Advanced Electron Microscopy Techniques and Applications

Towards inferring atomic scale conformation landscape of biomolecules from cryo-electron tomography data

This paper introduces DeepMDTOMO, a deep learning framework for predicting atomic coordinates from cryo-ET subtomograms, showing it works well with noise and missing-wedge artifacts.

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta

CryoZeta improves cryo-EM structure modeling by integrating density features with sequence data using a diffusion-based deep learning model, achieving higher accuracy than existing methods.

Direct from the Seed: An Atomic-Resolution Protein Structure by Ab Initio MicroED

The paper solves an atomic-resolution protein structure using ab initio microED from spontaneously formed nanocrystals, achieving 0.85 Å resolution and resolving individual hydrogen atoms.

Connecting the dots: deep learning-based automated model building methods in cryo-EM

This paper reviews deep learning methods for automating atomic model building in cryo-EM density maps, discussing their classification, limitations, and future directions.

CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking

CryoVirusDB provides a labeled cryo-EM dataset for training AI to identify virus particles in micrographs, aiding in 3D structural modeling.

Robust quality assessment of cryo-EM maps, tomograms and micrographs by statistics-based local resolution estimation

The paper introduces a statistics-based method for local resolution estimation in cryo-EM maps, tomograms, and micrographs to improve quality assessment and reconstruction.

Breaking Barriers: Transitioning from X-ray Crystallography to Cryo-EM for Structural Studies

This paper describes a laboratory's transition from X-ray crystallography to cryo-EM for studying ATAD2B, detailing challenges and strategies in sample preparation, data processing, and model building.

Enhancing interpretability of cryo-EM maps with hybrid attention Transformers

This paper introduces DEMO-EMReF, a Transformer-based framework for refining cryo-EM density maps, improving resolution and atomic model accuracy.

CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX

The paper introduces cryoJAX, a cryo-EM image simulation library built on JAX for developing data analysis techniques in cryo-EM.

PartiNet is a dynamic adaptive neural network for high-performance particle picking in cryo-electron microscopy

PartiNet improves particle picking in cryo-EM with a dynamic neural network that adapts to micrograph quality, enhancing efficiency and particle yield without sacrificing accuracy.

Ultrathin Liquid Cells for Microsecond Time-Resolved Cryo-EM

This paper introduces ultrathin liquid cells for microsecond time-resolved cryo-EM, enabling longer observation windows and improved resolution for studying protein dynamics.

Point-Cloud Enhancement and Structural Interpretation Framework for Cryo-EM Maps

This paper introduces CryoPC, a framework that enhances cryo-EM maps by incorporating global structural context, improving enhancement quality and providing a quality assessment framework.

Assembly and glycosylation of Helicobacter pylori sheathed flagella

This study determines the near-atomic structure of H. pylori sheathed flagella using cryo-EM, revealing how flagellins and glycans contribute to filament stability and motility.

MorphoLearn: A morphology-driven workflow to decipher 3D electron microscopy segmentation in diatoms

This paper introduces MorphoLearn, an AI framework for 3D FIB-SEM segmentation of diatoms, showing that whole-cell segmentation reveals architectural differences and that transfer learning and contrast-aware strategies improve performance.

Fully genetically encoded low-molecular-weight protein tags with defined shapes for direct molecular identification by cryo-electron tomography

This paper introduces genetically encoded protein tags with defined shapes for direct molecular identification by cryo-ET, demonstrating their effectiveness in identifying proteins in situ without disrupting native structures.

Gradient based refinement of CryoET tilt series alignment improves tomogram contrast and structure resolution

This study improves CryoET tomogram contrast and protein structure resolution by refining tilt-series alignment using gradient descent.

TomoSegNet: Augmented membrane segmentation for cryo-electron tomography by simulating the cellular context

TomoSegNet improves membrane segmentation in cryo-electron tomography by using synthetic data generated with a biophysical simulator, outperforming existing methods in recovering distorted membranes.

EXPLICIT CORRECTION OF SEVERELY NON-UNIFORM DISTRIBUTIONS OF CRYO-EM VIEWS

This paper improves 3D cryo-EM reconstructions by explicitly correcting non-uniform distributions of 2D projections using the VUE program.

QUANTIFYING DISTRIBUTIONS OF CRYO-EM PROJECTIONS

The paper introduces a numerical measure to quantify the deviation of cryo-EM 2D view distributions from uniformity, replacing traditional 2D diagrams with 1D curves for standardized analysis.

Hierarchical Assembly of Native Cytoplasmic Lattices Revealed by Cryo-EM

The paper uses cryo-EM to reveal the high-resolution structure of mouse oocyte cytoplasmic lattices, identifying their components and hierarchical assembly mechanism.

Thermophilic bacteria employ a contractile injection system in hot spring microbial mats

The paper identifies a novel contractile injection system in thermophilic bacteria from hot spring mats using cryoET and metagenomics.

Structure from Noise: Confirmation Bias in Particle Picking in Structural Biology

The paper analyzes bias in particle picking for cryo-EM and cryo-ET, showing that noise can lead to deterministic structure artifacts in downstream tasks.

In situ structure of bacterial 50S ribosomes at 3.0 A resolution from vitreous sections.

The paper demonstrates high-resolution in situ structures of bacterial 50S ribosomes using vitreous sections, achieving 3.0 Å resolution.

Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

The paper compares methods for analyzing heterogeneity in TRPV1 cryo-EM data and finds that different methods detect different types of heterogeneity.

SmartEM: machine-learning guided electron microscopy

SmartEM accelerates electron microscopy image acquisition by using machine learning to intelligently allocate imaging time, achieving up to 7-fold speedup in connectomic samples.

A Generative Foundation Model for Cryo-EM Densities

This paper introduces cryoFM, a generative foundation model for cryo-EM densities that improves reconstruction and refinement by combining data-driven priors with dataset-specific constraints.

Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images

This paper introduces a Sliced Wasserstein loss function to improve optimization robustness in cryo-EM, showing it outperforms MSE in handling noisy data and conformational heterogeneity.

Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii

Automated cryogenic plasma-focused ion beam milling and cryo-electron tomography of Chlamydomonas reinhardtii yield 1,829 annotated cellular tomograms and sub-nanometer in situ structures of six macromolecular complexes.

Capsid flexibility during Ty1 virus-like particle assembly

This study uses cryo-ET and sub-tomogram averaging to analyze Ty1 virus-like particles, revealing diverse capsomere arrangements and the role of CA-CTD flexibility in VLP heterogeneity.

ColorSTEM: An easy and convenient approach to Multicolor Electron Microscopy of Labeled Biological Specimens

ColorSTEM improves multicolor electron microscopy by using metal-conjugated DAB to enhance signal and simplify imaging.