Pilar Cossio

Quantifying RNA Folding Equilibria from Unclassified Cryo-EM Particle Images

This paper uses Bayesian ensemble reweighting on unclassified cryo-EM images to quantify RNA folding equilibria, showing agreement with bulk solution measurements.

The CAHRA Challenge: A Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms

The paper introduces the CAHRA Challenge, a community-wide assessment of cryo-EM heterogeneous reconstruction algorithms using three benchmark datasets.

Deep Learning-based Modeling Enhances Efficacy of Natural Ligand CAR Binders Targeting CD70

This study uses deep learning and physics-based modeling to engineer a CD27 variant that improves the efficacy of CD70-targeting CAR T-cells across multiple cancer models.

Cryo-electron microscopy ensemble optimization using individual particles and physical constraints

This paper introduces a Bayesian optimization method for cryo-EM ensemble optimization, directly inferring structures and population weights from particle images and physical constraints.

Cooling fast and slow: Characterising the effects of vitrification in cryo-EM and the subsequent recovery of equilibrium populations

This study uses molecular dynamics simulations to investigate how vitrification affects the conformational ensemble of Trp-cage miniprotein and develops a thermodynamic inference framework to recover equilibrium populations from vitrified samples.

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.

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.

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.

CryoLike: A python package for cryo-electron microscopy image-to-structure likelihood calculations

CryoLike evaluates image-to-structure likelihoods for cryo-EM data using Fourier-Bessel representations to improve computational efficiency.

Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics

This study evaluates the quality of machine learned reaction coordinates using the gamma metric and shows an inverse correlation with accelerated times.

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.

Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference

This paper introduces cryoSBI, a method using simulation-based inference to infer biomolecular conformations from cryo-EM images, achieving fast and accurate results.

Counting particles could give wrong probabilities in Cryo-Electron Microscopy

The paper warns that counting particle images in cryo-EM can lead to biased estimates of conformational state populations due to noise and orientation uncertainty, and suggests using full image datasets for more accurate modeling.

New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM

This paper introduces a new statistical metric, 2DTM p-value, to improve target detection in cryo-EM by combining SNR and z-score, showing better performance for complex targets.