Overview

Digital Biomedicine is an emerging interdisciplinary field that bridges computer science, life sciences, and basic medicine. It primarily uses digital technologies and computer simulations to study life systems and processes, thereby understanding the essence of life phenomena from a systemic perspective. Digital Biomedicine leverages computer simulation, big data analysis, and artificial intelligence to model dynamic life processes at various levels of biological systems, enabling the simulation and prediction of physiological and pathological phenomena. This approach provides essential tools for biomedical and life science research, supports new drug development, and advances disease diagnosis, driving innovation in biotechnology and healthcare.


Digital Biomedicine is divided into subfields based on the levels of life systems it models, such as protein structure, gene transcription, cell fate, and organ system homeostasis. In addition to constructing reductionist digital models at each level, it also aims to simulate dynamic changes across multiple levels of life systems. This is the core scientific objective of our center.


Given the intense global competition in biotechnology and healthcare, our country has prioritized the development of autonomous digital biotechnology. Data autonomy, algorithm autonomy, and application autonomy are key components of this goal. Leveraging the institute's advanced background in biological and medical research and the construction of the national human cell lineage facility, our center is poised for continuous high-quality data support. Our focus will be on dynamic life simulations based on cells as the fundamental unit of life, addressing information integration issues in multi-modal cell data, and providing intelligent models that combine "black box" and "white box" approaches to simulate dynamic life changes at various levels. By constructing causal models and applying large models, we aim to integrate and transfer prior knowledge to achieve high-quality simulations under perturbations, supporting drug and disease research.



Research

The Center for Digital Biomedicine collaborates with the major national science and technology infrastructure for Human Cell Lineage Atlas Facility (CLAF) to pioneer mathematical and biomedical technologies and develop advanced algorithms for multi-omics analysis of cell lineages. We also focus on creating cell lineage visualization technologies to solve challenges in multi-omics data integration. By seamlessly integrating artificial intelligence and big data analytics, we aim to construct comprehensive, autonomous models of cell lineages with both data and algorithmic independence. These models support the effective integration and transfer of prior knowledge through causality, enabling dynamic simulations grounded in cellular chassis of biological processes under diverse perturbations. 

Resources

1.Software:

scDIOR: single cell RNA-seq data IO software 

https://github.com/JiekaiLab/scDIOR

  • scDIOR: single cell RNA-seq data IO software 
  • https://github.com/JiekaiLab/scDIOR

scTE (single-cell TE processing pipeline) 

https://github.com/JiekaiLab/scTE

  • scTE (single-cell TE processing pipeline) 
  • https://github.com/JiekaiLab/scTE

IReNA (Integrated Regulatory Network Analysis)  

https://github.com/jiang-junyao/IReNA

  • IReNA (Integrated Regulatory Network Analysis)  
  • https://github.com/jiang-junyao/IReNA

 

CACIMAR (Cross-species Analysis of Cell Identities, Markers and Regulations)

https://github.com/jiang-junyao/CACIMAR

  • CACIMAR (Cross-species Analysis of Cell Identities, Markers and Regulations)
  • https://github.com/jiang-junyao/CACIMAR

ScReNI (single-cell regulatory network inference) 

https://github.com/Xuxl2020/ScReNI

  • ScReNI (single-cell regulatory network inference) 
  • https://github.com/Xuxl2020/ScReNI

  • sgRNA online 
  • https://crispr.zhaopage.com


2.Databases

scRetinaDB (Single-cell sequencing data for retinal tissues.)  

Dataset:http://192.168.83.112:10000/

TFSyntax (Database of transcription factors (TFs) binding syntax in mammalian genomes.) 

Dataset:https://tfsyntax.zhaopage.com/

  • TFSyntax (Database of transcription factors (TFs) binding syntax in mammalian genomes.) 
  • Dataset: https://tfsyntax.zhaopage.com/


History

In 2024, the Biomedical Digital Science Center of the Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, was officially established.

2024
Acknowledging Support

The authors gratefully acknowledge support from the Center for Biomedical Digital Science of Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences.

Contact

Technical Support and Communication

People
Email
Address
CHEN Jiekai
chen_jiekai@gibh.ac.cn
No.15 Luoxuan 2nd Road, Guangzhou International Bio Island, Guangdong, China