Author
European Bioinformatics InstituteORCID 0000-0002-5331-3604Unclaimed ORCID profile · follow to get notified of new preprints
5 papers
Recent·Most cited
Vanessa Molin Paynter, Sinan U. Umu, Jack A. S. Tierney, Francesca Floriana Tricomi, Leanne S. Haggerty, Bastian Fromm
MirMachine 2 annotates microRNAs across thousands of animal genomes, revealing methodological biases in apparent microRNA absence.
bioRxiv · May 21, 2026 · PreprintBioinformatics
Eric W. Deutsch, Leron W. Kok, Jonathan M. Mudge, Cristian Valls, Irwin Jungreis, Jorge Ruiz‐Orera, Zhi Sun, Ulrike Kusebauch, Ivo Fierro-Monti, Jennifer G. Abelin, M. Mar Albà, Julie L. Aspden, Sreejan Bandyopadhyay, Kaushik Banerjee, Pavel V. Baranov, , Sebastiaan van Heesch
The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.
Nature · May 6, 2026Peer-reviewedMolecular Biology
Javan Okendo, Sergey Koren, Arang Rhie, Aranza Torrado-Tapias, Brandon D. Pickett, Shelise Y. Brooks, Gerard G. Bouffard, Juyun Crawford, Christina Sison, Vinita Joardar, Terence D. Murphy, Jack A. S. Tierney, Leanne S. Haggerty, Fergal J. Martin, CATHERINE A. WILSON, , Shawn Michael Burgess
The paper presents a new zebrafish genome assembly with increased sequence coverage and improved annotation, along with a pangenome resource for variant analysis.
bioRxiv · Nov 17, 2025 · PreprintGenomics
Sonia Pankaj Chothani, Jorge Ruiz‐Orera, Jack A. S. Tierney, Jim Clauwaert, Eric W. Deutsch, M. Mar Albà, Julie L. Aspden, Pavel V. Baranov, Ariel Bazzini, Elspeth A. Bruford, Marie A. Brunet, Tristan Cardon, Anne‐Ruxandra Carvunis, Claudio Casola, Jyoti Sharma Choudhary, , Owen J. L. Rackham
The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.
bioRxiv · Jul 3, 2025 · PreprintGenomics
Jack A. S. Tierney, Michał I. Świrski, Håkon Tjeldnes, Jonathan M. Mudge, Joanna Kufel, Nicola Whiffin, Eivind Valen, Pavel V. Baranov
This paper introduces Ribosome Decision Graphs (RDGs) to represent eukaryotic RNA translation complexity, enabling analysis of translation patterns and genetic variation effects.
Genome Research · May 7, 2024Peer-reviewedGenomics