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

Nature communications, 2023-01, Vol.14 (1), p.154-10, Article 154

2023

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Nonsmooth nonnegative matrix factorization (nsNMF)

IEEE transactions on pattern analysis and machine intelligence, 2006-03, Vol.28 (3), p.403-415

2006

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Two-step demodulation based on the Gram-Schmidt orthonormalization method

Optics letters, 2012-02, Vol.37 (3), p.443

2012

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Two-step interferometry by a regularized optical flow algorithm

Optics letters, 2011-09, Vol.36 (17), p.3485

2011

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Integration of Cryo-EM Model Building Software in Scipion

Journal of chemical information and modeling, 2020-05, Vol.60 (5), p.2533-2540

2020

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Local resolution estimates of cryoEM reconstructions

Current opinion in structural biology, 2020-10, Vol.64, p.74-78

2020

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Marker-free image registration of electron tomography tilt-series

BMC bioinformatics, 2009-04, Vol.10 (124), p.124-124, Article 124

2009

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XMIPP: a new generation of an open-source image processing package for electron microscopy

Journal of structural biology, 2004-11, Vol.148 (2), p.194-204

2004

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Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis

Scientific reports, 2017-07, Vol.7 (1), p.6307-14, Article 6307

2017

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Image processing tools for the validation of CryoEM maps

Faraday discussions, 2022-11, Vol.24, p.21-227

2022

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BIPSPI: a method for the prediction of partner-specific protein–protein interfaces

Bioinformatics, 2019-02, Vol.35 (3), p.470-477

2019

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A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

BioMed research international, 2017-01, Vol.2017 (2017), p.1-17

2017

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Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

Journal of structural biology, 2016-07, Vol.195 (1), p.93-99

2016

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Xmipp 3.0: An improved software suite for image processing in electron microscopy

Journal of structural biology, 2013-11, Vol.184 (2), p.321-328

2013

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MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning

Journal of structural biology, 2020-06, Vol.210 (3), p.107498-107498, Article 107498

2020

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Local defocus estimation in single particle analysis in cryo-electron microscopy

Journal of structural biology, 2023-12, Vol.215 (4), p.108030-108030, Article 108030

2023

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Cryo-Electron Microscopy: The field of 1,000+ methods

Journal of structural biology, 2022-09, Vol.214 (3), p.107861-107861, Article 107861

2022

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BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

Journal of molecular biology, 2022-06, Vol.434 (11), p.167556-167556, Article 167556

2022

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ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis

Journal of molecular biology, 2023-05, Vol.435 (9), p.168088-168088, Article 168088

2023

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A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions

Journal of structural biology, 2024-03, Vol.216 (1), p.108056-108056, Article 108056

2024

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A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Journal of structural biology, 2023-12, Vol.215 (4), p.108024-108024, Article 108024

2023

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DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM

Journal of structural biology, 2021-06, Vol.213 (2), p.107712-107712, Article 107712

2021

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Generalization of the Principal Component Analysis algorithm for interferometry

Optics communications, 2013-01, Vol.286, p.130-134

2013

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3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations

Bioinformatics, 2019-09, Vol.35 (18), p.3512-3513

2019

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Cryo-EM density maps adjustment for subtraction, consensus and sharpening

Journal of structural biology, 2021-12, Vol.213 (4), p.107780-107780, Article 107780

2021

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

Nonsmooth nonnegative matrix factorization (nsNMF)

Two-step demodulation based on the Gram-Schmidt orthonormalization method

Two-step interferometry by a regularized optical flow algorithm

Integration of Cryo-EM Model Building Software in Scipion

Local resolution estimates of cryoEM reconstructions

Marker-free image registration of electron tomography tilt-series

XMIPP: a new generation of an open-source image processing package for electron microscopy

Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis

Image processing tools for the validation of CryoEM maps

BIPSPI: a method for the prediction of partner-specific protein–protein interfaces

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

Xmipp 3.0: An improved software suite for image processing in electron microscopy

MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning

Local defocus estimation in single particle analysis in cryo-electron microscopy

Cryo-Electron Microscopy: The field of 1,000+ methods

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis

A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM

Generalization of the Principal Component Analysis algorithm for interferometry

3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations

Cryo-EM density maps adjustment for subtraction, consensus and sharpening

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