Author

Pooja Dasgupta

University of Washington

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Bioinformatics· 1

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Organism:human· 1 Assay:proteomics· 1 Research Focus:software / tool· 1 Approach:transformer / foundation model· 1 Organism:yeast· 1

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Bo WeniD· 1 shared Chris HsuiD· 1 shared Michael J. MacCossiD· 1 shared Shreyash SonthaliaiD· 1 shared William Stafford NobleiD· 1 shared

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2026-2026 · peak 1/yr

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1 shared paperBioinformatics

Bo WenORCID

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1 paper

Recent·Most cited

Prioritizing peptides for targeted mass spectrometry experiments using deep learning

Shreyash Sonthalia, Bo Wen, Pooja Dasgupta, Chris Hsu, Michael J. MacCoss, William Stafford Noble

Bromo, a pairwise transformer, ranks a protein's peptide precursors by expected mass spectrometry response, beating XGBoost, PREGO and PeptideRanger on held-out yeast data, and can be fine-tuned per instrument.

bioRxiv · Aug 31, 2026 · PreprintBioinformatics✦ In-depth digest