Author

Martin Machyna

Yale UniversityORCID 0000-0002-3624-3472Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Research Focus:software / tool· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Alexandra ZhangiD· 2 shared Isaac W. VockiD· 2 shared J. Robert HoggiD· 2 shared Justin W. MabiniD· 2 shared Matthew D. SimoniD· 2 shared Ganesha RaiiD· 1 shared Isabelle Nathalie-Marie LeibleriD· 1 shared James IngleseiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersMolecular Biology

Alexandra ZhangORCID

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2 papers

Recent·Most cited

Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR

Justin W. Mabin, Isaac W. Vock, Martin Machyna, Nazmul Haque, Poonam Thakran, Alexandra Zhang, Ganesha Rai, Isabelle Nathalie-Marie Leibler, James Inglese, Matthew D. Simon, J. Robert Hogg

The paper introduces a method to infer isoform-level kinetics of nonsense-mediated mRNA decay using short-read NR-seq data, revealing variability in NMD efficiency and decay rates of transcripts with and without PTCs.

Genome biology · Jul 15, 2026Peer-reviewedMolecular Biology

Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite

Isaac W. Vock, Justin W. Mabin, Martin Machyna, Alexandra Zhang, J. Robert Hogg, Matthew D. Simon

The paper introduces EZbakR and fastq2EZbakR tools to enhance NR-seq data analysis by supporting multi-label modeling, improved variance accounting, and flexible statistical comparisons.

PLoS Computational Biology · Jul 3, 2025Peer-reviewedBioinformatics