Publications by authors named "Jonathan Mudge"

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The 2025 Report on the Human Proteome from the HUPO Human Proteome Project.
Eric W Deutsch, Cecilia Lindskog, Bogdan Budnik, Claudia Ctortecka, Tiannan Guo, Jonathan M Mudge

J Proteome Res· January 2026

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Ensembl 2026.
Andrew D Yates, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Jonathan M Mudge

Nucleic Acids Res· November 2025

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Programmed ribosomal frameshifting during mRNA decoding generates a constitutively active proteoform that supports myocardial function.
Gary Loughran, Raffaella De Pace, Ningyu Ding, Jianchao Zhang, Irwin Jungreis, Jonathan M Mudge

Sci Adv· October 2025

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High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Eric W Deutsch, Leron W Kok, Jonathan M Mudge, Jorge Ruiz-Orera, Ivo Fierro-Monti

bioRxiv· July 2025

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Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment.
Aaron Wacholder, Eric W Deutsch, Leron W Kok, Jip T van Dinter, Jiwon Lee, Jonathan M Mudge

bioRxiv· July 2025

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Evaluation of PE5 Entries on the Human Proteome Project Target List.
Clarissa Zheng, Marie Andken, Jonathan M Mudge, Michele Magrane, Sandra Orchard

J Proteome Res· July 2025

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An expanded reference catalog of translated open reading frames for biomedical research.
Sonia Chothani, Jorge Ruiz-Orera, Jack A S Tierney, Jim Clauwaert, Eric W Deutsch, Jonathan Mudge

bioRxiv· July 2025

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Programmed ribosomal frameshifting during mRNA decoding generates a constitutively active proteoform that supports myocardial function.
Gary Loughran, Raffaella De Pace, Ningyu Ding, Jianchao Zhang, Irwin Jungreis, Jonathan M Mudge

bioRxiv· January 2025

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GENCODE 2025: reference gene annotation for human and mouse.
Jonathan M Mudge, Sílvia Carbonell-Sala, Mark Diekhans, Jose Gonzalez Martinez, Toby Hunt

Nucleic Acids Res· January 2025

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Ensembl 2025.
Sarah C Dyer, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Jonathan M Mudge

Nucleic Acids Res· January 2025

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The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.
Gilbert S Omenn, Sandra Orchard, Lydie Lane, Cecilia Lindskog, Charles Pineau, Jonathan M Mudge

J Proteome Res· December 2024

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Triple coding in human SRD5A1 mRNA.
Martina M Yordanova, Conor Slattery, Mirriam Baranova-Gurvich, Manon Engels, Oscar Ting, Jonathan Mudge

Res Sq· December 2024

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GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.
Gazaldeep Kaur, Tamara Perteghella, Sílvia Carbonell-Sala, Jose Gonzalez-Martinez, Toby Hunt, Jonathan M Mudge

bioRxiv· October 2024

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Biophysical characterization of high-confidence, small human proteins.
A M Whited, Irwin Jungreis, Jeffre Allen, Christina L Cleveland, Jonathan M Mudge

Biophys Rep (N Y)· September 2024

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Jonathan M Mudge

Nat Methods· July 2024

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Ribosome decision graphs for the representation of eukaryotic RNA translation complexity.
Jack A S Tierney, Michał Świrski, Håkon Tjeldnes, Jonathan M Mudge, Joanna Kufel

Genome Res· May 2024

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Biophysical characterization of high-confidence, small human proteins.
A M Whited, Irwin Jungreis, Jeffre Allen, Christina L Cleveland, Jonathan M Mudge

bioRxiv· April 2024

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Ensembl 2024.
Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, Jonathan M Mudge

Nucleic Acids Res· January 2024

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Addendum: Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals.
Alla D Fedorova, Stephen J Kiniry, Dmitry E Andreev, Jonathan M Mudge, Pavel V Baranov

Nat Commun· January 2024

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Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity.
Jack A S Tierney, Michał Świrski, Håkon Tjeldnes, Jonathan M Mudge, Joanna Kufel

bioRxiv· November 2023

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What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?
John R Prensner, Jennifer G Abelin, Leron W Kok, Karl R Clauser, Jonathan M Mudge

Mol Cell Proteomics· September 2023

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Jonathan M Mudge

bioRxiv· July 2023

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What can Ribo-seq and proteomics tell us about the non-canonical proteome?
John R Prensner, Jennifer G Abelin, Leron W Kok, Karl R Clauser, Jonathan M Mudge

bioRxiv· May 2023

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Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.
Clara-L Sandmann, Jana F Schulz, Jorge Ruiz-Orera, Marieluise Kirchner, Matthias Ziehm, Jonathan M Mudge

Mol Cell· March 2023

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The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.
Joel Rozowsky, Jiahao Gao, Beatrice Borsari, Yucheng T Yang, Timur Galeev, Jonathan Mudge

Cell· March 2023

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