Christina R. Steadman

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.

Resolving in vitro heterogeneity of host functional responses to HCoV-229E via single-cell analyses

The paper uses single-cell RNA sequencing and ATAC-seq to analyze host responses to HCoV-229E infection, revealing heterogeneous transcriptional and regulatory changes across infected cells.

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.

SLUR(M)-py: A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

SLUR(M)-py is a Python pipeline using SLURM for parallel processing of multi-omic epigenomic data, demonstrating improved speed and completeness over existing HPC pipelines.

PERCEPTIVE: an R Shiny pipeline for the prediction of epigenetic modulators in novel species

PERCEPTIVE predicts epigenetic modulators in novel species using genomic data and model species information, validated by wet-lab experiments showing high accuracy.

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.