Author

Stefan Prodic

Australian National UniversityORCID 0009-0009-9511-5727Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Genetics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:long-read sequencing· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Organism:human· 2 Organism:Arabidopsis· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Approach:deep learning· 1

Frequent Co-Authors

Eduardo EyrasiD· 3 shared Nicole M. MartíneziD· 2 shared Ronit Jain· 2 shared A.J. SethiiD· 1 shared Aaryan ChhabraiD· 1 shared Agin RavindraniD· 1 shared Aiswarya Balakrishnan· 1 shared Akanksha SrivastavaiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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3 shared papersBioinformatics

Eduardo EyrasORCID

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4 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJun 17, 2026

ModkitOpt: An optimised workflow for RNA modification stoichiometry estimation and site calling from nanopore sequencing

Alexandra Sneddon, Stefan Prodic, Eduardo Eyras

ModkitOpt optimizes RNA modification site calling by selecting the best parameters and stoichiometry cutoff for nanopore sequencing data, improving precision and recall across modification types.

DOI 10.64898/2025.12.19.695383

long-read sequencingstatistical model

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BioinformaticsbioRxivPreprintJun 4, 2026

SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation

Stefan Prodic, Alice Cleynen, Shafi Mahmud…·Eduardo Eyras

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

2 citations

humanmouse

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Molecular BiologybioRxivPreprintOct 30, 2025

Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7

Rebecca Rodell, Ronit Jain, Hossein Shenasa…·Nicole M. Martínez

The paper develops Nano-Mod-Amp, a Nanopore sequencing tool, to analyze PUS7-dependent pseudouridylation, revealing structural and cell-type specific regulatory mechanisms.

1 citation

long-read sequencingexperimental assay

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GeneticsbioRxivPreprintMar 21, 2024

A basic framework governing splice-site choice in eukaryotes

Craig Dent, Stefan Prodic, Aiswarya Balakrishnan…·Sureshkumar Balasubramanian

The paper quantifies splice-site usage variation across species and identifies intronic hexamer sequences as key determinants of splice-site choice through GWAS and experimental validation.

1 citation

ArabidopsisDrosophila

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