📃 Publications

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

2026

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 . Nature Communications (2026).

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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).

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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).

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2025

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 . bioRxiv (2025).

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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).

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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).

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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).

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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 . Briefing In Bioinformatics (2025).

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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).

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A multistage, multitask transformer-based framework for multi-disease diagnosis and prediction using personal proteomes. Han LI, Yongkang LI, Yukuan LIU, Johnathan COOPER-KNOCK, Prof. Peng GAO, Xiaotao SHEN, Shengquan CHEN, Xudong XING, Prof. Sai ZHANG . medRxiv (2025).

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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).

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Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy. Xiaotao SHEN, Dr. Songjie Chen, Prof. Liang LIANG, Monika Avina, Hanyah Zackriah, Laura Jelliffe-Pawlowski, Larry Rand, Michael P SNYDER . Briefings in Bioinformatics (2025).

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Maternal lipidomic signatures of preterm and small-for-gestational-age newborn infants in low-and middle-income countries. Ivana MARIĆ, Ali MAHZARNIA, Hilda A MUJURU, Gwendoline CHIMHINI, Samir K SAHA, Mohammad Shameem HASSAN, Nancy A OTIENO, Steven HAWKEN, Kumanan WILSON, Xiaotao SHEN, Samuel LANCASTER, Ronald J WONG, Jonathan D REISS, John KERNER, Michael P SNYDER, William HAY, Gary M SHAW, David K STEVENSON, Victoria WARD, Gary L DARMSTADT . Science Advances (2025).

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MetaNet: a scalable and integrated tool for reproducible omics network analysis. Chen Peng, Zinuo HUANG, Xin WEI, Liuyiqi Jiang, Xiaoping ZHU, Zhen LIU, Qiong Chen, Xiaotao SHEN, Prof. Peng GAO, Prof. Chao Jiang . bioRxiv (2025).

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2024

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 . Nature Aging (2024).

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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).

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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 . Nature (2024).

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Generalized reporter score-based enrichment analysis for omics data. Chen Peng, Qiong Chen, Shangjin Tan, Xiaotao SHEN, Prof. Chao Jiang . Briefings in Bioinformatics (2024).

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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 . Cell Host Microbe (2024).

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Interindividual variability in postprandial plasma fructose patterns in adults. Mia GLADDING, Xiaotao SHEN, Michael P SNYDER, Peter J HAVEL, Sean H ADAMS . Nutrients (2024).

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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, Prof. Chao Jiang . bioRxiv (2024).

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2023

microbiomedataset A tidyverse-style framework for organizing and processing microbiome data. Xiaotao SHEN, Prof. Michael SNYDER . bioRxiv (2023).

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Semi-supervised Cooperative Learning for Multiomics Data Fusion. Daisy Yi Ding, Xiaotao SHEN, Prof. Michael SNYDER, Robert Tibshirani . arXiv (2023).

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Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Sanjay Jain, Liming Pei, Jeffrey M Spraggins, Michael Angelo, Prof. Michael SNYDER . Nature Cell Biology (2023).

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Organism-wide, cell-type-specific secretome mapping of exercise training in mice. Wei Wei, Nicholas M Riley, Xuchao Lyu, Xiaotao SHEN, Jing Guo, Steffen H Raun, Meng Zhao, Maria Dolores Moya-Garzon, Himanish Basu, Alan Sheng-Hwa Tung, Veronica L Li, Wentao Huang, Amanda L Wiggenhorn, Katrin J Svensson, Prof. Michael SNYDER, Carolyn R Bertozzi, Jonathan Z Long . Cell Metabolism (2023).

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Multi-omics microsampling for the profiling of lifestyle-associated changes in health. Xiaotao SHEN, Dr. Ryan KELLOGG, Daniel J Panyard, Dr. Nasim BARAPOUR, Kevin Erazo Castillo, Brittany Lee-McMullen, Alireza Delfarah, Jessalyn Ubellacker, Sara Ahadi, Yael Rosenberg-Hasson, Ariel Ganz, Kévin Contrepois, Basil Michael, Ian Simms, Prof. Chuchu Wang, Daniel Hornburg, Prof. Michael SNYDER . Nature Biomedical Engineering (2023).

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Semi-supervised Cooperative Learning. Daisy Yi Ding, Xiaotao SHEN, Prof. Michael SNYDER, Robert Tibshirani . Machine Learning for Multimodal Healthcare Data: First International … (2023).

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Systems and Methods for Evaluating Gestational Progress and Applications Thereof. Jürgen HOWALDT, Michael SCHWARZ . US Patent App. (2023).

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2022

massDatabase utilities for the operation of the public compound and pathway database. Xiaotao SHEN, Prof. Chuchu Wang, Prof. Michael SNYDER . Bioinformatics (2022).

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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).

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Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity. Prof. Sai ZHANG, Johnathan COOPER-KNOCK, Annika K Weimer, Minyi Shi, Lina Kozhaya, Derya Unutmaz, Calum Harvey, Thomas H Julian, Simone Furini, Elisa Frullanti, Francesca Fava, Alessandra Renieri, Prof. Peng GAO, Xiaotao SHEN, Ilia Sarah Timpanaro, Kevin P Kenna, J Kenneth Baillie, Mark M Davis, Philip S Tsao, Prof. Michael SNYDER . Cell systems (2022).

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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 . Briefings in Bioinformatics (2022).

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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 . Nature Communications (2022).

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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 . Genome Research (2022).

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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 . The Journal of Immunology (2022).

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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 . Bioinformatics (2022).

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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).

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2021

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 . medRxiv (2021).

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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 . bioRxiv (2021).

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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 . Clinical and Translational Medicine (2021).

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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).

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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).

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2020

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 . Cell (2020).

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2019

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

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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).

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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).

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2018

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).

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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 . Radiotherapy and Oncology (2018).

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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).

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2017

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).

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2016

Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry. Zhou Zhiwei, Shen Xiaotao, Tu Jia, Zhu Zheng-Jiang . Analytical chemistry (2016).

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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).

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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).

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