 187, no. 3, pp. 782–796, 2024. == Abstract == The rapid kinetics of biological processes and associated short-lived conformational changes pose a significant challenge in attempts to structurally visualize biomolecules during a reaction in real time. Conventionally, on-...")
• 07:50, 3 January 2025 WikiSysop talk contribs created page 2024Tuijtel Lamellae (Created page with "== Citation == M. W. Tuijtel et al., “Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging,” Science Advances, vol. 10, no. 17, p. eadk6285, 2024. == Abstract == Cryo–electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imagin...")
• 07:45, 3 January 2025 WikiSysop talk contribs created page 2023Grassetti Graphene (Created page with "== Citation == A. V. Grassetti, M. B. May, and J. H. Davis, “Enhancing CryoEM Sample Preparation Using Graphene Monolayer on Microscopy Grids (Video)| JoVE,” JoVE (Journal of Visualized Experiments), no. 201, p. e66023, 2023. == Abstract == In cryogenic electron microscopy (cryoEM), purified macromolecules are applied to a grid bearing a holey carbon foil; the molecules are then blotted to remove excess liquid and rapidly frozen in a roughly 20-100 nm thick layer...")
• 07:58, 27 December 2024 WikiSysop talk contribs created page 2023DiIorio AbInitio (Created page with "== Citation == M. C. DiIorio and A. W. Kulczyk, “Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy,” Micromachines, vol. 14, no. 9, p. 1674, 2023. == Abstract == Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. Howe...")
• 07:53, 27 December 2024 WikiSysop talk contribs created page 2023Langeberg RNAScaffold (Created page with "== Citation == C. J. Langeberg and J. S. Kieft, “A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM,” Nucleic Acids Research, vol. 51, no. 20, pp. e100–e100, 2023. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules remain challenging targets due to their intrinsic low signal to noise ratio. Methods to resolve small proteins...")
• 07:37, 27 December 2024 WikiSysop talk contribs created page 2023Riahi Transport (Created page with "== Citation == A. T. Riahi, G. Woollard, F. Poitevin, A. Condon, and K. D. Duc, “Alignot: An optimal transport based algorithm for fast 3d alignment with applications to cryogenic electron microscopy density maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023. == Abstract == Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step re...")
• 07:19, 27 December 2024 WikiSysop talk contribs created page 2024Singer Wasserstein (Created page with "== Citation == A. Singer and R. Yang, “Alignment of density maps in Wasserstein distance,” Biological Imaging, vol. 4, p. e5, 2024. == Abstract == In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function en...")
• 11:01, 26 December 2024 WikiSysop talk contribs created page 2023Forsberg Filter (Created page with "== Citation == B. O. Forsberg, P. N. Shah, and A. Burt, “A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps,” Nature Communications, vol. 14, no. 1, p. 5802, 2023. == Abstract == Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great eff...")
• 10:50, 26 December 2024 WikiSysop talk contribs created page 2023Dai CryoFEM (Created page with "== Citation == X. Dai, L. Wu, S. Yoo, and Q. Liu, “Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps,” Briefings in Bioinformatics, vol. 24, no. 6, p. bbad405, 2023. == Abstract == Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3-D atomic models of biological molecules. AlphaFold-predicted models generate initial 3-D coordinates; however, model inaccuracy and conformational heterogeneity o...")
• 10:44, 26 December 2024 WikiSysop talk contribs created page 2023Afonine Varref (Created page with "== Citation == P. V. Afonine, A. Gobet, L. Moissonnier, J. Martin, B. K. Poon, and V. Chaptal, “Conformational space exploration of cryo-EM structures by variability refinement,” Biochimica et Biophysica Acta (BBA)-Biomembranes, vol. 1865, no. 4, p. 184133, 2023. == Abstract == Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local...")
• 10:40, 26 December 2024 WikiSysop talk contribs created page 2023Yee Ot2Rec (Created page with "== Citation == N. B.-y. Yee, E. M. Ho, M. Darrow, and M. Basham, “Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow,” Biophysical Journal, vol. 122, no. 3, p. 462a, 2023. == Abstract == Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With...")
• 20:13, 23 December 2024 WikiSysop talk contribs created page 2023Zhang Denoising (Created page with "== Citation == D. Zhang et al., “Unsupervised Cryo-EM Images Denoising and Clustering based on Deep Convolutional Autoencoder and K-Means++,” IEEE Trans. Medical Imaging, vol. 42, pp. 1509–1521, 2023. == Abstract == Cryo-electron microscopy (cryo-EM) is a widely used structural determination technique. Because of the extremely low signal-to-noise ratio (SNR) of images captured by cryo-EM, clustering single-particle cryo-EM images with high accuracy is challengin...")
• 20:03, 23 December 2024 WikiSysop talk contribs created page 2024Bendory Complexity (Created page with "== Citation == T. Bendory and D. Edidin, “The Sample Complexity of Sparse Multireference Alignment and Single-Particle Cryo-Electron Microscopy,” SIAM J. on Mathematics of Data Science, vol. 6, no. 2, pp. 254–282, 2024. == Abstract == Multireference alignment (MRA) is the problem of recovering a signal from its multiple noisy copies, each acted upon by a random group element. MRA is mainly motivated by single-particle cryo–electron microscopy (cryo-EM) that ha...")
• 19:58, 23 December 2024 WikiSysop talk contribs created page 2024Liu DeepETPicker (Created page with "== Citation == G. Liu, T. Niu, M. Qiu, Y. Zhu, F. Sun, and G. Yang, “DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning,” Nature Communications, vol. 15, no. 1, p. 2090, 2024. == Abstract == To solve three-dimensional structures of biological macromolecules in situ, large numbers of particles often need to be picked from cryo-electron tomograms. However, adoption of automated particle-picking meth...")
• 19:54, 23 December 2024 WikiSysop talk contribs created page 2023Rice TomoTwin (Created page with "== Citation == G. Rice, T. Wagner, M. Stabrin, O. Sitsel, D. Prumbaum, and S. Raunser, “TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining,” Nature methods, vol. 20, no. 6, pp. 871–880, 2023. == Abstract == Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volu...")
• 19:50, 23 December 2024 WikiSysop talk contribs created page 2023Weiss Noise (Created page with "== Citation == G. Weiss-Dicker, A. Eldar, Y. Shkolinsky, and T. Bendory, “Unsupervised particle sorting for cryo-EM using probabilistic PCA,” in 2023 IEEE 20th Intl. Symposium on Biomedical Imaging (ISBI), IEEE, 2023, pp. 1–5. == Abstract == Single-particle cryo-electron microscopy (cryo-EM) is a leading technology to resolve the structure of molecules. Early in the process, the user detects potential particle images in the raw data. Typically, there are many fa...")
• 19:43, 23 December 2024 WikiSysop talk contribs created page 2024Jamali Modelangelo (Created page with "== Citation == K. Jamali, L. Käll, R. Zhang, A. Brown, D. Kimanius, and S. H. Scheres, “Automated model building and protein identification in cryo-EM maps,” Nature, vol. 628, no. 8007, pp. 450–457, 2024. == Abstract == Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learnin...")
• 19:34, 23 December 2024 WikiSysop talk contribs created page 2023Beton Fitting (Created page with "== Citation == J. G. Beton, T. Cragnolini, M. Kaleel, T. Mulvaney, A. Sweeney, and M. Topf, “Integrating model simulation tools and cryo-electron microscopy,” Wiley Interdisciplinary Reviews: Computational Molecular Science, vol. 13, no. 3, p. e1642, 2023. == Abstract == The power of computer simulations, including machine-learning, has become an inseparable part of scientific analysis of biological data. This has significantly impacted the field of cryogenic elec...")
• 19:27, 23 December 2024 WikiSysop talk contribs created page 2023Geva AbInitio (Created page with "== Citation == A. S. Geva and Y. Shkolnisky, “A common lines approach for ab initio modeling of molecules with tetrahedral and octahedral symmetry,” SIAM J. on Imaging Sciences, vol. 16, no. 4, pp. 1978–2014, 2023. == Abstract == A main task in cryo-electron microscopy single particle reconstruction is to nd a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy projection-images. In this work, we propose an algorithm f...")
• 08:16, 19 December 2024 WikiSysop talk contribs created page 2023Harpaz Alignment (Created page with "== Citation == Y. Harpaz and Y. Shkolnisky, “Three-dimensional alignment of density maps in cryo-electron microscopy,” Biological Imaging, vol. 3, p. e8, 2023. == Abstract == A common task in cryo-electron microscopy data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps, which exploits common lines between projection images of the maps. The algorithm is ful...")
• 08:02, 19 December 2024 WikiSysop talk contribs created page 2022Bharadwaj Scattering (Created page with "== Citation == A. Bharadwaj and A. J. Jakobi, “Electron scattering properties of biological macromolecules and their use for cryo-EM map sharpening,” Faraday Discussions, vol. 240, pp. 168–183, 2022. == Abstract == Resolution-dependent loss of contrast in cryo-EM maps may obscure features at high resolution that are critical for map interpretation. Post-processing of cryo-EM maps can improve the interpretability by adjusting the resolution-dependence of structur...")
• 08:40, 12 December 2024 WikiSysop talk contribs created page 2024Karimi Vesicle (Created page with "== Citation == R. Karimi, C. E. Coupland, and J. L. Rubinstein, “Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles,” J. Structural Biology, vol. 216, no. 4, p. 108148, 2024. == Abstract == Electron cryomicroscopy (cryo-EM) has recently allowed determination of near-atomic resolution structures of membrane proteins and protein complexes embedded in lipid vesicles. However, particle selection from electron micrographs of t...")
• 08:35, 12 December 2024 WikiSysop talk contribs created page 2024Remis Damage (Created page with "== Citation == J. Remis et al., “Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage,” Journal of Structural Biology, p. 108150, 2024. == Abstract == Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 Å resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-p...")
• 08:30, 12 December 2024 WikiSysop talk contribs created page 2024Hsieh MinIce (Created page with "== Citation == C.-C. Hsieh, Z.-J. Lin, and L.-J. Lai, “Minimizing ice contamination during specimen preparation for cryo-soft X-ray tomography and cryo-electron tomography,” Journal of Structural Biology: X, vol. 10, p. 100113, 2024. == Abstract == Cryo-soft X-ray tomography (cryo-SXT) is a newly developed technique for imaging 3D whole cells in nearly native states. Cryo-SXT users require the preparation of numerous cryo-sample grids to use the allocated beamtime...")
• 08:04, 12 December 2024 WikiSysop talk contribs created page 2024Schiotz Review (Created page with "== Citation == O. H. Schiøtz, S. Klumpe, J. M. Plitzko, and C. J. Kaiser, “Cryo-electron tomography: en route to the molecular anatomy of organisms and tissues,” Biochemical Society Transactions, p. BST20240173, 2024. == Abstract == Cryo-electron tomography (cryo-ET) has become a key technique for obtaining structures of macromolecular complexes in their native environment, assessing their local organization and describing the molecular sociology of the cell. Whi...")
• 06:34, 12 December 2024 WikiSysop talk contribs created page 2024Harley 40 (Created page with "== Citation == I. Harley, F. Mazzotta, X. Shaulli, F. Scheffold, K. Landfester, and I. Lieberwirth, “Practical considerations for plunge freezing samples over 40° C for Cryo-EM,” Micron, p. 103745, 2024. == Abstract == Cryo-EM is now an established tool for examining samples in their native, hydrated states—a leap made possible by vitrification. Utilising this sample preparation method to directly visualise temperature-responsive samples allows for deeper insig...")
• 15:07, 18 November 2024 WikiSysop talk contribs created page 2024deLaRosa EMHub (Created page with "== Citation == J. M. de la Rosa-Trevin et al., “EMhub: a web platform for data management and on-the-fly processing in scientific facilities,” Biological Crystallography, vol. 80, no. 11, 2024. == Abstract == Most scientific facilities produce large amounts of heterogeneous data at a rapid pace. Managing users, instruments, reports and invoices presents additional challenges. To address these challenges, EMhub, a web platform designed to support the daily operatio...")
• 10:31, 8 November 2024 WikiSysop talk contribs created page 2024Cameron REPIC (Created page with "== Citation == C. J. Cameron, S. J. Seager, F. J. Sigworth, H. D. Tagare, and M. B. Gerstein, “REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers,” Communications Biology, vol. 7, no. 1, p. 1421, 2024. == Abstract == Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computa...")
• 10:28, 8 November 2024 WikiSysop talk contribs created page 2024Li EM2NA (Created page with "== Citation == T. Li, H. Cao, J. He, and S.-Y. Huang, “Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps,” Nature Communications, vol. 15, no. 1, p. 9367, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) is one of the most powerful experimental methods for macromolecular structure determination. However, accurate DNA/RNA structure modeling from cryo-EM maps is still challenging especially for protein-DNA/RNA or multi-chai...")
• 10:22, 8 November 2024 WikiSysop talk contribs created page 2024Ermel DataPortal (Created page with "== Citation == U. Ermel et al., “A data portal for providing standardized annotations for cryo-electron tomography,” Nature Methods, pp. 1–3, 2024. == Abstract == We present the cryoET Data Portal (https://cryoetdataportal. czscience.com/), containing annotated cryoET datasets in standardized formats, as a resource for the cryoET community == Keywords == == Links == https://www.nature.com/articles/s41592-024-02477-2 == Related software == == Related methods...")
• 10:16, 8 November 2024 WikiSysop talk contribs created page 2024Wang DiffModeller (Created page with "== Citation == X. Wang, H. Zhu, G. Terashi, M. Taluja, and D. Kihara, “DiffModeler: large macromolecular structure modeling for cryo-EM maps using a diffusion model,” Nature Methods, pp. 1–11, 2024. == Abstract == Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multichain protein complexes. However, modeling a large complex structure, such as those with more than ten chains, is challenging, particularly when the map resolution de...")
• 10:11, 8 November 2024 WikiSysop talk contribs created page 2024Anuk Auction (Created page with "== Citation == S. Anuk, T. Bendory, and A. Painsky, “Image detection using combinatorial auction,” IEEE Open J. Signal Processing, 2024. == Abstract == This paper studies the optimal solution of the classical problem of detecting the location of multiple image occurrences in a two-dimensional, noisy measurement. Assuming the image occurrences do not overlap, we formulate this task as a constrained maximum likelihood optimization problem.We show that the maximum li...")
• 10:06, 8 November 2024 WikiSysop talk contribs created page 2024Chen EModelX (Created page with "== Citation == S. Chen, S. Zhang, X. Fang, L. Lin, H. Zhao, and Y. Yang, “Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences,” Nature Communications, vol. 15, no. 1, p. 8808, 2024. == Abstract == Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation...")
• 10:00, 8 November 2024 WikiSysop talk contribs created page 2024Moriya GoToCloud (Created page with "== Citation == T. Moriya, Y. Yamada, M. Yamamoto, and T. Senda, “GoToCloud optimization of cloud computing environment for accelerating cryo-EM structure-based drug design,” Communications Biology, vol. 7, no. 1, p. 1320, 2024. == Abstract == Cryogenic electron microscopy (Cryo-EM) is a widely used technique for visualizing the 3D structures of many drug design targets, including membrane proteins, at atomic resolution. However, the necessary throughput for struct...")
• 09:46, 8 November 2024 WikiSysop talk contribs created page 2024Joosten Roodmus (Created page with "== Citation == M. Joosten, J. Greer, J. Parkhurst, T. Burnley, and A. J. Jakobi, “Roodmus: A toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions,” IUCrJ, vol. 11, no. 6, 2024. == Abstract == Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be...")
• 09:37, 8 November 2024 WikiSysop talk contribs created page 2024Li Subtraction (Created page with "== Citation == S. Li, M. Li, Y. Wang, and X. Li, “Subtraction of liposome signals in cryo-EM structural determination of protein-liposome complexes,” Chinese Physics B, 2024. == Abstract == Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy (cryo-EM). However, the strong signal of liposomes under cryo-EM imaging conditions often...")
• 14:48, 22 October 2024 WikiSysop talk contribs created page 2024Lander Validation (Created page with "== Citation == G. C. Lander, “Single particle cryo-EM map and model validation: It’s not crystal clear,” Current Opinion in Structural Biology, vol. 89, p. 102918, 2024. == Abstract == The application of single particle cryogenic electron microscopy (cryo-EM) to structure determination continues to have a transformative impact on our understanding on biological systems. While there has been a great deal of algorithmic development focused on improving attainable...")
• 06:52, 18 October 2024 WikiSysop talk contribs created page 2023Sazzed Struwwel (Created page with "== Citation == S. Sazzed, P. Scheible, J. He, and W. Wriggers, “Untangling irregular actin cytoskeleton architectures in tomograms of the cell with struwwel tracer,” Intl. J. Molecular Sciences, vol. 24, no. 24, p. 17183, 2023. == Abstract == In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellu...")
• 06:40, 18 October 2024 WikiSysop talk contribs created page 2024Sanchez Anisotropy (Created page with "== Citation == R. Sanchez-Garcia, G. Gaullier, J. M. Cuadra-Troncoso, and J. Vargas, “Cryo-EM map anisotropy can be attenuated by map post-processing and a new method for its estimation,” Intl. J. Molecular Sciences, vol. 25, no. 7, p. 3959, 2024. == Abstract == One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection...")
• 05:55, 18 October 2024 WikiSysop talk contribs created page 2024vanVeen Missing (Created page with "== Citation == D. Van Veen et al., “Missing wedge completion via unsupervised learning with coordinate networks,” Intl. J. Molecular Sciences, vol. 25, no. 10, p. 5473, 2024. == Abstract == Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction qua...")
• 05:31, 18 October 2024 WikiSysop talk contribs created page 2023Ling Synch (Created page with "== Citation == S. Ling, “Solving orthogonal group synchronization via convex and low-rank optimization: Tightness and landscape analysis,” Mathematical Programming, vol. 200, no. 1, pp. 589–628, 2023. == Abstract == Group synchronization aims to recover the group elements from their noisy pairwise measurements. It has found many applications in community detection, clock synchronization, and joint alignment problem. This paper focuses on the orthogonal group syn...")
• 10:54, 8 October 2024 WikiSysop talk contribs created page 2024Huang MiLoPYP (Created page with "== Citation == Q. Huang, Y. Zhou, and A. Bartesaghi, “MiLoPYP: self-supervised molecular pattern mining and particle localization in situ,” Nature Methods, pp. 1–10, 2024. == Abstract == Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules w...")
• 17:03, 7 October 2024 WikiSysop talk contribs created page 2024Abe LEA (Created page with "== Citation == K. M. Abe, G. Li, Q. He, T. Grant, and C. J. Lim, “Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing,” Nature Communications, vol. 15, no. 1, p. 7705, 2024. == Abstract == Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Em...")
• 06:56, 6 September 2024 WikiSysop talk contribs created page 2022Levy CryoAI (Created page with "== Citation == Levy, Axel / Poitevin, Frédéric / Martel, Julien / Nashed, Youssef / Peck, Ariana / Miolane, Nina / Ratner, Daniel / Dunne, Mike / Wetzstein, Gordon. Cryoai: Amortized inference of poses for ab initio reconstruction of 3d molecular volumes from real cryo-em images. 2022. European Conference on Computer Vision, p. 540-557 == Abstract == Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us unde...")
• 06:49, 6 September 2024 WikiSysop talk contribs created page 2023Rangan Fast (Created page with "== Citation == Rangan, Aaditya V. Radial recombination for rigid rotational alignment of images and volumes. 2023. Inverse Problems, Vol. 39, No. 1, p. 015003 == Abstract == A common task in single particle electron cryomicroscopy (cryo-EM) is the rigid alignment of images and/or volumes. In the context of images, a rigid alignment involves estimating the inner product between one image of N × N pixels and another image that has been translated by some displaceme...")
• 06:38, 6 September 2024 WikiSysop talk contribs created page 2022Ganguly SparseAlign (Created page with "== Citation == Ganguly, Poulami Somanya / Lucka, Felix / Kohr, Holger / Franken, Erik / Hupkes, Hermen Jan / Batenburg, Kees Joost. Sparsealign: A grid-free algorithm for automatic marker localization and deformation estimation in cryo-electron tomography. 2022. IEEE Transactions on Computational Imaging, Vol. 8, p. 651-665 == Abstract == Tilt-series alignment is crucial to obtaining high-resolution reconstructions in cryo-electron tomography. Beam-induced local defor...")