Publications

All the publications can be found on google scholar
Bold: Shen lab member
2026 23 articles
MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi‐Omics Data
Yifei GE, Feifan ZHANG, Yijiang LIU, Chao JIANG, Peng GAO, Nguan Soon TAN, Sai ZHANG, Yuchen SHEN, Qianyi ZHOU, Xin ZHOU, Xiao WANG, Fangqing ZHAO, Chuchu WANG, Xiaotao SHEN
Advanced Science (2026).

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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
Briefings in Bioinformatics (2026).

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).

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).

17

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).

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).

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 WONG, Brian J LEE, Seung-Min PARK
Nature Protocols (2026).

1

Distinct Gut Microbiome Signatures in Ethnically Diverse Populations within a Shared Urban Asian Geography
Ruwen ZHOU, Xiaotao SHEN, Theresia Handayani MINA, Kajal Rupesh AGRAWAL, Dorrain Yanwen LOW, Jason Xing KANG, Jonathan Jin Yuan TEO, Shaun Hong Chuen HOW, Benjamin Chih Chiang LAM, Tong WANG, Chun-Wie CHONG, HELIOS Study TEAM, Joseph Jao Yiu SUNG, Niranjan NAGARAJAN, Yusuf ALI, John Campbell CHAMBERS, Sunny WONG
medRxiv (2026).

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eBiota: Designing microbial communities from large seed pools with desired function using rapid optimization and deep learning
Xiaoqing JIANG, Jiaheng HOU, Haoyu ZHANG, Jinyuan GUO, Shaohua GU, Doris VANDEPUTTE, Yulin LIAO, Qian GUO, Xinrun YANG, Yiyan ZHOU, Peter X GENG, Chunhui WANG, Mo LI, Alexandre JOUSSET, Xiaotao SHEN, Zhong WEI, Huaiqiu ZHU
bioRxiv (2026).

1

FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis
Yijiang LIU, Yuting WANG, Tao HUAN, Xiaotao SHEN
bioRxiv (2026).

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).

1

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).

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Integrated intraocular–plasma proteomics reveals conserved biomarkers for diabetic retinopathy progression: a multi-fluid biopsy study
Jiahui CAO, Fenghao LIU, Huiqian KONG, Chunran LAI, Zijing DU, Zhi Da SOH, Ting SU, Chenxiao SHEN, Qinyi LI, Ying FANG, Yijun HU, Xianwen SHANG, Xiaotao SHEN, Mingguang HE, Ching-Yu CHENG, Zhuoting ZHU, Meijuan ZHOU, Xiayin ZHANG, Honghua YU
Diabetologia (2026).

1

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).

4

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).

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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).

1

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).

7

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).

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Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes
Tianyuan ZHANG, Jia LI, Chao TANG, You WU, Hao WU, Xi‐Tong ZHU, Ziyang LUO, Hang QIN, Lishan DING, Yu ZENG, Shiou Yih LEE, Xiaotao SHEN, Shiwen GAO, Zhaoyang TIAN, Qian TANG, Mian LI, Muhammad Tahir Ul QAMAR, Yang DONG, Komivi DOSSA, Yaxuan ZHANG, Hu CHEN, Sanqi AN, Xiang YU, Lu CHEN, Dingjie WANG, Shengli LI, Ling‐Ling CHEN, Yanqiang LI
iMeta, e (2026).

9

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).

1

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).

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).

1

Trihalomethane Exposure, Seminal Plasma Metabolomics, and Semen Quality in Healthy Men: A Meet-in-the-Middle Approach
Xixi CHEN, Li-Li HUANG, Guangming LI, Audrey J GASKINS, Chong LIU, Chengliang XIONG, Tianqing MENG, Vicente MUSTIELES, Carmen MESSERLIAN, Jie ZHANG*, Xiaotao SHEN*, Yi-Xin WANG*
Environmental Science & Technology (2026).

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Before NTU