Computational and Integrative Biology Group

Decoding complex biological systems through data, algorithms, and computational models.

We are a bioinformatics-focused research group working at the intersection of biology, computer science, and data science. Our mission is to develop computational methods and software tools to understand complex biological systems across scales.

Our current research focuses on:

  • Data-driven approaches to developmental, aging, and evolutionary biology
  • Machine learning methods for biomedical research
  • Bioinformatics software and database development
  • Artificial intelligence in drug discovery and precision medicine
  • Educational data mining and its applications in biology teaching

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Ongoing Projects

Research Summary

Clustering in single-cell RNA-sequencing

As one of the core steps of single-cell transcriptome data analysis, clustering plays a crucial role in identifying cell types and interpreting cellular heterogeneity. We summarize applications and challenges of the clustering ensemble method in single-cell transcriptome data analysis, and provide constructive thoughts and references for researchers. (Nie X., et al. Computers in Biology and Medicine, 2023).

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Additives and Toxicological Mechanisms

Additives have the potential to affect the survival and lifespan of insects, but the full molecular mechanisms behind mortality and infertility remain unclear. By integrating molecular biology and multi-omics approaches, we focuses on uncovering the potential adverse effects of different food additives on the growth and developmental pathways of fruit flies. (Li L., et al. Int J Mol Sci, 2024).

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Computational Drug Repurposing

In the field of drug discovery, how to efficiently mine transcriptome data and identify new indications for old drugs remains a critical challenge. discussed the irreplaceable role of transcriptome data in computational drug repurposing and summarized some representative databases, tools and strategies. (He H., Duo H., et al. Computers in Biology and Medicine, 2023)

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LAB MEMBERS: Teachers

Faculty Members

Youjin HAO 

 Professor, College of Life Sciences, CQNU

Dr. Hao the Director of the Department of Biology at College of Life Sciences, Chongqing Normal University. He graduated with a Bachelor of Science degree from Ludong University in 1998, followed by Master's and Ph.D. degrees from Nankai University in 2001 and 2005. With experience as a Postdoctoral researcher at the University of the Azores, Portugal, and as an Assistant Researcher at the University of Chicago, USA, he also served as a Senior Visiting Scholar at the University of Colorado, USA from 2017 to 2018. Proficient in teaching courses such as Cell Biology, Cell Engineering, Enzyme Engineering, Professional English, and Advanced Molecular Biology, his current research focuses on biological big data mining and analysis. He has led or participated in over 10 scientific research projects globally, published more than 80 papers in prestigious journals, holds 3 utility model patents, and was awarded one third prize in Natural Science from Chongqing City.

Bo LI 

 Associate Professor, College of Life Sciences, CQNU

Dr. Li currently holds the positions of Associate Professor and Master's Supervisor. He obtained his bachelor's degree from Northwest A&F University in 2003, followed by earning a master's degree in Biophysics and a Ph.D. in Bioinformatics from Chongqing University. With expertise in bioinformatics, machine learning, and biological data mining, he actively contributes to teaching and research in these areas. Li has been involved in leading or collaborating on various provincial and ministerial-level projects, including an educational reform initiative. He has also authored a textbook and published over 50 academic papers in prestigious international journals such as Nucleic Acids Research, Trends in Food Science & Technology, Bioinformatics, Briefings in Bioinformatics, and Molecular & Cellular Proteomics.

Lab members: Students

Graduate Student

Jing SUN

Graduate student
(2023)

Yingxue XIAO

Graduate student
(2023)

Hanyue HU

Graduate student
(2023)

Lingling XIE

Graduate student
(2024)

Fan HE

Graduate student
(2024)

Tong LI

Graduate student
(2024)

Shiqi LIN

Graduate student
(2024)

Yuyan LIU

Graduate student
(2024)

Ziqi MA

Graduate student
(2024)

Xiaojiao TANG

Graduate student
(2024)

Ting WEI

Graduate student
(2024)

Yi WU

Graduate student
(2024)

Kunhong SONG

Graduate student
(2025)

Yue ZOU

Graduate student
(2025)

Yingying LIU

Graduate student
(2025)

Yitong ZHAI

Graduate student
(2025)

Minyi ZHANG

Graduate student
(2025)

Yujie DU

Graduate student
(2025)

Yao LI

Graduate student
(2025)

Renqi LIU

Graduate student
(2025)

Yatong LIAO

Graduate student
(2025)

Sha QIU

Graduate student
(2025)

Yanqing LUO

Graduate student
(2025)

Miao PENG

Graduate student
(2025)

Jiabao YUAN

Graduate student
(2025)

Undergraduates

Chen XU

Undergraduate
(2022)

Qiuyue HU

Undergraduate
(2023)

Yun Huang

Undergraduate
(2023)

Feifei LI

Undergraduate
(2023)

Dandan LIU

Undergraduate
(2023)

Nan CHEN

Undergraduate
(2024)

Yuting HUANG

Undergraduate
(2024)

Alumni

Hongrui DUO
PhD Student at NUS
CibLab:
2020~2025
Yujie Zeng
High School Teacher in Deyang
CibLab:
2022~2025
Xiaoxi Zhang
School Teacher in Chongqing
CibLab:
2022~2025

Zixuan ZHANG
Master Student at UESTC
CibLab:
2023~2024
Guangyi CHEN
Master Student at UESTC
CibLab:
2023~2024
Lei LI
Bioinformatics Engineer in CQ
CibLab:
2021~2024

Xiner NIE
PhD Student at WMU
CibLab:
2018~2023
Jingxin TAO
Bioinformatics Engineer at BGI
CibLab:
2019~2022
Dan YANG
School Teacher in Chongqing
CibLab:
2020~2022

Hao HE
PhD Student at FDU
CibLab:
2020~2022
Jinyi WEI
Master Student at UESTC
CibLab:
2019~2021

Publications

Selected Publications

# Equal contribution; * Corresponding author


2026

Single-cell differential abundance detection: A new angle on dissecting tumor heterogeneity

Xiao Y., Sun J., Xie L., Zou Y., Li T., Hao Y., Li B.*

World Journal of Clinical Oncology, 17(1): 113244, 2026  

Identification of Tissue Marker Genes in Drosophila melanogaster Based on Gene Expression Profiling

Sun J., Xiao Y., Xie L., Qin D., Zou Y., Liu Y., Zhai Y., Zhang M., Li T., Hao Y., Li B.*

BioTech, 15(1): 7, 2026  

2025

Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives

Yin H.#, Duo H.#, Li S., Qin D., Xie L., Xiao Y., Sun J,, Tao J., Zhang X., Li Y., Zou Y., Yang Q., Yang X., Hao Y.* & Li B.*

Journal of Advanced Research, 76: 135-157, 2025  

Spatial transcriptomics meets diabetic kidney disease: Illuminating the path to precision medicine

Liu D., Hu H., Li F., Hu Q., Liu M., Hao Y., Li B.*

World Journal of Diabetes, 16(9): 107663, 2025  

Efficient fine-tuning of small-parameter large language models for biomedical bilingual multi-task applications

Li Y.#, Yan Y.#, Tong Z., Wang Y., Yang Y., Bai M., Pu D, Xie J., Liu C., Li B.*, Liu M., Shu K*.

Applied Soft Computing, 175: 113084, 2025  

Lung Cancer Biomarker Database (LCBD): a comprehensive and curated repository of lung cancer biomarkers

Li Y.#, Tong Z.#, Yang Y.#, Wang Y., Wen L., Li Y., Bai M., Xie Y., Li B.*, Shu K*.

BMC cancer, 25: 478, 2025  

TMED4 maintains Treg cell suppressive function through modulating ROS homeostasis via balancing BiP-IRE1α-XBP1 signaling axis and NRF2 antioxidant stress response

Jiang Z.#, Wang H.#, Wang X.#, Duo H.#, Tao Y., Li J., Li X., Liu J., Ni J., Wu J., Xiang H., Guan C., Wang X., Zhang K., Zhang P., Hou Z., Liu Y., Wang Z., Su B., Li B., Hao Y.*, Li B.* & Wu X*.

Journal of Clinical Investigation, 135(1): e179874, 2025  

2024

Identification of Tissue Marker Genes in Drosophila melanogaster Based on Gene Expression Profiling (in Chinese)

Li L., Duo H., Li B., Li Y. & Hao Y.*

Journal of Chongqing Normal University (Natural Science), 1-6[2024-12-29], 2024  

Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios

Duo H.#, Li Y.#, Lan Y.#, Tao J., Yang Q., Xiao Y., Sun J., Li L., Nie X., Zhang X., Liang G., Liu M., Hao Y.* & Li B*.

Genome Biology, 25: 145, 2024  

Common Methods for Phylogenetic Tree Construction and Their Implementation in R

Zou Y.#, Zhang Z.#, Zeng Y., Hu H., Hao Y., Huang S.* & Li B*.

Bioengineering, 11(5): 480, 2024  

A Comparative Benchmarking and Evaluation Framework for Heterogeneous Network-Based Drug Repositioning Methods

Li Y.#,*, Yang Y.#,, Tong Z., Wang Y., Mi Q., Bai M., Liang G., Li B.* & Shu K*.

Briefings in Bioinformatics, 25(3): bbae172, 2024  

Comparative Transcriptomic Analysis Revealing the Potential Mechanisms of Erythritol-Caused Mortality and Oviposition Inhibition in Drosophila melanogaster

Li L., Duo H., Zhang X., Gong H., Li B.* & Hao Y*.

International Journal of Molecular Sciences, 25(7): 3738, 2024  

Strategy for Identifying a Robust Metabolomic Signature Reveals the Altered Lipid Metabolism in Pituitary Adenoma

Tang J.#, Mou M.#, Zheng X.#, Yan J., Pan Z., Zhang J., Li B., Yang Q., Wang Y., Zhang Y., Gao J., Li S.*, Yang H.* & Zhu F*.

Analytical Chemistry, 96(12): 4745–4755, 2024  

A Comparison and Benchmarking for Data Simulation Algorithms of Cellular Dynamic Differentiation in Single-Cell Transcriptomics (in Chinese)

Duo H., Li Y. & Li B.*.

Journal of Chongqing Normal University (Natural Science), 41(1): 125-132, 2024  

2023

Symbiosis between Dendrobium catenatum protocorms and Serendipita indica involves the plant hypoxia response pathway

Xu Z.-X.#, Zhu X.-M.#, Yin H., Li B., Chen X.-J., Fan X.-L., Li N.-Q., Selosse M.-A., Gao J.-Y.* & Han J.-J*

Plant Physiology, 192(3): 2554-2568, 2023  

Clustering ensemble in scRNA-seq data analysis: methods, applications and challenges

Nie X., Qin D,, Zhou X., Duo H., Hao Y., Li B.*, Liang G*.

Computers in Biology and Medicine, 159: 106939, 2023  

A Novel Exosome-derived Prognostic Signature and Risk Stratification for Breast Cancer Based on Multi-omics and Systematic Biological Heterogeneity

Long F.#, Ma H.#, Hao Y.#, Tian L., Li Y., Li B., Chen J., Tang Y., Li J., Deng L., Xie G.*, Liu M*.

Computational and Structural Biotechnology Journal, 21: 3010-3023, 2023  

Computational drug repurposing by exploiting large-scale gene expression data: Strategy, methods and applications

He H.#, Duo H.#, Hao Y., Zhang X., Zhou X., Zeng Y., Li Y., Li B.*.

Computers in Biology and Medicine, 155: 106671, 2023  

See full publications

Popular Resources

Classes for Students

Bioinformatics-B2024

for Undergraduates
Undergraduate students majoring in Biology, autumn semester, CQNU
Class Hours
32 lessons
Class Time
08:30 - 10:10, Monday
Class Location
12305#, Hongde Building

CibStarter-Master 2025

for beginners in CibLab
the ABC Knowledgebase for Beginners in Bioinformatics
Class Hours
54 lessons
Class Time
09:00 - 12:10, Friday
Class Location
Room 233, Jixian Building, CQNU

Bioinformatics-D2023

for Ph.D candidates
Ph.D students majoring in Biology, autumn semester, CQNU
Class Hours
32 lessons
Class Time
14:30 - 18:10, Monday
Class Location
Room 233, Jixian Building, CQNU

Software and Tools

NOREVA
MMEASE
DEGMiner
simshiny

Under construction

Downloading Zone

CibLab

Literature

  Lukas M,  GB-2019
  Thomas G,  NRG-2024
  Clemens K,  GB-2019

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Toolkits

  EditPlus 3.0 
  Sublime Text 
  Endnote X8 

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Datasets





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News

2024 May: Hongrui's paper has been accepted by Genome Biology! Congrats Hongrui!

2024 May: Yue's paper has been published online by Bioengineering! Congrats Yue!

2024 Apr: Qian's site in Bilibili was public, showing many movies for teaching biology at high school Click here! !

2024 Mar: Bo's collaboration paper (with Li Y. & Shu K.) is accepted in Briefings in Bioinformatics! Congrats Bo!

2024 Mar: Lei Li's paper is accepted in Int. J. Mol. Sci.! Congrats Li!

2023 Sep: Welcome our new graduate students, Yingxue Xiao, Jing Sun & Hanyue Hu!

2023 Jun: Yin's collaboration paper (with Xu Z. & Han J.) is accepted in Plant Physiology! Congrats Yin!

2023 May: We started hiring!

2023 Mar: Welcome our new intern students!

Contact

Join us!

We are looking for passionate (graduate students and undergraduates to develop together. Please do not hesitate to contact us ( libcell@cqnu.edu.cn) or ( haoyoujin@hotmail.com) if you are interested in bioinformatics or computational biology.

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