Eric M. Small

A reference genome without a virus: cDNA reconstruction reveals the provenance and function of the MS2 phage sequence

The paper reconstructs the MS2 phage genome using cDNA and shows that the current NCBI reference genome does not produce infectious phage, highlighting the need to verify reference genome infectivity.

The phage stress test: a proving ground for genome language models in biological prediction

This study evaluates a genome language model's ability to predict the effects of sequence changes in phages using experimental data, finding mixed success in distinguishing functional from nonfunctional mutations.

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.

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.

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.

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.