📃 Publications

All the publications can be found on google scholar
Bold: Shen lab member

Author

Year

Type

2026 16 articles

LagCI Enables Inference of Temporal Causal Relationships from Dense Multi-Omic Time Series

Yifei GE, Shunpeng BAI, Zirui QIANG, Yijiang LIU, Yitong WU, Xiaotao SHEN

bioRxiv (2026).

Link 0

Cross-body site microbial interactions influence the human plasma metabolome

Jingxiang ZHANG, Chao Jiang, Xin ZHOU, Peng GAO, Sunny WONG, Michael SNYDER, Xiaotao SHEN

Microbiome (2026).

Link 0

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 5

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 0

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).

Link 0

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).

Link 0

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).

Link 0

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).

Link 0

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).

Link 0

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 3

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).

Link 0

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 1

2025 10 articles

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

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).

Link PDF 1

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 21

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 11

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 6

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).

Link PDF 1

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 17

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

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

medRxiv (2025).

Link 2

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).

Link 0

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).

Link PDF 1

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 59

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

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 169

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 6

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).

Link 0

2023 7 articles

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

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).

Link PDF 1

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).

Link 0

Systems and Methods for Evaluating Gestational Progress and Applications Thereof

Jürgen HOWALDT, Michael SCHWARZ

US Patent App. (2023).

Link 1

2022 9 articles

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

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 103

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 21

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 93

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 84

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).

Link PDF 1

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 54

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).

Link 1

2021 5 articles

Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity

Sai ZHANG, Johnathan COOPER-KNOCK, Annika K Weimer, Calum Harvey, Thomas H Julian, Cheng Wang, Jingjing Li, Simone Furini, Elisa Frullanti, Francesca Fava, Alessandra Renieri, Cuiping Pan, Jina Song, Paul Billing-Ross, Peng GAO, Xiaotao SHEN, Ilia Sarah Timpanaro, Kevin P Kenna, VA Million Veteran Program, GEN-COVID Network, Mark M Davis, Philip S Tsao, Michael SNYDER

medRxiv (2021).

Link PDF 5

Integration and comparison of multi-omics profiles of NGLY1 deficiency plasma and cellular models to identify clinically relevant molecular phenotypes

Songjie Chen, Guangwen Wang, Xiaotao SHEN, Daniel Hornburg, Rene Hoffman, Stephanie Nevins, Xun Cheng, Michael SNYDER

bioRxiv (2021).

Link PDF 4

A serum metabolomics analysis reveals a panel of screening metabolic biomarkers for esophageal squamous cell carcinoma

Jiali Lv, Jialin Wang, Xiaotao SHEN, Jia Liu, Deli Zhao, Mengke Wei, Xia Li, Bingbing Fan, Yawen Sun, Fuzhong Xue, Zheng-Jiang ZHU, Tao Zhang

Clinical and Translational Medicine (2021).

Link PDF 18

The mediation effect of serum metabolites on the relationship between long-term smoking exposure and esophageal squamous cell carcinoma

Mengke Wei, Lihong Zhao, Jiali Lv, Xia Li, Guangshuai Zhou, Bingbing Fan, Xiaotao SHEN, Deli Zhao, Fuzhong Xue, Jialin Wang, Tao Zhang

BMC cancer (2021).

Link PDF 18

Serum metabolomics analysis for the progression of esophageal squamous cell carcinoma

Xia Li, Lihong Zhao, Mengke Wei, Jiali Lv, Yawen Sun, Xiaotao SHEN, Deli Zhao, Fuzhong Xue, Tao Zhang, Jialin Wang

Journal of Cancer (2021).

Link PDF 32

2020 1 article

Metabolic dynamics and prediction of gestational age and time to delivery in pregnant women

Liang LIANG, Marie-Louise Hee Rasmussen, Brian Piening, Xiaotao SHEN, Songjie Chen, Hannes Röst, John K Snyder, Robert Tibshirani, Line Skotte, Norman CY Lee, Kévin Contrepois, Bjarke Feenstra, Hanyah Zackriah, Michael SNYDER, Mads Melbye

Cell (2020).

Link PDF 322

2019 3 articles

MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery

Xiaotao SHEN, Zheng-Jiang Zhu

Bioinformatics (2019).

Link PDF 44

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics

Xiaotao SHEN, Ruohong Wang, Xin Xiong, Yandong Yin, Yuping Cai, Zaijun Ma, Nan Liu, Zheng-Jiang Zhu

Nature communications (2019).

Link PDF 393

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

Bioinformatics (2019).

Link PDF 82

2018 3 articles

Development of a correlative strategy to discover colorectal tumor tissue derived metabolite biomarkers in plasma using untargeted metabolomics

Zhuozhong Wang, Binbin Cui, Fan Zhang, Yue Yang, Xiaotao SHEN, Zhong Li, Weiwei Zhao, Yuanyuan Zhang, Kui Deng, Zhiwei Rong, Kai Yang, Xiwen Yu, Kang Li, Peng Han, Zheng-Jiang Zhu

Analytical chemistry (2018).

Link PDF 51

Predicting the pathological response to neoadjuvant chemoradiation using untargeted metabolomics in locally advanced rectal cancer

Huixun Jia, Xiaotao SHEN, Yun Guan, Meimei Xu, Jia Tu, Miao Mo, Li Xie, Jing Yuan, Zhen Zhang, Sanjun Cai, Ji Zhu, Zheng-Jiang ZHU

Radiotherapy and Oncology (2018).

Link PDF 65

Metabolic reaction network-based recursive metabolite identification for untargeted metabolomics

Xiaotao SHEN, Xin Xiong, Ruohong Wang, Yandong Yin, Yuping Cai, Zaijun Ma, Nan Liu, Zheng-Jiang Zhu

bioRxiv (2018).

Link 2

2017 1 article

LipidCCS prediction of collision cross-section values for lipids with high precision to support ion mobility–mass spectrometry-based lipidomics

Zhiwei Zhou, Jia Tu, Xin Xiong, Xiaotao SHEN, Zheng-Jiang Zhu

Analytical chemistry (2017).

Link PDF 250

2016 3 articles

Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry

Zhou Zhiwei, Xiaotao SHEN, Tu Jia, Zhu Zheng-Jiang

Analytical chemistry (2016).

Link PDF 240

Serum metabolomics for early diagnosis of esophageal squamous cell carcinoma by UHPLC-QTOF/MS

Jialin Wang, Tao Zhang, Xiaotao SHEN, Jia Liu, Deli Zhao, Yawen Sun, Lu Wang, Yingjun Liu, Xiaoyun Gong, Yanxun Liu, Zheng-Jiang Zhu, Fuzhong Xue

Metabolomics (2016).

Link PDF 366

Normalization and integration of large-scale metabolomics data using support vector regression

Xiaotao SHEN, Xiaoyun Gong, Yuping Cai, Yuan Guo, Jia Tu, Hao Li, Tao Zhang, Jialin Wang, Fuzhong Xue, Zheng-Jiang Zhu

Metabolomics (2016).

Link PDF 198

📃 Publications

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