MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery. - Xiaotao Shen; Zheng-Jiang Zhu (Bioinform., 2019)

LipidIMMS Analyzer: integrating multi-dimensional information to support lipid identification in ion mobility - mass spectrometry based lipidomics. - Zhiwei Zhou; Xiaotao Shen; Xi Chen; Jia Tu; Xin Xiong; Zheng-Jiang Zhu (Bioinform., 2019)

Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine. - Xiaotao Shen; Wei Shao 008; Chuchu Wang; Liang Liang; Songjie Chen; Sai Zhang; Mirabela Rusu; Michael P. Snyder (Briefings Bioinform., 2022)

metID: an R package for automatable compound annotation for LC-MS-based data. - Xiaotao Shen; Si Wu; Liang Liang; Songjie Chen; Kévin Contrepois; Zheng-Jiang Zhu; Michael P. Snyder (Bioinform., 2022)

massDatabase: utilities for the operation of the public compound and pathway database. - Xiaotao Shen; Chuchu Wang; Michael P. Snyder (Bioinform., 2022)

Semi-supervised Cooperative Learning for Multiomics Data Fusion. - Daisy Yi Ding; Xiaotao Shen; Michael Snyder 001; Robert Tibshirani (ML4MHD, 2023)

Generalized reporter score-based enrichment analysis for omics data. - Chen Peng; Qiong Chen; Shangjin Tan; Xiaotao Shen; Chao Jiang (Briefings Bioinform., 2024)

Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy. - Xiaotao Shen; Songjie Chen; Liang Liang; Monika Avina; Hanyah Zackriah; Laura Jelliffe-Pawlowski; Larry Rand; Michael P. Snyder (Briefings Bioinform., 2024)