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TidyMass2 Advancing LC-MS Untargeted Metabolomics Through Metabolite Origin Inference and Metabolic Feature-based Functional Module Analysis

Xiao WANG, Yijiang LIU, Chao Jiang, Zinuo HUANG, Hong YAN, Sunny WONG, Caroline H. Johnson, Jingxiang ZHANG, Yifei GE, Feifan ZHANG, Renfu Lai, Peng GAO, Xuebin Zhang, Xiaotao SHEN

Nature Communications (2026).

Link PDF 15

Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation

Qi SU, Sizhe CHEN, Louis HS LAU, Rashid N LUI, Yun WANG, Zhilu XU, Chun Pan CHEUNG, Jessica YL CHING, Xiaotao SHEN, Ye PENG, Hein Min TUN, Gianluca IANIRO, David RUBIN, Eugene B CHANG, Francis Ka Leung CHAN, Siew Chien NG

Cell Reports (2026).

Link 5

Bridging Sequence and Graph Structure for Epigenetic Age Prediction

Yao LI, Xikun ZHANG, Xiaotao SHEN, Sonika TYAGI, Xin ZHENG, Jiaxing HUANG, Feng XIA

arXiv preprint arXiv: (2026).

Deployment of a cloud-based passive defecation monitoring system for continuous gut health monitoring

Zhiquan SONG, Minso KIM, Jeung LEE, Tae Hyung KWON, Juhwan KIM, Ji Hong KIM, Seong-Geon KIM, Soh KIM, Bong-Hyun JUN, Sang Hun LEE, Walter G PARK, Irene SONU, Michael J ROSEN, Chi Wei ONG, Xiaotao SHEN, Leonard Wei Tat NG, Gun KIM, Sang Hoon CHAE, Kewin Tien Ho SIAH, Dean HO, Shang Wei SONG, Nicole MARTINEZ-MARTIN, Juha SONG, Kuo Chao YEW, Munho KIM, Hen-Wei HUANG, Sunny H WONG, Brian J LEE, Seung-min PARK

Nature Protocols (2026).

FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis

Yijiang LIU, Yuting WANG, Tao HUAN, Xiaotao SHEN

bioRxiv (2026).

Identification of antimicrobial peptides from ancient gut microbiomes

Sizhe CHEN, Yue YUAN, Yun WANG, Ye PENG, Hein Min TUN, Zhimin JIANG, Yinglei MIAO, Sunjae LEE, Xiaole YIN, Xiaotao SHEN, Orlando DELEON, Eugene B CHANG, Francis Ka Leung CHAN, Yang SUN, Siew Chien NG, Qi SU

Nature Communications (2026).

Insulin resistance modifies longitudinal multi-omics responses to habitual diet

Heyjun PARK, Xiaotao SHEN, Dalia PERELMA, Pranav BERRY, Yingzhou LU, Rachel BATTERSBY, Sophia Miryam Schussler FIORENZA, Alessandra CELLI, Caroline BEJIKIAN, Michael SNYDER

bioRxiv (2026).

Kun-peng enables scalable and accurate pan-domain metagenomic classification

Qiong Chen, Boliang ZHANG, Chen Peng, Jiajun HUANG, Zhen LIU, Xiaotao SHEN, Chao Jiang

Briefings in Bioinformatics (2026).

Link 3

Learning Multi-Relational Graph Representations for DNA Methylation-Based Biological Age Estimation

Qing QING, Xikun ZHANG, Zhongyuan ZHANG, Jiarui LIU, Xingtong YU, Xiaotao SHEN, Ziqi XU, Qixin ZHANG, Zhe WANG, Renqiang LUO

arXiv preprint arXiv: (2026).

LOESS and DE-SWAN can induce artifactual "waves" of molecular aging

Madeleine CARBONNEAU, Katherine H SHUTTA, Jeffrey MILLER, Xiaotao SHEN, Michael SNYDER, John QUACKENBUSH

bioRxiv (2026).

MetaNet: a scalable and integrated tool for reproducible omics network analysis

Chen Peng, Liuyiqi Jiang, Zinuo HUANG, Xin WEI, Xiaoping ZHU, Zhen LIU, Qiong Chen, Xiaotao SHEN, Peng GAO, Chao Jiang

Bioinformatics (2026).

Link 6

Microbial Dark Matter, A Multi-layer Mystery

Xiaopan MA, Enhui WU, Yuanyuan GUO, Zheng WEI, Qianyi Zhou, Anita VOIGT, Yijiang LIU, Xiaotao SHEN, Lihui FENG, Shaymaa A ISMAIL, Sridhar MANI, Mingguang HE, Michael P SNYDER, Liang QIAO, Xin ZHOU

Phenomics (2026).

Per-and polyfluoroalkyl substances, seminal plasma metabolome, and sperm telomere length and mitochondrial DNA copy number: a cohort study

Guangming LI, Keyi SI, Jie ZHANG, Xixi CHEN, Xiaotao SHEN, Vicente MUSTIELES, Audrey J GASKINS, Miao LI, Fengjiang SUN, Tian-Qing MENG, An PAN, Chong LIU, Da CHEN, Lili HUANG, Xiaocui LI, Yi-Xin WANG

Journal of Hazardous Materials (2026).

The Expanding Landscape of Microbiota Medicine: Indications, Therapeutic Modalities, and the Path Towards Integrative Microbiome‐Targeting Healthcare

Min DAI, Yisha LIN, Renyou GAN, Xiaotao SHEN, Shin Young PARK, Sunjae LEE, Qi SU

Microbiota Medicine Research (2026).

Link 2

The gut microbiome organ

Yang BI, Weibin SONG, Maria GLYMENAKI, Jie HU, Xiru LI, Heng HUANG, Yousong PENG, Shuaishuai NI, Ornuma HAONON, Zhu LIU, Krai DAOWTAK, Xiaotao SHEN, Huadong PENG, Jutarop PHETCHARABURANIN, Huiru TANG, Yulan WANG, Jia V LI, Mizu JIANG, Nick POWELL, Victor W ZHONG, Elaine HOLMES, Yunlei XIANYU, Zhigang LIU

iMeta, e (2026).

Leveraging Large Language Models for Redundancy-Aware Pathway Analysis and Deep Biological Interpretation

2025 10 articles

Yifei GE, Yijiang LIU, Feifan ZHANG, Chao Jiang, Peng GAO, Nguan Soon Tan, Sai ZHANG, Yuchen SHEN, Qianyi Zhou, Xin ZHOU, Xiao WANG, Chuchu Wang, Xiaotao SHEN

bioRxiv (2025).

Metabolomics and proteomics reveal blocking argininosuccinate synthetase 1 alleviates colitis in mice

Shijia Liu, Haijian Sun, Zijing DU, Shuai Lu, Chenwen Wang, Ye Zhang, Zichen Luo, Lu Wang, Zhimin Fan, Peng Wei, Yujiao Yan, Junzhi Zhang, Shusheng Yin, Tongtong Liu, Qiongzi He, Xi Guo, Kang Ding, Jingjie Zhou, Haibing Hua, Chengli Yu, Weichen Xu, Jinjun Shan, Yongming Li, Yi Xu, Xiaotao SHEN, Gang Cao, Wei Zhou

Nature Communications (2025).

Link PDF 28

Application of LLMs/Transformer-Based Models for Metabolite Annotation in Metabolomics

Yijiang LIU, Feifan ZHANG, Yifei GE, Qiao Liu, Siyu he, Xiaotao SHEN

Health and Metabolism (2025).

Link PDF 12

Application of Wearable Devices in Diabetes Management

Zijing DU, Feifan ZHANG, Yifei GE, Yijiang LIU, Honghua Yu, Yong Wang, Rinkoo Dalan, Xiaotao SHEN

Health and Metabolism (2025).

Link PDF 7

Longitudinal Urine Metabolic Profiling and Gestational Age Prediction in Pregnancy

Xiaotao SHEN, Songjie Chen, Liang LIANG, Monika Avina, Hanyah Zackriah, Laura Jelliffe-Pawlowski, Larry Rand, Michael SNYDER

Briefing In Bioinformatics (2025).

A multistage, multitask transformer-based framework for multi-disease diagnosis and prediction using personal proteomes

Food recommendation towards personalized wellbeing

Guanhua Qiao, Dachuan Zhang, Nana Zhang, Xiaotao SHEN, Xidong Jiao, Wenwei Lu, Daming Fan, Jianxin Zhao, Hao Zhang, Wei Chen, Jinlin Zhu

Trends in Food Science & Technology (2025).

Link PDF 21

Han LI, Yongkang LI, Yukuan LIU, Johnathan COOPER-KNOCK, Peng GAO, Xiaotao SHEN, Shengquan CHEN, Xudong XING, Sai ZHANG

medRxiv (2025).

Link 3

Identification of Early and Mid-Pregnancy Maternal Lipidomics and Metabolomics Signatures of Preterm and Small-for-Gestational Age Infants from Low-and Middle-income Countries …

I MARIC, H MUJURU, G CHIMHINI, SK SAHA, N OTIENO, S HAWKEN, K WILSON, X SHEN, S LANCASTER, RJ WONG, J REISS, JA KERNER, M SNYDER, WW HAY, GM SHAW, DK STEVENSON, V WARD, GL DARMSTADT

JOURNAL OF INVESTIGATIVE MEDICINE (2025).

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 in Bioinformatics (2025).

Link 6

Before NTU

2024 6 articles

Exploring the underlying molecular mechanisms of acute myocardial infarction after SARS-CoV-2 infection

Enrui Xie, Xiaotao SHEN, Yee Hui Yeo, Zixuan Xing, Joseph E. Ebinger, Yixuan Duan, Yue Zhang, Susan Cheng, Fanpu Ji, Jie Deng

American Heart Journal Plus Cardiology Research and Practice (2024).

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

Generalized reporter score-based enrichment analysis for omics data

Chen Peng, Qiong Chen, Shangjin Tan, Xiaotao SHEN, Chao Jiang

Briefings in Bioinformatics (2024).

Link PDF 72

Xin ZHOU, Xiaotao SHEN, Jethro S Johnson, Daniel J Spakowicz, Melissa Agnello, Wenyu Zhou, Monica Avina, Alexander Honkala, Faye Chleilat, Shirley Jingyi Chen, Kexin Cha, Shana Leopold, Chenchen Zhu, Lei Chen, Lin Lyu, Daniel Hornburg, Si Wu, Xin-Yue ZHANG, Chao Jiang, Liuyiqi Jiang, Lihua Jiang, Ruiqi Jian, Andrew W Brooks, Meng Wang, Kévin Contrepois, Peng GAO, Sophia Miryam Schüssler-Fiorenza Rose, Thi Dong Binh Tran, Hoan Nguyen, Alessandra CELLI, Bo-Young Hong, Eddy J Bautista, Yair Dorsett, Paula B Kavathas, Yanjiao Zhou, Erica Sodergren, George M Weinstock, Michael SNYDER

Cell Host Microbe (2024).

Link PDF 198

Interindividual variability in postprandial plasma fructose patterns in adults

Mia GLADDING, Xiaotao SHEN, Michael P SNYDER, Peter J HAVEL, Sean H ADAMS

Nutrients (2024).

Link 7

Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all

Qiong Chen, Boliang ZHANG, Chen Peng, Jiajun HUANG, Xiaotao SHEN, Chao Jiang

bioRxiv (2024).

microbiomedataset A tidyverse-style framework for organizing and processing microbiome data

2023 7 articles

Xiaotao SHEN, Michael SNYDER

bioRxiv (2023).

Link PDF 2

Semi-supervised Cooperative Learning for Multiomics Data Fusion

Daisy Yi Ding, Xiaotao SHEN, Michael SNYDER, Robert Tibshirani

arXiv (2023).

Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Sanjay Jain, Liming Pei, Jeffrey M Spraggins, Michael Angelo, Michael SNYDER

Nature Cell Biology (2023).

Link PDF 0

Semi-supervised Cooperative Learning

Daisy Yi Ding, Xiaotao SHEN, Michael SNYDER, Robert Tibshirani

Machine Learning for Multimodal Healthcare Data: First International … (2023).

Systems and Methods for Evaluating Gestational Progress and Applications Thereof

Jürgen HOWALDT, Michael SCHWARZ

US Patent App. (2023).

massDatabase utilities for the operation of the public compound and pathway database

2022 9 articles

Xiaotao SHEN, Chuchu Wang, Michael SNYDER

Bioinformatics (2022).

Link PDF 10

State-of-the-art methods for exposure-health studies: Results from the exposome data challenge event

Léa Maitre, Jean-Baptiste Guimbaud, Charline Warembourg, Nuria Güil-Oumrait, Paula Marcela Petrone, Marc Chadeau-Hyam, Martine Vrijheid, Xavier Basagaña, Juan R Gonzalez, Exposome Data Challenge Participant Consortium

Environment international (2022).

Link PDF 115

Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine

Xiaotao SHEN, Wei SHAO, Chuchu Wang, Liang LIANG, Songjie Chen, Sai ZHANG, Mirabela Rusu, Michael SNYDER

Briefings in Bioinformatics (2022).

Link PDF 23

TidyMass an object-oriented reproducible analysis framework for LC–MS data

Xiaotao SHEN, Hong YAN, Chuchu Wang, Peng GAO, Caroline JOHNSON, Michael SNYDER

Nature Communications (2022).

Link PDF 101

Precision environmental health monitoring by longitudinal exposome and multi-omics profiling

Peng GAO, Xiaotao SHEN, Xin-Yue ZHANG, Chao Jiang, Sai ZHANG, Xin ZHOU, Sophia Miryam Schüssler-Fiorenza Rose, Michael SNYDER

Genome Research (2022).

Link PDF 92

Longitudinal interactions between levels of serum cytokine and the microbiome from four body sites

Xin ZHOU, Xiaotao SHEN, Jethro Johnson, Daniel J Spakowicz, Chenchen Zhu, Wenyu Zhou, Yanjiao Zhou, George Weinstock, Michael SNYDER

The Journal of Immunology (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 SNYDER

Bioinformatics (2022).

Link PDF 57

Organism-wide secretome mapping uncovers pathways of tissue crosstalk in exercise

Wei Wei, Nicholas M Riley, Xuchao Lyu, Xiaotao SHEN, Jing Guo, Meng Zhao, Maria Dolores Moya-Garzon, Himanish Basu, Alan TUNG, Veronica L Li, Wentao Huang, Katrin J Svensson, Michael P SNYDER, Carolyn R Bertozzi, Jonathan Z Long

bioRxiv (2022).