HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes

LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure

(2020) Xiaobo Zhai et al.   Scientific Reports

The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type

(2019) Mohammed Kaplan et al.   eLife

In situ and high‐resolution cryo‐EM structure of a bacterial type VI secretion system membrane complex

(2019) Chiara Rapisarda et al.   EMBO JOURNAL

In situ structure determination by subtomogram averaging

(2019) Daniel Castaño-Díez et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

(2019) Mohamad Harastani et al.   PROTEIN SCIENCE

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment

(2018) Qiang Guo et al.   CELL

Structure and Conformational Dynamics of the Human Spliceosomal B act Complex

(2018) David Haselbach et al.   CELL

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Conserved in situ arrangement of complex I and III2in mitochondrial respiratory chain supercomplexes of mammals, yeast, and plants

(2018) Karen M. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Variability from Noisy Tomographic Projections

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

In situ architecture of the algal nuclear pore complex

(2018) Shyamal Mosalaganti et al.   Nature Communications

Structure of the membrane-assembled retromer coat determined by cryo-electron tomography

(2018) Oleksiy Kovtun et al.   NATURE

emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging

(2018) Benjamin A. Himes et al.   NATURE METHODS

Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape

(2018) Joshua Hutchings et al.   Nature Communications

Visualization of the type III secretion mediated Salmonella–host cell interface using cryo-electron tomography

(2018) Donghyun Park 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

Native structure of a retroviral envelope protein and its conformational change upon interaction with the target cell

(2017) Christiane Riedel et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure and assembly of the Ebola virus nucleocapsid

(2017) William Wan et al.   NATURE

Proteasomes tether to two distinct sites at the nuclear pore complex

(2017) Sahradha Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In situ architecture, function, and evolution of a contractile injection system

(2017) Désirée Böck et al.   SCIENCE

Dissecting the molecular organization of the translocon-associated protein complex

(2017) Stefan Pfeffer et al.   Nature Communications

The structure of the COPI coat determined within the cell

(2017) Yury S Bykov et al.   eLife

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

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

Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation

(2016) Slavica Jonic et al.   IEEE Journal of Selected Topics in Signal Processing

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

(2016) J.M. de la Rosa-Trevín et al.   JOURNAL OF STRUCTURAL BIOLOGY

Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM

(2016) Joachim Frank et al.   METHODS

Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION

(2016) Tanmay A M Bharat et al.   Nature Protocols

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

(2016) Florian K. M. Schur et al.   SCIENCE

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition

(2016) S. Banerjee et al.   SCIENCE

The structure and flexibility of conical HIV-1 capsids determined within intact virions

(2016) Simone Mattei et al.   SCIENCE

Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome

(2016) Priyanka D Abeyrathne et al.   eLife

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

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

Single particle tomography in EMAN2

(2015) Jesús G. Galaz-Montoya 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

Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM

(2015) Anna Zhou et al.   eLife

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol

(2014) Carlos Oscar S. Sorzano et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

Autofocused 3D Classification of Cryoelectron Subtomograms

(2014) Yuxiang Chen et al.   STRUCTURE

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

Fast and accurate reference-free alignment of subtomograms

(2013) Yuxiang Chen et al.   JOURNAL OF STRUCTURAL BIOLOGY

3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy

(2013) R. Nogales-Cadenas et al.   NUCLEIC ACIDS RESEARCH

Contribution of histone N-terminal tails to the structure and stability of nucleosomes

(2013) Wakana Iwasaki et al.   FEBS Open Bio

High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching

(2012) Min Xu et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

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

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

(2011) Pawel A. Penczek et al.   STRUCTURE

Maximum likelihood based classification of electron tomographic data

(2010) Michael Stölken et al.   JOURNAL OF STRUCTURAL BIOLOGY

The Nucleosome Family: Dynamic and Growing

(2009) Jordanka Zlatanova et al.   STRUCTURE

Averaging of Electron Subtomograms and Random Conical Tilt Reconstructions through Likelihood Optimization

(2009) Sjors H.W. Scheres et al.   STRUCTURE

Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections

(2007) Nadav Elad et al.   JOURNAL OF STRUCTURAL BIOLOGY

Classification of cryo-electron sub-tomograms using constrained correlation

(2007) Friedrich Förster et al.   JOURNAL OF STRUCTURAL BIOLOGY