Khanh Dao Duc

Mapping the Functional Landscape and Viral Diversity of 2A Peptides

The paper develops a FRET-based system to analyze 2A peptides' activity, identifies key residues, and discovers a novel subclass with high StopGo efficiency.

Fast and interpretable quantification of biological shape heterogeneity via stratified Wasserstein kernel

The paper introduces a method to quantify biological shape heterogeneity using a stratified Wasserstein kernel, demonstrating its application to 2D and 3D biological datasets.

Learning Continuous Morphological Trajectories via Latent Principal Curves

The paper introduces MorphCurveVAE, a method to infer continuous morphological trajectories from static 3D microscopy images, demonstrating its effectiveness on mitosis data.

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.

Advanced coarse-grained model for fast simulation of nascent polypeptide chain dynamics within the ribosome

This paper develops a coarse-grained model for simulating nascent polypeptide dynamics in the ribosome, enabling efficient simulation of elongation and escape processes.

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge

The paper presents a cryo-EM conformational heterogeneity challenge to evaluate and improve methods for analyzing molecular motions in heterogeneous samples.

Detection of prokaryotic-like ribosome exit tunnels within eukaryotic kingdoms

The paper identifies prokaryotic-like ribosome exit tunnels in eukaryotic protists by analyzing structural and sequence data from 725 ribosome models.

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-EM density maps

This study benchmarks deep learning methods for building atomic models from cryo-EM density maps, showing their superiority over traditional methods and the benefits of integrating AlphaFold.

Quantifying the organization and dynamics of M. smegmatis morphology from Long-Term Time-Lapse Atomic Force Microscopy

This study quantifies M. smegmatis morphology dynamics using LTTL-AFM and identifies bi-phasic pole growth and wave-form propagation, supported by a reaction-diffusion model.

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

This paper introduces DeCOr-MDS, a robust MDS method that detects and corrects orthogonal outliers to improve embedding quality in biological datasets.

CAT PETR: A Graphical User Interface for Differential Analysis of Phosphorylation Data

CAT PETR is a web application for differential analysis of phosphorylation data from antibody microarrays, offering improved data input and visualization compared to existing tools.

RiboXYZ: A comprehensive database for visualizing and analyzing ribosomestructures

RiboXYZ provides a database and tools for organizing, visualizing, and comparing ribosome structures from multiple sources with standardized nomenclature.

MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX

MorphOT interpolates between EM maps using optimal transport to generate morphing trajectories, avoiding blending by displacing densities.

The key parameters that govern translation efficiency

The paper develops a stochastic model of translation dynamics to identify key parameters governing translation efficiency and validates findings with ribosome profiling data from yeast.

Dynamics of ion fluxes between neurons, astrocytes and the extracellular space during neurotransmission

The paper reviews a tri-compartment model of potassium dynamics between neurons, astrocytes, and the extracellular space, showing how astrocytes buffer potassium and how channel disruptions affect neuronal activity.

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

The paper quantifies factors affecting translation elongation rates using ribosome profiling data and shows exit tunnel interactions and nascent polypeptide hydropathy are key determinants.

Theoretical analysis of the distribution of isolated particles in the TASEP: Application to mRNA translation rate estimation

The paper analyzes the distribution of isolated particles in the TASEP model to estimate mRNA translation rates and identifies potential biases in ribosome profiling data.