Mohammadreza Paraan

Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography

The paper describes a Kaggle challenge for particle picking in cryo-electron tomography, resulting in improved algorithms and highlighting the need for better annotation quality measures.

A Crossed Laser Phase Plate for CryoEM

This paper introduces a crossed laser phase plate (xLPP) for cryoEM, demonstrating improved contrast and resolution in imaging biological samples.

AreTomoLive: Automated reconstruction of comprehensively-corrected and denoised cryo-electron tomograms in real-time and at high throughput

AreTomo3 and DenoisET form an automated GPU pipeline that reconstructs cryo-electron tomograms with tile-based contrast transfer function correction, screens their quality, and denoises them during acquisition.

Characterization Standard for In-situ Cryo-electron Tomography

The paper introduces PP7 virus-like particles as a standardized benchmark for cryo-electron tomography, enabling rapid validation and resolution assessment of tomographic pipelines.

Dose-Efficient Cryo-Electron Microscopy for Thick Samples using Tilt-Corrected Scanning Transmission Electron Microscopy, Demonstrated on Cells and Single Particles

This paper introduces tilt-corrected bright-field scanning-TEM (tcBF-STEM) for cryo-EM, showing improved contrast and efficiency for thick samples, with a subnanometer resolution SPA map of a virus-like particle.

Cationic amino acid identity and net charge influence condensate properties in E. coli

This study shows that cationic amino acid identity and net charge affect condensate properties in E. coli, with arginine promoting better encapsulation and stability than lysine.

Open-source Tools for CryoET Particle Picking Machine Learning Competitions

The paper introduces open-source tools for a machine learning competition focused on particle picking in cryo-electron tomography data.

Annotating CryoET Volumes: A Machine Learning Challenge

The paper introduces a phantom sample and annotated 3D volumes for a machine learning challenge to improve cryoET volume annotation.

The structure of a Type III-A CRISPR-Cas effector complex reveals conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems

The paper presents the structure of a Type III-A CRISPR-Cas effector complex from S. epidermidis, revealing interactions with target RNA and crRNA and highlighting differences among related systems.