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Nature Communications|December 12, 2025
FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectraYuhui Hong, Sujun Li, Yuzhen Ye, et al.Molecular & Cellular Proteomics : MCP|May 31, 2019
A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic VariationSujun Li, Haixu Tang, Yuzhen YeBioinformatics (Oxford, England)|May 30, 2023
3DMolMS: prediction of tandem mass spectra from 3D molecular conformationsYuhui Hong, Sujun Li, Christopher J Welch, et al.Plos Computational Biology|December 6, 2016
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in MetaproteomicsHaixu Tang, Sujun Li, Yuzhen YeAnnual Review of Analytical Chemistry (Palo Alto, Calif.)|February 27, 2025
Machine Learning in Small-Molecule Mass SpectrometryYuhui Hong, Yuzhen Ye, Haixu TangNature Communications|December 2, 2023
Accurate de novo peptide sequencing using fully convolutional neural networksKaiyuan Liu, Yuzhen Ye, Sujun Li, et al.Analytical Chemistry|February 14, 2020
Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural NetworkKaiyuan Liu, Sujun Li, Lei Wang, et al.Bioinformatics (Oxford, England)|August 31, 2015
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysisYuzhen Ye, Haixu TangJournal of Bioinformatics and Computational Biology|June 10, 2009
An ORFome assembly approach to metagenomics sequences analysisYuzhen Ye, Haixu TangComputational Systems Bioinformatics. Computational Systems Bioinformatics Conference|August 1, 2009
An ORFome assembly approach to metagenomics sequences analysisYuzhen Ye, Haixu TangPageof 28