A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions |
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Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM |
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A Fijivirus Major Viroplasm Protein Shows RNA-Stimulated ATPase Activity by Adopting Pentameric and Hexameric Assemblies of Dimers |
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A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis |
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Local defocus estimation in single particle analysis in cryo-electron microscopy |
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ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis |
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Umbrella Data Management Plans to Integrate FAIR Data : Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness |
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Performance and Quality Comparison of Movie Alignment Software for Cryogenic Electron Microscopy |
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Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials |
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Emerging Themes in CryoEM─Single Particle Analysis Image Processing |
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ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation |
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Cryo-Electron Microscopy: The field of 1,000+ methods |
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On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy |
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BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction |
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Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools |
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New Tools and Pipelines for Continuous Heterogeneity Analysis from Cryo-EM using Normal Modes and 3D Zernike Polynomials |
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Image processing tools for the validation of CryoEM maps |
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Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0 |
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Structural analysis of receptors and actin polarity in platelet protrusions |
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Identification of incorrectly oriented particles in cryo-EM single particle analysis |
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DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM |
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Cryo-EM and Single-Particle Analysis with Scipion |
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Algorithmic robustness to preferred orientations in single particle analysis by CryoEM |
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Cryo-EM density maps adjustment for subtraction, consensus and sharpening |
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DeepEMhancer: a deep learning solution for cryo-EM volume post-processing |
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Self-assembly and regulation of protein cages from pre-organised coiled-coil modules |
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FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation |
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PDBe-KB: collaboratively defining the biological context of structural data |
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Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials |
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Advances in xmipp for cryo–electron microscopy: From xmipp to scipion |
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Principal component analysis is limited to low-resolution analysis in cryoEM |
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3DBionotes COVID-19 Edition. |
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Author Correction: Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. |
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Integration of Cryo-EM Model Building Software in Scipion |
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Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells |
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Automatic local resolution-based sharpening of cryo-EM maps |
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Measuring local-directional resolution and local anisotropy in cryo-EM maps |
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Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures |
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Local resolution estimates of cryoEM reconstructions |
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State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps |
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Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data |
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Measurement of local resolution in electron tomography |
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MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning |
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FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy |
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Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening |
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A GPU acceleration of 3-D Fourier reconstruction in cryo-EM |
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The Molecular Control of Calcitonin Receptor Signaling |
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Structural basis for cooperativity of human monoclonal antibodies to meningococcal factor H-binding protein |
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DeepRes: A new deep-learning- and aspect-based local resolution method for electron-microscopy maps |
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Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion |
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Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy |
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3DBIONOTES v3.0: Crossing molecular and structural biology data with genomic variations |
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Validation of electron microscopy initial models via small angle X-ray scattering curves |
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Cryo-Electron Tomography and Proteomics studies of centrosomes from differentiated quiescent thymocytes |
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BIPSPI: a method for the prediction of partner-specific protein-protein interfaces |
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West-Life: A Virtual Research Environment for structural biology |
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MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps |
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Map challenge: Analysis using a pair comparison method based on Fourier shell correlation |
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Using Scipion for stream image processing at Cryo-EM facilities |
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A new algorithm for high-resolution reconstruction of single particles by electron microscopy |
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Deep Consensus, a deep learning-based approach for particle pruning in cryo-electron microscopy |
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The first single particle analysis Map Challenge: A summary of the assessments |
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Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead |
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X-ray structure of full-length human RuvB-Like 2-mechanistic insights into coupling between ATP binding and mechanical action |
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Blind estimation of DED camera gain in Electron Microscopy |
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Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis |
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Agricultural residues are efficient abrasive tools for weed control |
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Scipion web tools: Easy to use cryo-EM image processing over the web |
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3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures |
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3DBIONOTES v2.0: A web server for the automatic annotation of macromolecular structures |
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Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo |
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ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds |
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A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy |
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Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap |
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Quantitative analysis of 3D alignment quality: Its impact on soft-validation, particle pruning and homogeneity analysis |
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Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors |
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XTEND: Extending the depth of field in cryo soft X-ray tomography |
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Electron microscopy structural insights into CPAP oligomeric behavior: A plausible assembly process of a supramolecular scaffold of the centrosome |
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A review of resolution measures and related aspects in 3D Electron Microscopy. |
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Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope |
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Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution |
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Fast and automatic identification of particle tilt pairs based on Delaunay triangulation. |
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Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ |
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Local analysis of strains and rotations for macromolecular electron microscopy maps |
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Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy |
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Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions |
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3DBIONOTES: A unified, enriched and interactive view of macromolecular information |
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The Electron Microscopy eXchange (EMX) initiative. |
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StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes |
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Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography |
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3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling |
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Particle alignment reliability in single particle electron cryomicroscopy: a general approach. |
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A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function |
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Fast and accurate conversion of atomic models into electron density maps |
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Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited |
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Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k |
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Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data |
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Using neighborhood cohesiveness to infer interactions between protein domains |
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CTF Challenge: Result summary |
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Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star |
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A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy |
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Alignment of direct detection device micrographs using a robust Optical Flow approach |
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Outlier detection for single particle analysis in Electron Microscopy |
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The soft x-ray transform |
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Efficient initial volume determination from electron microscopy images of single particles |
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Error analysis of the principal component analysis demodulation algorithm |
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Xmipp 3.0: An improved software suite for image processing in electron microscopy |
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A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs |
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Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques |
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Fringe pattern denoising by image dimensionality reduction |
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Structure and Non-Structure of Centrosomal Proteins |
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On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy |
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FASTDEF: Fast defocus and astigmatism estimation for high-throughput transmission electron microscopy |
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Generalization of the Principal Component Analysis algorithm for interferometry |
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Image processing for Cellular tomography using soft X-rays |
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Data management challenges in three-dimensional EM |
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Corrigendum to "Fast, robust and accurate determination of transmission electron microscopy contrast transfer function" [J. Struct. Biol. 160 (2007) 249-262] |
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Shack-Hartmann centroid detection using the spiral phase transform |
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Image formation in cellular X-ray microscopy |
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Two-step demodulation based on the Gram-Schmidt orthonormalization method |
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Integrating human and murine anatomical gene expression data for improved comparisons |
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Two-step interferometry by a regularized optical flow algorithm |
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Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA |
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PRIDEViewer: A novel user-friendly interface to visualize PRIDE XML files |
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Maximum likelihood based classification of electron tomographic data |
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Non-rigid consistent registration of 2D image sequences |
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OmicsHub Proteomics Software Tool. |
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Data Management, Analysis, Standardization and Reproducibility in a ProteoRed Multicentric Quantitative Proteomics Study with the OmicsHub Proteomics Software Tool. |
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A clustering approach to multireference alignment of single-particle projections in electron microscopy |
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MARQ: An online tool to mine GEO for experiments with similar or opposite gene expression signatures |
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Dynamic Effects of Cofactors and DNA on the Oligomeric State of Human Mitochondrial DNA Helicase |
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Conformational Rearrangements of SV40 Large T Antigen during Early Replication Events |
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Moara: A Java library for extracting and normalizing gene and protein mentions |
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tmRNA·SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes |
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Averaging of Electron Subtomograms and Random Conical Tilt Reconstructions through Likelihood Optimization |
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aGEM: An integrative system for analyzing spatial-temporal gene-expression information |
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Automatic particle selection from electron micrographs using machine learning techniques |
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Insights into the molecular architecture of the 26S proteasome |
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Introducing robustness to maximum-likelihood refinement of electron-microsopy data |
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SENT: Semantic features in text |
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GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information |
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Maximum likelihood refinement of electron microscopy data with normalization errors |
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Marker-free image registration of electron tomography tilt-series |
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A theoretical model for EM-ML reconstruction algorithms applied to rotating PET scanners |
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Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra |
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Comparison of molecular dynamics and superfamily spaces of protein domain deformation |
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CentrosomeDB: A human centrosomal proteins database |
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Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs |
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Image processing for electron microscopy single-particle analysis using XMIPP |
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Crystal structure of a near-full-length archaeal MCM: Functional insights for an AAA plus hexameric helicase |
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Assessment of protein set coherence using functional annotations |
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Design and analysis of an object-oriented discrete-event simulation engine for ATM telecommunication networks |
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Interoperability with Moby 1.0 - It\'s better than sharing your toothbrush! |
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ChIPCodis: Mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data |
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Volumetric restrictions in single particle 3DEM reconstruction |
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Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function |
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Modeling experimental image formation for likelihood-based classification of electron microscopy |
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GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists |
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Quaternary structures of tumor suppressor p53 and a specific p53-DNA complex |
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Parameter optimization in 3D reconstruction on a large scale grid |
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Integrating electron microscopy information into existing Distributed Annotation Systems |
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Quasi-atomic model of bacteriophage T7 procapsid shell: Insights into the structure and evolution of a basic fold |
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Loading a ring: Structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase |
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Electron tomography of complex biological specimens on the Grid |
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Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization |
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On the nature of 2D crystal unbending |
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Optimization problems in electron microscopy of single particles |
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Parallelization of reconstruction algorithms in three-dimensional electron microscopy |
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BioNMF: A versatile tool for non-negative matrix factorization in biology |
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A literature-based similarity metric for biological processes |
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Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies |
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Image processing and 3-D reconstruction in electron microscopy |
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Quaternary polymorphism of replicative helicase G40P: Structural mapping and domain rearrangement |
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Structural basis for the cooperative assembly of large T antigen on the origin of replication |
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Nonsmooth nonnegative matrix factorization (nsNMF) |
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Biclustering of gene expression data by non-smooth non-negative matrix factorization |
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Integrated analysis of gene expression by association rules discovery |
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Discovering semantic features in the literature: a foundation for building functional associations |
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Double hexamer disruption and biochemical activities of Methanobacterium thermoautotrophicum MCM |
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Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum |
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Multiobjective algorithm parameter optimization using multivariate statistics in three-dimensional electron microscopy reconstruction |
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Fast maximum-likelihood refinement of electron microscopy images |
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Classification of single-projection reconstructions for cryo-electron microscopy data of icosahedral viruses |
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Maximum-likelihood multi-reference refinement for electron microscopy images |
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Mining association rules from biological databases |
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SPI-EM: Towards a tool for predicting CATH superfamilies in 3D-EM maps |
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Grid computing in structure determination of biological specimens by electron microscope tomography |
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XMIPP: a new generation of an open-source image processing package for electron microscopy |
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Normalizing projection images: A study of image normalizing procedures for single particle three-dimensional electron microscopy |
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Designing and executing scientific workflows with a programmable integrator |
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A multiresolution approach to orientation assignment in 3D electron microscopy of single particles |
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The potential of grid computing in three-dimensional electron microscopy |
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3-D reconstruction of 2-D crystals in real space |
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Transfer function restoration in 3D electron microscopy via iterative data refinement |
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Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing |
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High performance computing in electron microscope tomography of complex biological structures |
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Large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication |
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FEMME database: Topologic and geometric information of macromolecules |
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A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment |
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Engene: The processing and exploratory analysis of gene expression data |
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New electron microscopy database and deposition system |
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Spin images and neural networks for efficient content-based retrieval in 3D object databases |
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Volumetric constraints in 3D tomography applied to electron microscopy |
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3D reconstruction of 2D crystals from projections in real space |
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Modeling shape and topology of low-resolution density maps of biological macromolecules |
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Command-line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE) |
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High-performance electron tomography of complex biological specimens |
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Quantitative self-organizing maps for clustering electron tomograms |
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Smoothly distributed fuzzy c-means: A new self-organizing map |
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The DnaB center dot DnaC complex: a structure based on dimers assembled around an occluded channel |
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A novel neural network technique for analysis and classification of EM single-particle images |
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The effect of overabundant projection directions on 3D reconstruction algorithms |
|
pH-Controlled quaternary states of hexameric DnaB helicase |
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A new phase consistency criterion and its application in electron crystallography |
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Image processing approaches to biological three-dimensional electron microscopy |
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The need for a shared database infrastructure: Combining X-ray crystallography and electron microscopy |
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Mapping and fuzzy classification of macromolecular images using self-organizing neural networks |
|
Sequence-related protein export NTPases encoded by the conjugative transfer region of RP4 and by the cag pathogenicity island of Helicobacter pylori share similar hexameric ring structures |
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Large T-antigen double hexamers imaged at the simian virus 40 origin of replication |
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Helicases as nucleic acid unwinding machines |
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Application of the fuzzy kohonen clustering network to biological macromolecules images classification |
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A framework for querying a database for structural information on 3D images of macromolecules: A Web-based query-by-content prototype on the BioImage macromolecular server |
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The BioImage Database Project: Organizing multidimensional biological images in an object-relational database |
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The three-dimensional structure of a DNA translocating machine at 10 Å resolution |
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Organising multi-dimensional biological image information: The BioImage database |
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Effects of uneven sampling in 3D reconstructions. |
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Self-organizing tree-growing network for the classification of protein sequences |
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Polymorphic quaternary organization of the Bacillus subtilis bacteriophage SPP1 replicative helicase (G40P) |
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Automatic classification of biological particles from electron-microscopy images using conventional and genetic-algorithm optimized learning vector quantization |
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Computational space reduction and parallelization of a new clustering approach for large groups of sequences |
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Parallel implementation of DNAml program on message-passing architectures |
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Self-organizing free growing network for classifying amino acids |
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Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC |
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3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs) |
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A spectral estimation approach to contrast transfer function detection in electron microscopy |
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Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: Application of a new three- dimensional reconstruction algorithm and objective comparison with weighted backprojection |
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The RepA protein of plasmid RSF1010 is a replicative DNA helicase |
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A new type of unsupervised growing neural network for biological sequence classification that adopts the topology of a phylogenetic tree |
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Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel |
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Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree |
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Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system |
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Analysis of structural variability within two-dimensional biological crystals by a combination of patch averaging techniques and self organizing maps |
|
On a new computationally fast image invariant based on bispectral projections |
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Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy |
|
Xmipp: An image processing package for electron microscopy |
|
Confidence limits for resolution estimation in image averaging by random subsampling |
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AN IMAGE-PROCESSING APPROACH TO DOTPLOTS - AN X-WINDOW-BASED PROGRAM FOR INTERACTIVE ANALYSIS OF DOTPLOTS DERIVED FROM SEQUENCE AND STRUCTURAL DATA |
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A STRUCTURAL MODEL FOR THE ESCHERICHIA-COLI DNAB HELICASE BASED ON ELECTRON-MICROSCOPY DATA |
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Towards a data-bank of three-dimensional macromolecular structures: A WWW-based prototype |
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Pattern recognition and classification of images of biological macromolecules using neural networks |
|
Study of the collars extracted from T3 and 029 viral particles |
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Practical issues on invariant image averaging using the Bispectrum |
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On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures |
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Pattern recognition and classification of images of biological macromolecules using artificial neural networks |
|
Speech recognizer optimization and real-time implementation on a multitransputer array |
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Image reconstruction on hypercube computers: Application to electron microscopy |
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Three-dimensional structure of T3 connector purified from overexpressing bacteria |
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Detection, classification and 3D reconstruction of biological macromolecules on hypercube computers |
|
Electron microscopy study of GroEL chaperonin: Different views of the aggregate appear as a function of cell growth temperature |
|
Purity, purposes, and possibilities of classification techniques in electron microscopy: A reply to comments by Marin van Heel |
|
Filtered back projection on shared-memory multiprocessors |
|
Study of two related configurations of the neck of bacteriophage Ø29 |
|
Multidimensional fast Fourier transform into SIMD hypercubes |
|
Cluster validity based on the hard tendency of the fuzzy classification |
|
Image template matching on hypercube SIMD computers |
|
Three-dimensional reconstruction of the sevenfolded form of Bacillus subtilis Gro EL chaperonin |
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Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles. |
|
On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures |
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Variations of the three-dimensional structure of the Escherichia coli ribosome in the range of overlap views. An application of the methods of multicone and local single-cone three-dimensional reconstruction. |
|
Three-dimensional reconstruction of the ribosome from Escherichia coli. |
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Three-dimensional matching of macromolecular structures obtained from electron microscopy: an application to the 70S and 50S E. coli ribosomal particles. |
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Three-dimensional structure of 50 S Escherichia coli ribosomal subunits depleted of proteins L7/L12. |
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Bacteriophage T3 connector: Three-dimensional structure and comparison with other viral head-tail connecting regions |
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Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli. |
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A new non-crystallographic image-processing technique reveals the architecture of ribosomes. |
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Purification and Organization of the Gene 1 Portal Protein Required for Phage P22 DNA Packaging |
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Restoration of direct Fourier three-dimensional reconstructions of crystalline specimens by the method of convex projections. |
|
Information recovery in missing angular data cases: an approach by the convex projections method in three dimensions |
|
Three-dimensional reconstruction of the connector of bacteriophage φ29 at 1.8 nm resolution |
|
Computer graphic display method for visualizing three-dimensional biological structures |
|
Bacteriophage T3 gene 8 product oligomer structure |
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Study of the direct Fourier method for the three‐dimensional reconstruction of objects in the case of a missing angular data range |
|
Three-dimensional reconstruction of bacteriophage φ29 neck particles at 2.2 nm resolution |
|
Structure of phage φ29 connector protein assembled in Vivo |
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Structural study of tetragonal-ordered aggregates of phage φ29 necks |
|
GENERAL MORPHOLOGY AND CAPSID FINE-STRUCTURE OF AFRICAN SWINE FEVER VIRUS-PARTICLES |
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Structural localizaton of the proteins of the head to tail connecting region of bacteriophage φ29 |
|