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

Biochemistry and Biophysics Reports · Sep 11, 2026Peer-reviewedGenomics

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

Anna Hendrika Cornelia Vlot, Vrinda Venu, Samantha Adikari, Eric M. Small, Cullen Roth, Kyle A. Sullivan, Shawn R. Starkenburg, Daniel Jacobson, Christina R. Steadman

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.

bioRxiv · Apr 18, 2026 · PreprintMicrobiology

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

David Rogers, Cullen Roth, Cameron Tauxe, Jeannie T. Lee, Christina R. Steadman, Karissa Y. Sanbonmatsu, Anna Lappala, Shawn R. Starkenburg

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.

BMC Bioinformatics · Jan 8, 2026Peer-reviewedBioinformatics

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

Vrinda Venu, Eric M. Small, Cullen Roth, Samantha Adikari, Anna Hendrika Cornelia Vlot, Kyle A. Sullivan, Chanaka Roshan Abeyratne, Daniel Jacobson, Shawn R. Starkenburg, Karissa Y. Sanbonmatsu, Christina R. Steadman

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

Epigenetics & Chromatin · Oct 3, 2025Peer-reviewedCancer Biology

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

Cullen Roth, Vrinda Venu, Sasha Bacot, Shawn R. Starkenburg, Christina R. Steadman

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.

Epigenomics · Oct 3, 2025Peer-reviewedBioinformatics

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

Cullen Roth, Vrinda Venu, Vanessa Job, Nicholas Lubbers, Karissa Y. Sanbonmatsu, Christina R. Steadman, Shawn R. Starkenburg

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.

BMC Bioinformatics · Nov 21, 2023Peer-reviewedBioinformatics

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

Vrinda Venu, Cullen Roth, Samantha Adikari, Eric M. Small, Shawn R. Starkenburg, Karissa Y. Sanbonmatsu, Christina R. Steadman

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

bioRxiv · Nov 15, 2023 · PreprintGenomics

The telomere-to-telomere, gapless, phased diploid genome and methylome of the green alga Scenedesmus obliquus UTEX 3031 reveals significant heterozygosity and functional separation of the haplotypes

Thomas C. Biondi, Colin P. S. Kruse, Samuel I. Koehler, Taehyung Kwon, Wyatt Eng, Yuliya A. Kunde, Cheryl D. Gleasner, Kayley You Mak, Juergen E. W. Polle, Blake T. Hovde, Erik R. Hanschen, Shawn R. Starkenburg

The paper presents a gapless, phased diploid genome and methylome of Scenedesmus obliquus, revealing haplotype heterogeneity and functional divergence.

bioRxiv · Nov 30, 2022 · PreprintGenomics