Name：Ruixin Zhu

Degree：Ph.D.

Academic Title：Professor, Doctoral Supervisor

Research Field：Bioinformatics

Research Interests

1. AI-Powered Drug Discovery

• Therapeutic Areas: gastroenterology and gynecology

• Technical Innovations:

• HybridGNN: Structure-aware graph neural networks for precise binding affinity prediction

• CausalRL: Causal reinforcement learning for optimal multi-target dosing regimens

2. Intelligent Microbiome Engineering

•  Diagnostic Development:

• Clinically validated fecal metagenomics biomarkers for early cancer detection

• mmBERT: Advanced deep learning framework for strain-level microbiome analysis

• Therapeutic Innovation:

• Causal AI models elucidating host-microbe-drug interactions

• Federated learning-enabled design of next-generation engineered probiotics

3. End-to-End Biomedical AI Platform

• Key Features:

• Integrated pipeline from raw data analysis to FDA-ready submissions

• Production-grade tools for bias detection and model explain ability

• Technical Advantages:

• TorchBio: Open-source library for reproducible research (1.2k+ GitHub stars)

• Blockchain-secured medical knowledge graph with 1M+ auditable entities

Lab Website：cadd.tongji.edu.cn

E-mail：rxzhu@tongji.edu.cn

Biography

Dr. Ruixin Zhu is a Professor and Doctoral Advisor in the Department of Bioinformatics, School of Life Sciences and Technology at Tongji University. He concurrently serves as a Distinguished Researcher at the Obstetrics and Gynecology Hospital of Tongji University (Shanghai First Maternity and Infant Hospital).

Dr. Zhu received his B.S. in Chemistry from Lanzhou University in 2001, and his Ph.D. in Computational Chemistry from the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences in 2007. From 2007 to 2008, he conducted research at the Shanghai Center for Bioinformation Technology. Since 2008, he has been engaged in teaching and research at Tongji University.

Dr. Zhu has published 82 SCI-indexed papers (as of May 2025) as first or corresponding author (including co-first and co-corresponding) in high-impact journals such as Nature Microbiology, Nature Ecology & Evolution, Nature Protocols, Nature Communications, and Cell Reports Medicine. He is the author of China’s first undergraduate textbook on Computer-Aided Drug Design (CADD): Computer-Aided Drug Design: Fundamental Principles and Practical Applications (Dalian University of Technology Press, 2011, ISBN 978-7-5611-6104-3).

Currently, Dr. Zhu serves as associate editor for Frontiers in Pharmacology and Frontiers in Microbiology, and as an editorial board member of iMetaMed. He is also an invited reviewer for journals such as Nature Medicine, Nature Microbiology, Signal Transduction and Targeted Therapy, Briefings in Bioinformatics, Genomics, Proteomics & Bioinformatics, Journal of Chemical Information and Modeling, and Bioinformatics.

Dr. Zhu has led multiple national research projects related to the microbiome and gastrointestinal diseases. He has successfully mentored two Ph.D. students who are now independent principal investigators at Zhejiang University and Fudan University, respectively.

Selected Research Projects Led as Principal Investigator

1. 2023–2024

Subproject 2 of the Major Research Plan, National Natural Science Foundation of China (Grant No. 92251307).

2. 2022–2024

Subtask of the National Key Research and Development Program of China (Grant No. 2021YFF0703700/2021YFF0703702).

3. 2022–2025

National Natural Science Foundation of China (Grant No. 82170542).

4. 2018–2021

National Natural Science Foundation of China (Grant No. 81774152).

5. 2016–2019

Original Exploration Project, Shanghai Natural Science Foundation (Grant No. 16ZR1449800).

6. 2015–2016

Interdisciplinary Research Project, Fundamental Research Funds for the Central Universities (Grant No. 10247201546).

7. 2013–2015

National Natural Science Foundation of China (Grant No. 31200986).

8. 2013–2014

Young Talents Program, Fundamental Research Funds for the Central Universities (Grant No. 2000219083).

9. 2010–2012

Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20100072120050).

10. 2008–2009

Program for Young Excellent Talents, Tongji University (Grant No. 2008KJ073).

11. 2007–2010

Shanghai Natural Science Foundation (Grant No. 07ZR14085). 

Representative Publications

1. Wanning Chen$, Yichen Li$, Wenxia Wang$, Sheng Gao, Jun Hu, Bingjie Xiang, Dingfeng Wu, Na Jiao, Tao Xu, Min Zhi*, Lixin Zhu*, Ruixin Zhu* (2024). Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. Cell Reports Medicine, https://doi.org/10.1016/j.xcrm.2024.101624. (Highlighted in Cell Reports Medicine)                      

2. Na Jiao*, Lixin Zhu*, Ruixin Zhu*. (2024). The search for authentic microbiome–disease relationships. Nature Medicine, https://doi.org/10.1038/s41591-024-02920-z.  (Invited & Featured)

3. Wenxing Gao#, Weili Lin#, Qiang Li#, Wanning Chen, Wenjing Yin, Xinyue Zhu, Sheng Gao, Lei Liu, Wenjie Li, Dingfeng Wu, Guoqing Zhang*, Ruixin Zhu*, Na Jiao*. (2024). Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder, Nature Protocols, https://doi.org/10.1038/s41596-024-00999-9.

4. Xiang Gao#, Ruicong Sun#, Na Jiao#, Xiao Liang, Gengfeng Li, Han Gao, Xiaohan Wu, Muqing Yang, Chunqiu Chen, Liang Chen, Wei Wu, Zhong Li, Yingzi Cong, Ruixin Zhu*, Tiannan Guo*, Zhanju Liu*. (2023). Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn’s disease. Cell Reports Medicine, 4(6), 101050. DOI: https://doi.org/10.1016/j.xcrm.2023.101050.

5. Dingfeng Wu#, Lei Liu#, Na Jiao#, Yida Zhang, Li Yang, Chuan Tian, Ping Lan, Lixin Zhu*, Rohit Loomba*, and Ruixin Zhu*. (2022). Targeting Keystone Species Helps Restore the Dysbiosis of Butyrate‐Producing Bacteria in Nonalcoholic Fatty Liver Disease. iMeta, e61. https://doi.org/10.1002/imt2.61.

6. Ning-Ning Liu #, Na Jiao #, Jing-Cong Tan #, Ziliang Wang #, Dingfeng Wu, An-Jun Wang, Jie Chen, Liwen Tao, Chenfen Zhou, Wenjie Fang, Io Hong Cheong, Weihua Pan, Wanqing Liao, Zisis Kozlakidis, Christopher Heeschen, Geromy G. Moore, Lixin Zhu *, Xingdong Chen *, Guoqing Zhang *, Ruixin Zhu*, Hui Wang *. (2022). Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. Nature Microbiology, 7:238–250. DOI: https://doi.org/10.1038/s41564-021-01030-7. ESI  Highly Cited Paper

7.Yuanqi Wu #, Na Jiao #, Ruixin Zhu*, Yida Zhang, Dingfeng Wu, An-Jun Wang, Sa Fang, Liwen Tao, Yichen Li, Sijing Cheng, Xiaosheng He,Ping Lan, Chuan Tian *, Ning-Ning Liu *, Lixin Zhu *. (2021). Identification of microbial markers across populations in early detection of colorectal cancer. Nature Communications. DOI: https://doi.org/10.1038/s41467-021-23265-y.  ESI Highly Cited Paper

8.Dingfeng Wu #, Wenxing Gao #, Xiaoyi Li #, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu, Guoqing Zhang, Ruixin Zhu*. (2021). Dr AFC: drug repositioning through anti-fibrosis characteristic. Briefings in Bioinformatics. Volume 22, Issue 3, May 2021, bbaa115. DOI: https://doi.org/10.1093/bib/bbaa115.

9.Lu Fan†,*, Dingfeng Wu†, Vadim Goremykin†, Jing Xiao, Yanbing Xu, Sriram Garg, Chuanlun Zhang, William F. Martin*, Ruixin Zhu*. (2020). Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria. Nature Ecology & Evolution, DOI: https://doi.org/10.1038/s41559-020-1239-x. 

10. Na Jiao†, Susan S Baker*, Adrian Chapa-Rodriguez, Wensheng Liu, Colleen A Nugent, Maria Tsompana, Lucy Mastrandrea, Michael J Buck, Robert D Baker, Robert J Genco, Ruixin Zhu*, Lixin Zhu*. (2018). Suppressed hepatic bile acid signalling despite elevated production of primary and secondary bile acids in NAFLD. Gut. 67(10):1881-1891. ESI  Highly Cited Paper

Invention Patents

1. Biomarker, Kit, and Biomarker Screening Method for Crohn’s Disease. (Patent No.: ZL202210137717.5), Ruixin Zhu, Sheng Gao

2. Biomarker, Kit, and Biomarker Screening Method for Colorectal Adenomas (Patent No.: ZL202210011544.2), Ruixin Zhu, Wenxing Gao

Software Copyrights

1. Knowledgebase for Drug Discovery in Non-Alcoholic Fatty Liver Disease, Version 1.0 (Registration No.: 2023SR1522072), Ruixin Zhu, Tingjun Xu

2. Intelligent Drug Development Platform for Non-Alcoholic Fatty Liver Disease, Version 1.0 (Registration No.: 2023SR1522073), Ruixin Zhu, Tingjun Xu

3. Two-step Species Annotation Software Based on Phylogenetic Tree (TESLA) Version 1.0 (Registration No.: 2024SR0400643), Ruixin Zhu, Yulong Zheng

Author and Editor of the Textbook

Computer-Aided Drug Design: Fundamental Principles and Practical Applications (Ruixin Zhu, Ed., Dalian University of Technology Press, 2011, ISBN 978-7-5611-6104-3).

The first undergraduate professional textbook on Computer-Aided Drug Design in China, awarded the Excellent Undergraduate Textbooks by Tongji University.

Teaching Experience

1.2020–present — Metagenomics (for majors in Life Sciences, Medicine, Pharmacy, Earth Sciences, and Environmental Sciences)

2.2015–2017 — Computational Genomics (Bioinformatics)

3.2014–2015 — Bioinformatics II (Honors Class)

4.2011–2014 — Bioinformatics Laboratory (Biotechnology)

5.2010–present — Course Project Design (Bioinformatics)

6.2009–present — Computer-Aided Drug Design (Bioinformatics)

Awards

1. 2024, Shanghai Leading Talent Project (Education Platform)

2. 2024, Tongji University Distinguished Ph.D. Thesis Supervisor

3. 2023, Outstanding Faculty of the Year (School of Life Sciences and Technology, Tongji University)

4. 2022, Selected for Tongji University's 2021 Collection of Top 100 International Collaborative Research Papers

5. 2021, Tongji University Distinguished Master’s Thesis Supervisor

6. 2019, Tongji University Distinguished Ph.D. Thesis Supervisor

7. 2019, Tongji University Distinguished Graduation Project Supervisor (The only recipient in Bioinformatics; consecutively awarded)

8. 2018, Tongji University Distinguished Graduation Project Supervisor (The only recipient in Bioinformatics; consecutively awarded)

9. 2017, Outstanding Researcher of the Year (School of Life Sciences and Technology, Tongji University)

10. 2017, Tongji University Distinguished Graduation Project Supervisor (The only recipient in Bioinformatics; consecutively awarded)

11. 2016, Second Prize for Outstanding Undergraduate Textbooks (Tongji University)

12. 2016, Tongji University Distinguished Graduation Project Supervisor (The only recipient in Bioinformatics; consecutively awarded)

13. 2015, Advanced Worker (School of Life Sciences and Technology, Tongji University)

14. 2015, Outstanding Faculty of the Year (School of Life Sciences and Technology, Tongji University)

15. 2015, Ranked #1 in Tongji University's Annual Performance Evaluation (Top Tier)

16. 2015, Tongji University Distinguished Graduation Project Supervisor (The only recipient in Bioinformatics)

17. 2012, Second Prize in Teaching Award (Tongji University)

18. 2012, Tongji University Outstanding Young Faculty Support Program (Elite Talent Program)

19. 2012, Second Prize in the First Teaching Excellence Award (School of Life Sciences and Technology, Tongji University)

20. 2010, The First Tongji University Outstanding Young Faculty Development Program (Elite Talent Program)

Two or more postdoctoral positions are available in Artificial Intelligence, Bioinformatics, or Microbiome research!