Cyro-EM

Reviews

Year	Publisher	Title
2016	Microscopy	Principles of cryo-EM single-particle image processing
2015	Cell	A Primer to Single-Particle Cryo-Electron Microscopy
2015	Cell	Single-Particle Cryo-EM at Crystallographic Resolution
201	Methods in Enzymology	Automation in Single-Particle Electron Microscopy: Connecting the Pieces

Direct Electron Detector

Year	Publisher	Title
2011	Current Opinion in Structural Biology	Electronic detectors for electron microscopy
2013	Nature Methods	Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
2011	Journal of Structural Biology	[

Following is a list of computational methods that address challenges in cryo-EM 3D reconstruction problem.

3D Heterogeneous Analysis/Reconstruction

Year	Publisher	Title
2012	Journal of Optical Society	Three-dimensional reconstruction of the statistics of heterogeneous objects from a collection of one projection image of each object
2013	JSB	Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps
2014	ISBI	Covariance estimation using conjugate gradient for 3D classification in Cryo-EM
2014	National Academy of Sciences	Trajectories of the ribosome as a Brownian nanomachine
2014	Structure	Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes
2015	Open Journal of Statistics	Structure Sorting of Multiple Macromolecular States in Heterogeneous Cryo-EM Samples by 3D Multivariate Statistical Analysis
2015	JSB	Directly reconstructing principal components of heterogeneous particles from cryo-EM images
2016	Prtoein Cell	A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules
2016	Methods	Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM
2018	eLife	Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
2019	Inverse Problems	Cryo-em reconstruction of continuous heterogeneity by Laplacian spectral volumes
2019	Inverse Problems	Hyper-Molecules: on the Representation and Recovery of Dynamical Structures, with Application to Flexible Macro-Molecular Structures in Cryo-EM
2020	Nature	Retrieving functional pathways of biomolecules from single-particle snapshots
2020	ECCV	Multi-CryoGAN: Reconstruction of Continuous Conformations in Cryo-EM Using Generative Adversarial Networks
2020	Nature	Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction
2021	Nature	CryoDRGN: Reconstruction of heterogeneous cryo-EM structures using neural networks
2021	ICCV	CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images
2021	Nature	Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM
2021	JSB	3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM
2021	bioArxiv	3D flexible refinement: Structure and motion of flexible proteins from cryo-EM
2022	NeurIPS	Amortized Inference for Heterogeneous Reconstruction in Cryo-EM
2023	Nature	Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

3D Homogeneous Reconstruction

Year	Publisher	Title
2017	Nature	cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
2020	IEEE Transactions on Comp Imaging	CryoGAN: A New Reconstruction Paradigm for Single-Particle Cryo-EM via Deep Adversarial Learning
2021	ICCV	CryoPoseNet: End-to-End Simultaneous Learning of Single-Particle Orientation and 3D Map Reconstruction From Cryo-Electron Microscopy Data
2022	ECCV	CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images

Orientation Estimation

Year	Publisher	Title
1986	Soviet Physics Doklady	Determination of the spatial orientation of arbitrarily arranged identical particles of unknown structure from their projections
1987	Ultramicroscopy	Angular reconstitution: A posteriori assignment of projection directions for 3D reconstruction
2010	JSB	Detecting consistent common lines in cryo-EM by voting
2011	SIAM Journal on Imaging Sci	Viewing Angle Classification of Cryo-Electron Microscopy Images Using Eigenvectors
2011	SIAM Journal on Imaging Sci	Three-dimensional structure determination from common lines in cryo-EM by eigenvectors and semidefinite programming
2012	SIAM journal on imaging sciences	Viewing direction estimation in cryo-EM using synchronization
2012	Communications on pure and applied mathematics	Vector diffusion maps and the connection Laplacian
2013	SIAM journal on imaging sciences	Orientation determination of cryo-EM images using least unsquared deviations
2014	JSB	Rotationally invariant image representation for viewing direction classification in cryo-EM
2015	Arxiv	Non-unique games over compact groups and orientation estimation in cryo-EM
2016	IEEE Transactions on Comp Imaging	Fast steerable principal component analysis
2017	JSB	Common lines modeling for reference free ab-initio reconstruction in cryo-EM

Reviews

Year	Publisher	Title
2017	Current Opinion in Structural Biology	Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images
2020	Annual Reviews	Computational Methods for Single-Particle Cryo-EM

Multi-Scale Implicit Neural Representation

Following is a list of papers that propose multi-scale neural implicit representation learning. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy](https://www.sciencedirect.com/science/article/pii/S1047847711002577)|