Author

Varun Ananth

University of Washington

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Assay:proteomics· 3 Research Focus:benchmarking· 2 Research Focus:deconvolution· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Assay:metagenomics· 1

Frequent Co-Authors

Melih YilmaziD· 3 shared Sewoong OhiD· 3 shared William Stafford NobleiD· 3 shared Bo WeniD· 2 shared Justin Sanders· 2 shared William E. FondrieiD· 2 shared Wout BittremieuxiD· 2 shared Carlo MelendeziD· 1 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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3 shared papersBioinformatics

Melih YilmazORCID

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3 papers

Recent·Most cited

Improvements to Casanovo, a deep learning de novo peptidesequencer

Gwenneth Straub, Varun Ananth, William E. Fondrie, Chris Hsu, Daniela Klaproth-Andrade, Marina Pominova, Michael E. Riffle, Justin Sanders, Bo Wen, Lingwen Xu, Melih Yilmaz, Michael J. MacCoss, Sewoong Oh, Wout Bittremieux, William Stafford Noble

The paper improves Casanovo, a deep learning de novo peptidesequencer, by enhancing interpretability, generalizing its use in database search, speeding up performance, and adding tools for adoption and result interpretation.

Journal of Proteome Research · Dec 30, 2025Peer-reviewedMolecular Biology

Sequence-to-sequence translation from mass spectra to peptides with a transformer model

Melih Yilmaz, William E. Fondrie, Wout Bittremieux, Carlo Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble

Casanovo translates tandem mass spectra into peptide sequences using a transformer model, outperforming existing methods and improving analysis in immunopeptidomics and metaproteomics.

Nature Communications · Jul 30, 2024Peer-reviewedBioinformatics

A learned score function improves the power of mass spectrometry database search

Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh, William Stafford Noble

The paper re-purposes a machine learning model for de novo peptide sequencing as a score function for database search, improving detection power over existing methods.

Bioinformatics · Jun 28, 2024Peer-reviewedBioinformatics