Karissa Y. Sanbonmatsu

AI-Assisted Cryo-ET Workflow for 3D Visualization of Chromatin during Cellular Differentiation

This paper presents an AI-assisted cryo-ET workflow to visualize chromatin compaction during motor neuron differentiation and correlates findings with Hi-C data.

Structural Topology-based Electrostatic Model (STEM) Reveals Ion-Coordination Exchange as a Driver of RNA Folding Dynamics

The paper introduces STEM, a model that captures ion-coordination dynamics in RNA folding, showing how Mg2+ coordination drives conformational transitions and folding pathways.

Cleavage region organizes the structural architecture of the B2 SINE ribozyme

The paper determines the structural ensemble-to-function relations of the B2 SINE ribozyme using RNA chemical probing, X-ray scattering, and modeling, showing cleavage site dependency on its structure and function.

From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture

The paper introduces 4DGBWorkflow and 4DGB, open-source tools that use molecular dynamics simulations constrained by Hi-C data to generate 3D chromatin reconstructions and integrate them with epigenomic data for visualization.

Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression

The paper investigates how chromatin dynamics and gene expression change after epigenetic drug treatment, finding locus-specific chromatin remodeling and gene expression alterations.

Human Protein Synthesis Requires aminoacyl-tRNA Pivoting During Proofreading

This study identifies a pivotal aa-tRNA pivoting mechanism in human translation that enhances fidelity by navigating the constrained ribosomal accommodation corridor.

Widespread 3D genome reorganization precedes programmed DNA rearrangement in Oxytricha trifallax

The paper maps 3D genome organization in Oxytricha trifallax to understand its role in programmed DNA rearrangement during development.

Statistical relationships across epigenomes using large-scale hierarchical clustering

The paper uses hierarchical clustering to analyze over 3,000 epigenomes and characterize relationships among epigenetic modifiers, their modifiers, and immune cell types.

Improved Quality Metrics for Association and Reproducibility in Chromatin Accessibility Data Using Mutual Information

The paper evaluates correlation and association statistics for ATAC-seq data, finding that mutual information performs best in predicting replicate relationships after removing co-zeros.

Vaccinia virus infection induces concurrent alterations in host chromatin architecture, accessibility, and gene expression

This study shows that vaccinia virus infection causes coordinated changes in host chromatin structure, accessibility, and gene expression over time.