Computational Omics Lab

Shen Lab @ NTU

Multi-omics for human health

Research video

MAPA — Video introduction

Advanced Science

MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi‐Omics Data

Briefings in Bioinformatics

LagCI Enables Inference of Temporal Causal Relationships from Dense Multi-Omic Time Series

Microbiome

Cross-body site microbial interactions influence the human plasma metabolome

Nature Communications

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

RESEARCH

👉 Detailed Research

Our research is focused on the development of computational methods for the analysis of multi-omics data, with a particular emphasis on metabolomics and microbiome data. We are also interested in the application of these methods to precision medicine, aging, pregnancy, and other health-related areas.

Molecular & physiological dataComputational methodsHuman health

MetabolomicsMetabolic signatures & function MicrobiomeMicrobial communities & host interactions Wearable sensingLongitudinal physiology & digital biomarkers

AI & multi-omics Integrate · Model · Interpret

Precision medicine ↗Individualized prediction & intervention Aging ↗Biological age & health trajectories Pregnancy ↗Maternal health & early prediction

SOFTWARE

Pipeline

lagCI

Multi-omics 2025

AI tool

MAPA

Multi-omics 2025

Web app

TidyMassShiny

Metabolomics 2025

R ecosystem

TidyMicrobiome

Multi-omics 2022

Resource

R cookbook

Others 2020

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PUBLICATION

MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi‐Omics Data

Advanced Science

LagCI Enables Inference of Temporal Causal Relationships from Dense Multi-Omic Time Series

Briefings in Bioinformatics

Cross-body site microbial interactions influence the human plasma metabolome

Microbiome

Publication Summary

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NEWS

2026-09-30 Yifei GE and Feifan ZHANG present at HUPO 2026

2026-09-27 Chi Fang HSU presents her research

2026-09-23 Xiaotao SHEN presents at AI4Science, SJTU

2026-09-09 MAPA project accepted in Advanced Science

2026-09-09 NTU AI for X Postdoctoral Fellowship

2026-08-14 Xiaotao SHEN presents at MedTechX in Hong Kong

2026-08-08 Shen Lab joins the Microbial Engineering Conference

2026-08-06 Paper accepted in Briefings in Bioinformatics

2026-07-23 Xiaotao SHEN presents in Shanghai on pregnancy multi-omics

2026-06-26 Xiaotao SHEN presents at a genetics conference in Tianjin

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TEAM

👉 All Team Members

Principal Investigator

Xiaotao SHEN

Nanyang Assistant Professor

Researchers

Si-Si LIU

Visiting Scholar (2026-)

Yuanming YANG

Visiting Scholar (2025-)

Jingxiang ZHANG

Research Fellow (2024-)

Students

Yifei GE

PhD Candidate (2025-)

Chi Fang HSU

PhD Candidate (2025-)

Jiramet KINCHAGAWAT

PhD Candidate (2025-)

Yijiang LIU

PhD Candidate (2025-)

Yuting WANG

PhD Candidate (2025-)

Xicheng YANG

PhD Candidate (2026-)

Donghwee YUN

FYP Undergraduate (2026-2027)

Feifan ZHANG

PhD Candidate (2025-)

Shuli ZHANG

Visiting PhD Student (2026-2027)

Junqi ZHAO

Visiting PhD Student (2026–2027)

Co-supervised Students

Kajal AGRAWAL

PhD Candidate (Co-supervised with Prof. Sunny Wong)

Xiaoyu XU

PhD Candidate (Co-supervised with Prof. Kun Qian)

Ruwen ZHOU

PhD Candidate (Co-supervised with Prof. Sunny Wong)

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Open opportunities

Team Summary

Life in Shen Lab

2026

Prof. wenfeng zeng visited shen lab

2026

Yifei presented at hupo2026

2026

Prof. kun qian visited shen lab

2026

Lifespin germany visited spc

2026

Dinner with mike

2026

Prof ju sheng zheng visited shen lab

2026

Feifan presentation at hupo 2026

2026

Shen lab at hupo 2026

2026

Chi fang presentation

2026

Xiaotao presented at ai4science sjtu2

2026

Xiaotao presented at ai4science sjtu

2026

Prof. nick tellay visited lab

2026

Lab group photo

2026

Lab dinner

2026

Ha LAN last day in the lab

2026

Ntu bot members and lkc leadership visit spc

2026

Hk medteck x

2026

微生物工程会议

2026

Hit visiting shen lab

2026

Shanghai environment health

2026

Visiting macao university

2026

Tianjin genetics conference2

2026

Tianjin genetics conference

2026

Lab dinner2

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age cell gestational longitudinal metabolic metabolite metabolomics microbiome multi prediction