Jun Zhu

π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome

This paper introduces π-SPECFormer, a foundation model for mass spectrometry-based proteomics that decodes the dark proteome by pre-training on unannotated spectra and outperforms baselines in peptide sequencing and modification detection.

Decoding cell identity with multi-scale explainable deep learning

The paper introduces Cell Decoder, a deep learning model that provides multi-scale interpretability for cell type decoding and data integration, showing its effectiveness in human and mouse datasets.

Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics

The paper develops Quartet, a proteome reference material with built-in truths, to assess label-free proteomics reproducibility across platforms and labs.