TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining

Structures from intact myofibrils reveal mechanism of thin filament regulation through nebulin

(2022) Zhexin Wang et al.   SCIENCE

Structure of a bacterial Rhs effector exported by the type VI secretion system

(2022) Patrick Günther et al.   PLoS Pathogens

VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms

(2022) Yu Hao et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Solving the nuclear pore puzzle

(2022) Thomas U. Schwartz   SCIENCE

Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex

(2022) Xuechen Zhu et al.   SCIENCE

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

(2022) Shyamal Mosalaganti et al.   SCIENCE

Isotropic reconstruction for electron tomography with deep learning

(2022) Yun-Tao Liu et al.   Nature Communications

Parallel cryo electron tomography on in situ lamellae

(2022) Fabian Eisenstein et al.   NATURE METHODS

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

(2021) Dimitry Tegunov et al.   NATURE METHODS

The molecular basis for sarcomere organization in vertebrate skeletal muscle

(2021) Zhexin Wang et al.   CELL

A streamlined workflow for automated cryo focused ion beam milling

(2021) Sebastian Tacke et al.   JOURNAL OF STRUCTURAL BIOLOGY

Molecular-scale visualization of sarcomere contraction within native cardiomyocytes

(2021) Laura Burbaum et al.   Nature Communications

Locating macromolecular assemblies in cells by 2D template matching with cisTEM

(2021) Bronwyn A Lucas et al.   eLife

In situ cryo-ET structure of phycobilisome–photosystem II supercomplex from red alga

(2021) Meijing Li et al.   eLife

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

(2021) Dari Kimanius et al.   BIOCHEMICAL JOURNAL

Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms

(2021) Emmanuel Moebel et al.   NATURE METHODS

Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE

(2020) Andreas D. Schenk et al.   Journal of Chemical Information and Modeling

Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography

(2020) Felix R. Wagner et al.   Nature Protocols

Assembly intermediates of orthoreovirus captured in the cell

(2020) Geoff Sutton et al.   Nature Communications

A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue

(2019) Miroslava Schaffer et al.   NATURE METHODS

Deep Metric Learning: A Survey

(2019) Kaya et al.   Symmetry-Basel

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

(2019) D. Maluenda et al.   Acta Crystallographica Section D-Structural Biology

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

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

(2019) Tristan Bepler et al.   NATURE METHODS

Structure of a Tc holotoxin pore provides insights into the translocation mechanism

(2019) Daniel Roderer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in cryo-electron tomography for biology and medicine

(2018) Roman I. Koning et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

Deep Correlated Holistic Metric Learning for Sketch-Based 3D Shape Retrieval

(2018) Guoxian Dai et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Tc toxin activation requires unfolding and refolding of a β-propeller

(2018) Christos Gatsogiannis et al.   NATURE

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging

(2017) Wim J.H. Hagen et al.   JOURNAL OF STRUCTURAL BIOLOGY

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

(2017) Toshio Moriya et al.   Jove-Journal of Visualized Experiments

In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology

(2016) Shoh Asano et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Expression, purification, and characterization of recombinant human H-chain ferritin

(2016) Wenyan Zou et al.   PREPARATIVE BIOCHEMISTRY & BIOTECHNOLOGY

Cryo-electron tomography: The challenge of doing structural biology in situ

(2013) Vladan Lučić et al.   JOURNAL OF CELL BIOLOGY

Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments

(2012) Daniel Castaño-Díez et al.   JOURNAL OF STRUCTURAL BIOLOGY

Simulation of transmission electron microscope images of biological specimens

(2011) H. RULLGÅRD et al.   JOURNAL OF MICROSCOPY

PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis

(2011) Thomas Hrabe et al.   JOURNAL OF STRUCTURAL BIOLOGY