Xiaotao Shen

SHEN, XIAOTAO

BIOGRAPHY

Hello, my visitors! I am a phD student 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.

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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

  • 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, under review.

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

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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. PDF link

ORAL PRESENTATION

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

  • SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology. The 14th International Conference of the Metabolomics Society, 26th, June, 2018, Seattle, Washington, USA.

  • 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.

  • 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.

  • 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

  • X. Shen (Presenter), Z.-J Zhu, Metabolic Reaction Network based Metabolite Annotation in Untargeted Metabolomics. The 13th International Conference of the Metabolomics Society, June, 2017, Brisbane, Austria.


PROJECTS

  • omicsPie: An Open Platform to Sharing Omics Information

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

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

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

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

  • Biomarker Discovery for Early Diagnosis of Esophagus Cancer.

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

  • 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.