😁 Hello!

👋Welcome to Xiaotao Shen’s Personal Website!👋

CV

🧬 Research interest

I am broadly interested in Metabolomics, Multi-omics, Biostatistics, Systems Biology, and Bioinformatics, and their application in healthcare.

My publications

☕️ Record My life ☕️

😄Life with my family😄

Chuchu Wang

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Xiaotao Shen

Xiaotao Shen

Postdoctoral Research Fellow

Stanford University

👤 About me

I am a Postdoctoral Research Fellow in Prof. Michael Snyder’s lab at Stanford University School of Medicine. My overarching research interests are bioinformatics algorithms development for multi-omics data, and their application to precision medicine. Specifically, I am interested in bioinformatics algorithm development, including 1) Comprehensive analysis workflow and deep learning for LC-MS data, 2) Metabolic network analysis, 3) Wearable and multi-omics data integration, and 4) microbiome and metabolome data integration. I also employed the developed bioinformatics algorithms as a unique systems biology approach to study the potential biomarkers and mechanisms of 1) pregnancy and related diseases, 2) aging and related diseases, and 3) cancer. More tools and projects I developed can be found in the Projects part.

Now I am also the member of Stanford Chinese Postdoctral Association (SCPA). Feel free to let me know if you want to join us and contribute to the amazing community!

🐶 🏫 🈸 😄 👊 ✊ 👨‍👩‍👦 🐼 🌏 🎉 🇨🇳

📚 Statistics

Data from Google Scholar (9/21/2023)
34

Publications

1,243

Citations

13

H-index

🧑‍🎓 Experiences

 
 
 
 
 
Stanford University
Postdoctoral Research Fellow
Stanford University
April 2019 – Present Palo Alto, California 🇺🇸

👨‍🏫 Advisor: Prof. Michael P. Snyder

🧪 Research:

  • Metabolomics and System Biology
  • Multi-omics data analysis and their application in healthcare
  • Software and algorithm development for metabolomics and other omics data
 
 
 
 
 
Stanford Chinese Postdoctoral Association
Co-chair
Stanford Chinese Postdoctoral Association
August 2021 – July 2022 Palo Alto, California 🇺🇸
 
 
 
 
 
Chinese Academy of Sciences
Research Scientist
Chinese Academy of Sciences
January 2019 – March 2019 Shanghai, China 🇨🇳
👨‍🏫 Advisor: Prof. Zheng-Jiang Zhu
 
 
 
 
 
Chinese Academy of Sciences
Ph.D.
Chinese Academy of Sciences
September 2013 – December 2018 Shanghai, China 🇨🇳

👨‍🏫 Advisor: Prof. Zheng-Jiang Zhu

🧪 Research:

  • Metabolomics and System Biology
  • Bioinformatics
 
 
 
 
 
Inner Mongolia University
B.S.
Inner Mongolia University
September 2009 – July 2013 Hohhot, Inner Mongolia, China 🇨🇳

📃 Publications

🔗 Google scholar

microbiomedataset A tidyverse-style framework for organizing and processing microbiome data
microbiomedataset A tidyverse-style framework for organizing and processing microbiome data
Link PDF
microbiomedataset A tidyverse-style framework for organizing and processing microbiome data
Semi-supervised Cooperative Learning for Multiomics Data Fusion
Semi-supervised Cooperative Learning for Multiomics Data Fusion
Link PDF
Semi-supervised Cooperative Learning for Multiomics Data Fusion
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
Link PDF
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
Multi-omics microsampling for the profiling of lifestyle-associated changes in health
Multi-omics microsampling for the profiling of lifestyle-associated changes in health
Link PDF
Multi-omics microsampling for the profiling of lifestyle-associated changes in health
massDatabase utilities for the operation of the public compound and pathway database
massDatabase utilities for the operation of the public compound and pathway database
Link PDF
massDatabase utilities for the operation of the public compound and pathway database
See all publications

💻 Projects

*
All Metabolomics Multi-omics Others
TidyMicrobiome
TidyMicrobiome project is a comprehensive computational framework that can process the whole workflow of data processing and analysis for microbiome data using tidyverse principles.
Link Code
TidyMicrobiome
SCPA
The Stanford Chinese Postdoc Association is a vibrant community of the Chinese postdocs, across all disciplines, at Stanford University. Our mission is to create and hold a space of all Chinese postdocs, and help them in study, work and life as much as we can.
Link Code
SCPA
R cookbook
This is myself note book for R study.
Link Code
R cookbook
MetNormalizer
MetNormalizer is used to normalize large scale metabolomics data.
Link Code
MetNormalizer
deepPseudoMSI
The deepPseudoMSI project is the first method that convert LC-MS raw data to “images” and then process them using deep learning method for diagnosis.
Link Code
deepPseudoMSI
laggedCor
TidyMass project is a comprehensive computational framework that can process the whole workflow of data processing and analysis for LC-MS-based untargeted metabolomics using tidyverse principles.
Link Code
laggedCor
metID
metID is a R packge which is used for metabolite identification based on in-house database and public database based on accurate mass, retention time and/or MS2 spectra.
Link Code
metID
TidyMass
TidyMass project is a comprehensive computational framework that can process the whole workflow of data processing and analysis for LC-MS-based untargeted metabolomics using tidyverse principles.
Link Code
TidyMass
MetDNA
MetDNA characterizes initial seed metabolites using a small tandem spectral library, and utilize their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites which are subsequently served as the basis for recursive analysis.
Link Code
MetDNA
MetFlow
We developed an interactive web server, namely, MetFlow, to provide an integrated and comprehensive workflow for metabolomics data cleaning and differential metabolite discovery.
Link Code
MetFlow

🗣 Talks

Nonlinear Dynamic Changes During Human Aging Revealed in Multi-omics Profiles
Nonlinear Dynamic Changes During Human Aging Revealed in Multi-omics Profiles Health
Xiaotao Shen
Sep 21, 2023
Slides Video
Nonlinear Dynamic Changes During Human Aging Revealed in Multi-omics Profiles
Nonlinear Dynamic Changes During Human Aging Revealed in Multi-omics Profiles
Nonlinear Dynamic Changes During Human Aging Revealed in Multi-omics Profiles Health
Xiaotao Shen
Last updated on Sep 8, 2023
Slides Video
Nonlinear Dynamic Changes During Human Aging Revealed in Multi-omics Profiles
Multi-Omics Microsampling for The Profiling of Lifestyle-Associated Changes in Health
Multi-Omics Microsampling for The Profiling of Lifestyle-Associated Changes in Health
Xiaotao Shen
Last updated on Sep 6, 2023
Slides Video
Multi-Omics Microsampling for The Profiling of Lifestyle-Associated Changes in Health
See all

📖 Blog

脂质组学研究揭示健康、疾病和衰老过程中的动态变化
脂质组学研究揭示健康、疾病和衰老过程中的动态变化
Xiaotao Shen
Last updated on Sep 14, 2023 Chinese
tidytof:一种可扩展和可重现的高维细胞数据分析的整洁框架
依赖于tidyverse风格的组学数据处理软件越来越多了！期待我们的tidymicrobiome！
Xiaotao Shen
Last updated on Sep 8, 2023 R, Chinese
如何使用colorspace包选择合适的颜色方案
颜色是数据可视化中非常重要的一个元素，它可以传达信息，引起注意，增强美感，甚至影响情绪。但是，如何选择合适的颜色方案呢？有没有一种科学的方法，可以帮助我们在众多的颜色中找到最佳的组合呢?
Xiaotao Shen
Last updated on Sep 8, 2023 R, Chinese
See all posts

📥 Contact

📰 News

2023-09-08 Xiaotao Shen presented on 2023 BAMM.
Last updated on Sep 8, 2023
PDF
2023-09-08 Xiaotao Shen presented on 2023 BAMM.
2023-9-1 Xiaotao Shen presented the nonlinear aging work on 2023 Stanford University Biox Symposium.
Last updated on Sep 6, 2023
PDF
2023-9-1 Xiaotao Shen presented the nonlinear aging work on 2023 Stanford University Biox Symposium.
2023-8-29 Xiaotao Shen presented on CASMS2023.
Last updated on Sep 6, 2023
PDF
2023-8-29 Xiaotao Shen presented on CASMS2023.
2023-8-29 Xiaotao Shen received the CASMS Young Investigator Award!😀
Last updated on Sep 6, 2023
PDF
2023-8-29 Xiaotao Shen received the CASMS Young Investigator Award!😀

🐕‍🦺 Journal Referee

Nature Biotechnology
Link
Nature Biotechnology
Nature Communications
Link
Nature Communications
Briefing in Bioinformatics
Link
Briefing in Bioinformatics
Bioinformatics
Link
Bioinformatics
GigaScience
Link
GigaScience
See all

🏅 Awards

CASMS
Young Investigator Award 2023
CASMS Aug 2023
Chinese American Society of Mass Spectrometry
Stanford
SPORR 2023 Rigor and Reproducibility Awards
Stanford May 2023
Stanford Program on Research Rigor & Reproducibility
ISGlobal
Winner Selected by the Event Committee
ISGlobal May 2021
Exposome Data Challenge Event
metabolomics_society
Student Travel Award for Oral Presentation
metabolomics_society Jun 2018
The International Metabolomics Society
org
Student Travel Award for Oral Presentation
org Jun 2018
Journal Metabolites
China
China National Scholarship
China Jun 2017
Ministry of Education of the People’s Republic of China
org
Award for Outstanding Youth Report
org Jun 2017
The 3rd China MS Analysis Conference
CAS
Merit Student
CAS Jun 2016
University of Chinese Academy of Sciences
org
Award for Outstanding Youth Report
org Jun 2016
The 34th China MS Society Conference
org
Inner Mongolia Outstanding Graduate
org Jun 2016
Inner Mongolia Autonomous Region
IMU
National Encouragement Scholarship
IMU Jun 2011
Inner Mongolia University

🦮 Academic Service

 
 
 
 
 
Phenomics
Member of Youth Editorial Board
Phenomics
February 2023 – Present China 🇨🇳
 
 
 
 
 
Brain-X
Member of Youth Editorial Board
Brain-X
January 2023 – Present China 🇨🇳
 
 
 
 
 
iMeta
Member of Youth Editorial Board
iMeta
July 2022 – Present China 🇨🇳
 
 
 
 
 
npj women's health
Member of Editorial Board
npj women’s health
August 2023 – Present UK 🇬🇧

🤝 Collaborators

Academia

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Dr. Chuchu Wang

Postdoc
Stanford University

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Dr. Daniel Panyard

Postdoc
Stanford University

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Dr. Liang Liang

Research Scientist
Stanford University

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Dr. Nasim Barapour

Postdoc
Stanford University

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Dr. Wei Shao

Assistant Professor
University of Florida

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Dr. Xin Zhou

Postdoc
Stanford University

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Dr. Yan Hong

Postdoc
Yale University

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Prof. Caroline Johnson

Associate Professor
Yale University

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Prof. Michael Snyder

Professor
Stanford University

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Prof. Peng Gao

Assistant Professor
University of Pittsburgh

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Prof. Sai Zhang

Assistant Professor
University of Florida

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Prof. Zheng-Jiang Zhu

Professor
Chinese Academy of Sciences

Industry

Avatar

Dr. Daniel Hornburg

Vice President
Seer

Avatar

Dr. Ryan Kellogg

Founder/CEO
RTHM

Avatar

Dr. Si Wu

Research Scientist
AbbVie

Avatar

Dr. Songjie Chen

Research Scientist
Merck

Girl in a jacket

Map of Collaborators

📸 Photos

Academic Blog Chinese Metabolomics Multi-omics Others Paper R package 开源