Cullen Roth

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

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.

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.

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

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.

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

The paper tests the accidental pathogen hypothesis by identifying a QTL linked to amoeba resistance and melanization in Cryptococcus species, finding no correlation with macrophage resistance or virulence.

This study identifies genetic interactions governing morphogenesis in Cryptococcus fungi using QTL analysis, revealing epistatic relationships between genes involved in signaling pathways.

This paper identifies genetic loci and pathways underlying virulence traits in Cryptococcus deneoformans using QTL mapping and finds that key signaling pathways contribute to phenotypic variation.

The paper maps meiotic recombination in Cryptococcus deneoformans, finding lower recombination rates in unisexual reproduction compared to bisexual crosses.