The paper introduces RiboMarker, a method for comprehensive sRNA sequencing that detects all RNA fragment types, improving sensitivity for low-abundance biomarkers.

RNA · Apr 2, 2026Peer-reviewedMolecular Biology

Characterization of transcriptomic changes across Coccidioides morphologies using RiboMarker(R)-enhanced RNA sequencing

Jonathan M. Howard, Aidan C. Manning, Rachel C. Clark, Tahirah Williams, Clarissa J. Nobile, Sergei A. Kazakov, Sergio Barberán-Soler

This study characterizes transcriptomic changes in Coccidioides posadasii across different morphologies using RiboMarker-enhanced RNA sequencing, revealing small RNA and fragment expression patterns associated with life stage transitions.

bioRxiv · Feb 11, 2025 · PreprintMolecular Biology

Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs

Kejia Zhang, Aidan C. Manning, Jenna M. Lentini, Jonathan M. Howard, Jan Felix Dalwigk, Reza Maroofian, Stéphanie Efthymiou, Patricia P. Chan, Sergei I. Eliseev, Zi F. Yang, Hayley Chang, Ehsan Ghayoor Karimiani, Behnoosh Bakhshoodeh, Henry Houlden, Stefanie Kaiser, , Dragony Fu

The paper identifies the roles of TRMT1 and TRMT1L in tRNA modifications, showing their impact on tRNA stability and function, and links TRMT1 variants to disease.

Cell Reports · Jan 1, 2025Peer-reviewedMolecular Biology

tRNA Analysis of eXpression (tRAX): A tool for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications

Andrew Holmes, Jonathan M. Howard, Patricia P. Chan, Todd M. Lowe

tRAX is a tool for analyzing tRNAs and tRNA-derived small RNAs, demonstrating its effectiveness in characterizing these transcriptomes in mouse tissues.

bioRxiv · Jul 2, 2022 · PreprintBioinformatics

Predicting transfer RNA gene activity from sequence and genome context

Bryan P. Thornlow, Joel C. Armstrong, Andrew Holmes, Jonathan M. Howard, Russell B Corbett-Detig, Todd M. Lowe

The paper predicts tRNA gene activity using sequence and genomic context features, finding strong correlations with G+C content and CpG density.

Genome Research · Jan 1, 2020Peer-reviewedGenomics

HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo

Jonathan M. Howard, Hai Lin, Andrew J. Wallace, Garam Kım, Jolene M. Draper, Maximilian Haeussler, Sol J. Katzman, Masoud Toloue, Yunlong Liu, Jeremy R. Sanford

The paper investigates how HNRNPA1 influences U2AF2 RNA binding in vivo, showing it shifts U2AF2 to decoy splice site sequences and affects exon skipping.

Genome Research · May 1, 2018Peer-reviewedMolecular Biology