📃 Publications | Shen Lab@NTU

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

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

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

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

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

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

Application of Wearable Devices in Diabetes Management

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

Longitudinal Urine Metabolic Profiling and Gestational Age Prediction in Pregnancy

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

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

Nonlinear dynamics of multi-omics profiles during human aging

Xiaotao SHEN, Prof. Chuchu Wang, Prof. Xin ZHOU, Wenyu Zhou, Daniel Hornburg, Dr. Si Wu, Prof. Michael SNYDER

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

Structure and topography of the synaptic V-ATPase–synaptophysin complex

Prof. Chuchu Wang, Wenhong Jiang, Jeremy Leitz, Kailu Yang, Luis Esquivies, Xing Wang, Xiaotao SHEN, Richard Held, Daniel J. Adams, Tamara Basta, Lucas Hampton, Ruiqi Jian, Lihua Jiang, Michael H. B. Stowell, Wolfgang Baumeister, Qiang Guo, Axel T. Brunger

Generalized reporter score-based enrichment analysis for omics data

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

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

Prof. 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, Dr. Si Wu, Xinyue Zhang, Prof. Chao Jiang, Liuyiqi Jiang, Lihua Jiang, Ruiqi Jian, Andrew W Brooks, Meng Wang, Kévin Contrepois, Prof. 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, Prof. Michael SNYDER

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

Xiaotao SHEN, Prof. Michael SNYDER

Semi-supervised Cooperative Learning for Multiomics Data Fusion

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

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

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

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

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

Xiaotao SHEN, Prof. Chuchu Wang, Prof. Michael SNYDER

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

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

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

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

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

Prof. Peng GAO, Xiaotao SHEN, Xinyue Zhang, Prof. Chao Jiang, Prof. Sai ZHANG, Prof. Xin ZHOU, Sophia Miryam Schüssler-Fiorenza Rose, Prof. Michael SNYDER

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

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

metID: an R package for automatable compound annotation for LC− MS-based data

Xiaotao SHEN, Dr. Si Wu, Prof. Liang LIANG, Dr. Songjie Chen, Kévin Contrepois, Zheng-Jiang Zhu, Prof. Michael SNYDER

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

Prof. 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, Prof. Peng GAO, Xiaotao SHEN, Ilia Sarah Timpanaro, Kevin P Kenna, VA Million Veteran Program, GEN-COVID Network, Mark M Davis, Philip S Tsao, Prof. Michael SNYDER

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

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

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, Prof. Zheng-Jiang ZHU, Tao Zhang

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

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

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

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

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

Xiaotao SHEN, Zheng-Jiang Zhu

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

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

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

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, Prof. Zheng-Jiang ZHU

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

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

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

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

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