4.6 Article

Toward Single Particle Reconstruction without Particle Picking: Breaking the Detection Limit

Related references

Note: Only part of the references are listed.
Article Engineering, Electrical & Electronic

Two-Dimensional Multi-Target Detection: An Autocorrelation Analysis Approach

Shay Kreymer et al.

Summary: The study addresses the multi-target detection problem by proposing a method for image recovery in high noise conditions, estimating the image through an autocorrelation analysis framework, and demonstrating accurate image recovery in high noise environments through extensive numerical experiments.

IEEE TRANSACTIONS ON SIGNAL PROCESSING (2022)

Article Computer Science, Interdisciplinary Applications

A molecular prior distribution for Bayesian inference based on Wilson statistics

Marc Aurele Gilles et al.

Summary: This paper discusses the applications of Wilson statistics in structural biology and introduces a novel prior based on statistical estimates for Bayesian inference of molecular structures. The results show that the new prior effectively suppresses noise, improves resolution in low SNR regions, and produces Fourier Shell Correlation curves that are insensitive to masking effects.

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2022)

Article Chemistry, Multidisciplinary

Random conical tilt reconstruction without particle picking in cryo-electron microscopy

Ti-Yen Lan et al.

Summary: This article presents a method for reconstructing 3D molecular structure from micrographs in cryo-electron microscopy, using autocorrelation analysis and circumventing the need for particle picking. The method is demonstrated with simulated data and the effect of missing-cone region is investigated.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2022)

Article Engineering, Electrical & Electronic

An Approximate Expectation-Maximization for Two-Dimensional Multi-Target Detection

Shay Kreymer et al.

Summary: We study the problem of two-dimensional multi-target detection, which involves estimating a target image from a noisy measurement containing randomly rotated and translated image copies. Our research is motivated by the structure reconstruction problem in single-particle cryo-electron microscopy. We propose an expectation-maximization framework to estimate the image and demonstrate its superior performance compared to previous autocorrelation analysis, especially in high noise regimes.

IEEE SIGNAL PROCESSING LETTERS (2022)

Article Engineering, Electrical & Electronic

The Generalized Method of Moments for Multi-Reference Alignment

Asaf Abas et al.

Summary: This paper studies the application of the generalized method of moments (GMM) to multi-reference alignment (MRA). The paper proves the asymptotic optimality of the GMM estimator for statistical models with group symmetry, including MRA, and demonstrates the significant improvement of GMM compared to the classical method of moments in MRA through comprehensive numerical experiments. The paper also presents the formulation of GMM for estimating a three-dimensional molecular structure using cryo-electron microscopy and provides numerical results on simulated data.

IEEE TRANSACTIONS ON SIGNAL PROCESSING (2022)

Review Biochemistry & Molecular Biology

Conquer by cryo-EM without physically dividing

Gabriel C. Lander et al.

Summary: This mini-review discusses the progress made in obtaining high-resolution structures for proteins and macromolecules smaller than 100 kDa using single-particle cryo-EM. It highlights the importance of establishing limits in particle size and resolution for future refinement approaches. Furthermore, it compares experimental achievements with theoretical estimates and identifies areas for further improvement in equipment and methods.

BIOCHEMICAL SOCIETY TRANSACTIONS (2021)

Editorial Material Biochemistry & Molecular Biology

Seeing Atoms by Single-Particle Cryo-EM

Xiao-chen Bai

Summary: Recent advancements in technology have enabled researchers to achieve atomic-resolution structure determination using single-particle cryo-electron microscopy for the first time, as demonstrated by Nakane et al. and Yip et al. This breakthrough now allows researchers to apply this technique to a wide range of protein complexes for obtaining atomic structural information.

TRENDS IN BIOCHEMICAL SCIENCES (2021)

Article Chemistry, Multidisciplinary

Exploiting prior knowledge about biological macromolecules in cryo-EM structure determination

Dari Kimanius et al.

Summary: This paper introduces a regularization framework for cryo-EM structure determination that utilizes prior knowledge about biological structures through a convolutional neural network trained on known macromolecular structures. The method yields better reconstructions than current state-of-the-art techniques for simulated data, and possibilities for extending this work to experimental cryo-EM data are discussed.

IUCRJ (2021)

Article Chemistry, Multidisciplinary

Wilson statistics: derivation, generalization and applications to electron cryomicroscopy

Amit Singer

Summary: This paper focuses on the importance of Wilson statistics in studying the power spectrum of proteins, as well as its applications in the fields of X-ray crystallography and cryo-EM. Through rigorous mathematical derivation, researchers have identified the valid regime of Wilson statistics and generalized the statistics to covariance and higher-order spectra. This provides a theoretical foundation for the Bayesian inference framework in three-dimensional refinement and explains the limitations of autocorrelation-based methods in cryo-EM.

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2021)

Article Mathematics, Applied

Multi-Reference Alignment in High Dimensions: Sample Complexity and Phase Transition

Elad Romanov et al.

Summary: The article focuses on the problem of multi-reference alignment in the high-dimensional regime. The analysis reveals a phase transition phenomenon controlled by the parameter alpha, where the problem becomes significantly harder when alpha is less than or equal to 2, and the sample complexity grows more quickly with the noise variance sigma(2).

SIAM JOURNAL ON MATHEMATICS OF DATA SCIENCE (2021)

Article Engineering, Electrical & Electronic

CryoGAN: A New Reconstruction Paradigm for Single-Particle Cryo-EM Via Deep Adversarial Learning

Harshit Gupta et al.

Summary: CryoGAN is a new paradigm for single-particle cryo-electron microscopy reconstruction based on unsupervised deep adversarial learning, achieving 3D structure reconstruction via distribution matching and skipping pose estimation or marginalization. It has shown success in recovering correct structures in an idealized mathematical model and achieving 10.8 angstrom resolution on a realistic synthetic dataset.

IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING (2021)

Article Engineering, Electrical & Electronic

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

Tamir Bendory et al.

IEEE SIGNAL PROCESSING MAGAZINE (2020)

Article Mathematics, Applied

Non-unique games over compact groups and orientation estimation in cryo-EM

Afonso S. Bandeira et al.

INVERSE PROBLEMS (2020)

Article Biochemistry & Molecular Biology

KLT picker: Particle picking using data-driven optimal templates

Amitay Eldar et al.

JOURNAL OF STRUCTURAL BIOLOGY (2020)

Article Microscopy

Reducing bias and variance for CTF estimation in single particle cryo-EM

Ayelet Heimowitz et al.

ULTRAMICROSCOPY (2020)

Review Biochemistry & Molecular Biology

How low can we go? Structure determination of small biological complexes using single-particle cryo-EM

Mengyu Wu et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Article Engineering, Electrical & Electronic

Multi-Target Detection With an Arbitrary Spacing Distribution

Ti-Yen Lan et al.

IEEE TRANSACTIONS ON SIGNAL PROCESSING (2020)

Article Multidisciplinary Sciences

High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM

Mark A. Herzik et al.

NATURE COMMUNICATIONS (2019)

Article Mathematics, Applied

Multi-target detection with application to cryo-electron microscopy

Tamir Bendory et al.

INVERSE PROBLEMS (2019)

Article Biochemical Research Methods

Laser phase plate for transmission electron microscopy

Osip Schwartz et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

Tristan Bepler et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

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

C. O. S. Sorzano et al.

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

Kaiming Zhang et al.

NATURE COMMUNICATIONS (2019)

Article Computer Science, Information Systems

Multireference Alignment Is Easier With an Aperiodic Translation Distribution

Emmanuel Abbe et al.

IEEE TRANSACTIONS ON INFORMATION THEORY (2019)

Article Mathematics, Applied

The Sample Complexity of Multireference Alignment

Amelia Perry et al.

SIAM JOURNAL ON MATHEMATICS OF DATA SCIENCE (2019)

Review Chemistry, Multidisciplinary

Single-Particle Reconstruction of Biological Molecules-Story in a Sample (Nobel Lecture)

Joachim Frank

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Multidisciplinary Sciences

Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system

Yuxi Liu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Biochemistry & Molecular Biology

APPLE picker: Automatic particle picking, a low-effort cryo-EM framework

Ayelet Heimowitz et al.

JOURNAL OF STRUCTURAL BIOLOGY (2018)

Article Computer Science, Artificial Intelligence

The Steerable Graph Laplacian and its Application to Filtering Image Datasets

Boris Landa et al.

SIAM JOURNAL ON IMAGING SCIENCES (2018)

Article Biochemistry & Molecular Biology

Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application

Giovanna Scapin et al.

CELL CHEMICAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Phase-plate cryo-EM structure of a class B GPCR-G-protein complex

Yi-Lynn Liang et al.

NATURE (2017)

Article Computer Science, Artificial Intelligence

Steerable Principal Components for Space-Frequency Localized Images

Boris Landa et al.

SIAM JOURNAL ON IMAGING SCIENCES (2017)

Article Multidisciplinary Sciences

Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate

Maryam Khoshouei et al.

NATURE COMMUNICATIONS (2017)

Letter Biochemical Research Methods

EMPIAR: a public archive for raw electron microscopy image data

Andrii Iudin et al.

NATURE METHODS (2016)

Article Engineering, Electrical & Electronic

Fast Steerable Principal Component Analysis

Zhizhen Zhao et al.

IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING (2016)

Article Biochemistry & Molecular Biology

Semi-automated selection of cryo-EM particles in RELION-1.3

Sjors H. W. Scheres

JOURNAL OF STRUCTURAL BIOLOGY (2015)

Letter Multidisciplinary Sciences

Finding trimeric HIV-1 envelope glycoproteins in random noise

Marin van Heel

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise

Richard Henderson

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

A method for the alignment of heterogeneous macromolecules from electron microscopy

Maxim Shatsky et al.

JOURNAL OF STRUCTURAL BIOLOGY (2009)

Article Statistics & Probability

Higher criticism for detecting sparse heterogeneous mixtures

D Donoho et al.

ANNALS OF STATISTICS (2004)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)