Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

(2023) D. Herreros et al.   Nature Communications

Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models

(2023) Muyuan Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements

(2022) Rémi Vuillemot et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity

(2022) Kira DeVore et al.   Biomolecules

Visualizing Conformational Space of Functional Biomolecular Complexes by Deep Manifold Learning

(2022) Zhaolong Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

3D Flexible Refinement: Structure and Motion of Flexible Proteins from Cryo-EM

(2022) Ali Punjani et al.   MICROSCOPY AND MICROANALYSIS

DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images

(2022) Ilyes Hamitouche et al.   Frontiers in Molecular Biosciences

Deep generative modeling for volume reconstruction in cryo-electron microscopy

(2022) Claire Donnat et al.   JOURNAL OF STRUCTURAL BIOLOGY

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

(2021) Ellen D. Zhong et al.   NATURE METHODS

Principal component analysis is limited to low-resolution analysis in cryoEM

(2021) Carlos Oscar S. Sorzano et al.   Acta Crystallographica Section D-Structural Biology

Continuous heterogeneity analysis of CryoEM images through Zernike polynomials and spherical harmonics

(2021) David Herreros Calero et al.   MICROSCOPY AND MICROANALYSIS

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

New tools for automated cryo-EM single-particle analysis in RELION-4.0

(2021) Dari Kimanius et al.   BIOCHEMICAL JOURNAL

Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review

(2021) Jia-Geng Wu et al.   IEEE Transactions on Neural Networks and Learning Systems

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

(2021) David Herreros et al.   IUCrJ

Single-Particle Cryo-Electron Microscopy: Mathematical Theory, Computational Challenges, and Opportunities

(2020) Tamir Bendory et al.   IEEE SIGNAL PROCESSING MAGAZINE

Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding

(2020) Suvrajit Maji et al.   Journal of Chemical Information and Modeling

Retrieving functional pathways of biomolecules from single-particle snapshots

(2020) Ali Dashti et al.   Nature Communications

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

(2020) Roberto Melero et al.   IUCrJ

A representation theory perspective on simultaneous alignment and classification

(2019) Roy R. Lederman et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Multi-target detection with application to cryo-electron microscopy

(2019) Tamir Bendory et al.   INVERSE PROBLEMS

Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes

(2019) Amit Moscovich et al.   INVERSE PROBLEMS

Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM

(2019) Roy R Lederman et al.   INVERSE PROBLEMS

Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy

(2018) Massimiliano Bonomi et al.   BIOPHYSICAL JOURNAL

Likelihood-based structural analysis of electron microscopy images

(2018) Pilar Cossio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Bispectrum Inversion With Application to Multireference Alignment

(2018) Tamir Bendory et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

Structural Variability from Noisy Tomographic Projections

(2018) Joakim Andén et al.   SIAM Journal on Imaging Sciences

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

(2018) C. O. S. Sorzano et al.   Acta Crystallographica Section F-Structural Biology Communications

Structures of transcription pre-initiation complex with TFIIH and Mediator

(2017) S. Schilbach et al.   NATURE

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes

(2016) Carlos Oscar Sanchez Sorzano et al.   BIOPHYSICAL JOURNAL

Method of the Year 2015

(2016)   NATURE METHODS

Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes

(2016) Slavica Jonić   Computational and Structural Biotechnology Journal

Directly reconstructing principal components of heterogeneous particles from cryo-EM images

(2015) Hemant D. Tagare et al.   JOURNAL OF STRUCTURAL BIOLOGY

Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem

(2015) E. Katsevich et al.   SIAM Journal on Imaging Sciences

Efficient Estimation of Three-Dimensional Covariance and its Application in the Analysis of Heterogeneous Samples in Cryo-Electron Microscopy

(2015) Hstau Y. Liao et al.   STRUCTURE

Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes

(2015) Serban L. Ilca et al.   Nature Communications

Sampling the conformational space of the catalytic subunit of human γ-secretase

(2015) Xiao-chen Bai et al.   eLife

Conformations of macromolecules and their complexes from heterogeneous datasets

(2014) P. Schwander et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Trajectories of the ribosome as a Brownian nanomachine

(2014) Ali Dashti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes

(2014) Qiyu Jin et al.   STRUCTURE

Likelihood-based classification of cryo-EM images using FREALIGN

(2013) Dmitry Lyumkis et al.   JOURNAL OF STRUCTURAL BIOLOGY

Empirical intrinsic geometry for nonlinear modeling and time series filtering

(2013) R. Talmon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Prevention of overfitting in cryo-EM structure determination

(2012) Sjors H W Scheres et al.   NATURE METHODS

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

Identifying Conformational States of Macromolecules by Eigen-Analysis of Resampled Cryo-EM Images

(2011) Pawel A. Penczek et al.   STRUCTURE

Mapping the conformations of biological assemblies

(2010) P Schwander et al.   NEW JOURNAL OF PHYSICS

On random tomography with unobservable projection angles

(2009) Victor M. Panaretos   ANNALS OF STATISTICS