Author

Philip Z. Johnson

University of Maryland, College ParkORCID 0000-0002-6689-8306Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Research Focus:software / tool· 2 Research Focus:benchmarking· 1 Research Focus:gene regulatory network inference· 1 Assay:long-read sequencing· 1 Organism:plant (other)· 1

Frequent Co-Authors

Anne E. SimoniD· 2 shared Aleksei NaideniD· 1 shared Anton I. PetroviD· 1 shared Anton S. PetroviD· 1 shared Blake SweeneyiD· 1 shared Caeden D. MeadeiD· 1 shared Carlos Eduardo RibasiD· 1 shared Craig L. ZirbeliD· 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 papersBioinformatics

Anne E. SimonORCID

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2 papers

Recent·Most cited

Ghost in the Machine: Evidence for Non-Random Errors During Direct RNA Nanopore Sequencing Due to Post-Translocated RNA Folding

Jason M. Needham, Philip Z. Johnson, Anne E. Simon

The paper shows that direct RNA nanopore sequencing has non-random error patterns linked to RNA folding and sequence complexity, not random distribution as previously assumed.

bioRxiv · May 27, 2026 · PreprintBioinformatics

R2DT: a comprehensive platform for visualising RNA secondary structure

Holly McCann, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Philip Z. Johnson, Anne E. Simon, David Hoksza, Eric P. Nawrocki, Patricia P. Chan, Todd M. Lowe, Carlos Eduardo Ribas, Blake Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, , Anton I. Petrov

R2DT is a software platform for visualizing RNA secondary structures with enhanced features like SNP display and template-free visualization.

Nucleic Acids Research · Feb 8, 2025Peer-reviewedBioinformatics