Xiaotao Shen, Ph.D.

Xiaotao Shen, Ph.D. in CAS

BIOGRAPHY

Hello, my visitors! I am a Ph.D. in Interdisciplinary Research Center on Biology and Chemistry (IRCBC), Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences (CAS). I am broadly interested in Metabolomics, Analytical chemistry, Biostatictics, System biology and Bioinformatics.

My research focuses on the development of bioinformatic algorithms and tools for large-scale metabolomics as well as its application in discovering new biomarkers related to human diseases. I have developed several algorithms and tools in the past five years. The first algorithm was MetNormalizer, which is a machine learning-based algorithm for data normalization and integration of large-scale metabolomics. Then I developed a web-based tool, MetFlow, aiming to provide a comprehensive pipeline for data cleaning and statistical analysis of large-scale metabolomics. The most important algorithm I have developed is called MetDNA, which is a novel algorithm for metabolite identification and dysregulated pathway analysis in untargeted metabolomics.

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INTERESTS

  • R programming

  • Metabolomics

  • Biostatistics & Bioinformatics

  • Biomarker Discovery for Diseases


EDUCATION

  • Ph.D. in Metabolomics and Bioinformatics (Advisor: Dr. Zheng-Jiang Zhu), Aug. 2013-2018, Chinese Academy of Sciences

  • BSs in Biotechnology, Aug. 2009-Jun. 2013, Inner Mongolia University


RESEARCH

  • Mass Spectrometry-based Metabolomics.

  • Metabolomics Data Processing Methods and Software Development.

  • Metabolomics Statistical Analysis.

  • Biomarker Discovery for Diseases.


HONORS AND AWARDS

  • Student Travel Award (500 US dollar), Metabolomics Society (2018)

  • Travel Award (800 Swiss France), Journal Metabolites (2018)

  • National Scholarship, University of Chinese Academy of Sciences (2017)

  • Award for Outstanding Youth Report, The third China Mass Spectrometry Analysis Conference (2017)

  • Merit Student, University of Chinese Academy of Sciences (2016)

  • Award for Outstanding Youth Report, The 34th China Mass Spectrometry Society Conference (2016)

  • Inner Mongolia Outstanding Graduate, Inner Mongolia Autonomous Region (2013)

  • National Encouragement Scholarship, Inner Mongolia University (2011)


PATENTS AND SOFTWARE COPYRIGHTS

  • A Method for Metabolite Identification and Pathway Network Analysis
    Dr. Zheng-Jiang Zhu and Xiaotao Shen (Software Copyright, 2018)

  • Software for Metabolite Identification and Pathway Network Analysis
    Dr. Zheng-Jiang Zhu and Xiaotao Shen (Patent, 2017)

  • Software for Data Cleaning for Metabolomics Data
    Dr. Zheng-Jiang Zhu and Xiaotao Shen (Software Copyright, 2018)


PUBLICATIONS

  1. X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, J. Ma, N. Liu and Z.-J. Zhu, Large-scale Metabolite Identification for Untargeted Metabolomics Using Metabolic Reaction Network, Nature Communications, in revision.

  2. X. Shen and Z.-J. Zhu, MetFlow: An Interactive and Integrated Workflow for Metabolomics Data Cleaning and Differential Metabolite Discovery, Bioinformatics, in revision.

  3. Z. Zhou, X. Shen, X. Chen, J. Tu, X. Xiong, and Z.-J. Zhu, LipidIMMS Analyzer: Integrating Multi-dimensional Information to Support Lipid Identification in Ion Mobility–Mass Spectrometry based Lipidomics, Bioinformatics, in press.

  4. H. Jia, X. Shen (Co-first author), Y. Guan, M. Xu, M. Mo, J. Zhu and Z.-J. Zhu, Assessment of The Response to Neoadjuvant Chemo-Radiation in Rectal Cancer Patients based on a Metabolomics Approach, Radiotherapy and Oncology, in press.

  5. Z. Zhou, J. Tu, X. Xiong, X. Shen, and Z.-J. Zhu, LipidCCS: Prediction of Collision Cross-Section Values for Lipids with High Precision to Support Ion Mobility-Mass Spectrometry based Lipidomics, Analytical Chemistry, 2017, 89, 9559–9566.

  6. Z. Zhou, X. Shen, J. Tu, and Z.-J. Zhu, Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility - Mass Spectrometry, Analytical Chemistry, 2016, 88, 11084-11091.

  7. J. Wang, T. Zhang, X. Shen (Co-first author), J. Liu, D. Zhao, Y. Sun, L. Wang, Y. Liu, X. Gong, Y. Liu, Z.-J. Zhu, F. Xue, Serum Metabolomics for Early Diagnosis of Esophageal Squamous Cell Carcinoma by UHPLC-QTOF/MS, Metabolomics, 2016, 12: 116.

  8. X. Shen, X. Gong, Y. Cai, Y. Guo, J. Tu, H. Li, T.Zhang, J. Wang, F. Xue, and Z.-J. Zhu, Normalization and Integration of Large-Scale Metabolomics Data Using Support Vector Regression, Metabolomics, 2016, 12: 89.

ORAL PRESENTATION

  1. Metabolic Reaction Network-based Recursive Metabolite Identification for Untargeted Metabolomics.
    The 14th International Conference of the Metabolomics Society, 28th, June, 2018, Seattle, Washington, USA.

  2. Assessment of the Response to Neoadjuvant Chemo-Radiation in Rectal Cancer Patients based on a Metabolomics Approach.
    The Third China Mass Spectrometry Analysis Conference, December, 2017, Xiamen, Fujian, China.

  3. Normalization and Integration of Large-Scale Mass Spectrometry-based Metabolomics Data Using Support Vector Regression.
    The 34th China Mass Spectrometry Society Conference, September, 2016, Xining, Qinghai, China.

  4. Normalization and Integration of Large-Scale Mass Spectrometry-based Metabolomics Data Using Support Vector Regression.
    The 64th American Society for Mass Spectrometry Conference, June, 2016, San Antonio, Texas, USA.

POSTER PRESENTATION

  • Metabolic Reaction Network based Metabolite Annotation in Untargeted Metabolomics.
    The 13th International Conference of the Metabolomics Society, June, 2017, Brisbane, Austria.


PROJECTS

  1. omicsPie: An Open Platform to Sharing Omics Information

  2. MetFlow: An Interactive and Integrated Workflow for Metabolomics Data Cleaning and Differential Metabolite Discovery.

  3. Metabolic Reaction Network Based Metabolite Annotation and Dysregulated Network Analysis.

  4. Biomarker Discovery for Early Diagnosis of Alzheimer’s Disease.

  5. Biomarker Discovery for Locally Advanced Rectal Cancer Patients’ Response to Neoadjuvant Chemo-Radiation Therapy.

  6. Biomarker Discovery for Early Diagnosis of Esophagus Cancer.

  7. Data Cleaning Methods and Software (MetCleaning) Development of Large-scale Metabolomics Data. Github link

  8. Normalization Method (MetNormalizer) Development for Large-scale Metabolomics Data Using Machine Learning Method.


TECHNICAL STRENGTH

  • Languages: Mandarin (Very fluent), English (Fluent), Henan dialect (Very fluent).

  • Programming Languages: R, Python.

  • Mass Spectrometry Analysis: Agilent QT0F 6550, Agilent QQQ 6495, 6460, Agilent IMMS 6560, AB sciex Triple TOF 5600, 6600, Bruker MALDI-TOF.

  • Bioinformatic Tools: Agilent MassHunter work station, AB sciex PeakView, XCMS, MS-DIAL.

  • Other Skills: Photoshop, Illustrator, Linux (Ubuntu and CentOS), Github, Shiny.


GET IN TOUCH

Following is my contact information at IRCBC (ShangHai), SIOC, CAS. Other socail-netwrok information can be found via the icons on the bottom of this web.

  • Address: 26 Qiuyue Rd, Building 6, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, China.