中国科学院机构知识库网格
Chinese Academy of Sciences Institutional Repositories Grid
首页 机构 成果 学者
  
  1. CAS IR Grid
  2. 计算技术研究所
  3. 中国科学院计算技术研究所
  4. 中国科学院计算技术研究所期刊论文
  5. 英文
GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model

文献类型：期刊论文

作者Yang, Xiaodong2,3,4,14; Liu, Guole5,6,11; Feng, Guihai2,7,8,13; Bu, Dechao3,4,9,14; Wang, Pengfei4,10; Jiang, Jie11; Chen, Shubai3,4,14; Yang, Qinmeng10; Miao, Hefan2; Zhang, Yiyang1,4,12
刊名CELL RESEARCH
出版日期2024-10-08
页码16
ISSN号1001-0602
DOI10.1038/s41422-024-01034-y
英文摘要Deciphering universal gene regulatory mechanisms in diverse organisms holds great potential for advancing our knowledge of fundamental life processes and facilitating clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms and does not integrate various cell types across species. Recent breakthroughs in single-cell sequencing and deep learning techniques present an unprecedented opportunity to address this challenge. In this study, we built an extensive dataset of over 120 million human and mouse single-cell transcriptomes. After data preprocessing, we obtained 101,768,420 single-cell transcriptomes and developed a knowledge-informed cross-species foundation model, named GeneCompass. During pre-training, GeneCompass effectively integrated four types of prior biological knowledge to enhance our understanding of gene regulatory mechanisms in a self-supervised manner. By fine-tuning for multiple downstream tasks, GeneCompass outperformed state-of-the-art models in diverse applications for a single species and unlocked new realms of cross-species biological investigations. We also employed GeneCompass to search for key factors associated with cell fate transition and showed that the predicted candidate genes could successfully induce the differentiation of human embryonic stem cells into the gonadal fate. Overall, GeneCompass demonstrates the advantages of using artificial intelligence technology to decipher universal gene regulatory mechanisms and shows tremendous potential for accelerating the discovery of critical cell fate regulators and candidate drug targets.
资助项目National Natural Science Foundation of China (National Science Foundation of China)[YSBR-076] ; National Natural Science Foundation of China (National Science Foundation of China)[YSBR-034] ; CAS Project for Young Scientists in Basic Research[31971289] ; CAS Project for Young Scientists in Basic Research[32341013] ; CAS Project for Young Scientists in Basic Research[91954201] ; CAS Project for Young Scientists in Basic Research[62202455] ; CAS Project for Young Scientists in Basic Research[32341019] ; National Natural Science Foundation of China[CAS-WX2021SF-0101] ; Informatization Plan of Chinese Academy of Sciences
WOS研究方向Cell Biology
语种英语
WOS记录号WOS:001327618200001
出版者SPRINGERNATURE
源URL[http://119.78.100.204/handle/2XEOYT63/39521]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Zhao, Yi; Zhou, Yuanchun; Li, Fei; Liu, Jing; Chen, Yiqiang; Yang, Ge; Li, Xin
作者单位1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China
2.Chinese Acad Sci, Inst Zool, State Key Lab Stem Cell & Reprod Biol, Beijing, Peoples R China
3.Chinese Acad Sci, Inst Comp Technol, Beijing Key Lab Mobile Comp & Pervas Device, Beijing, Peoples R China
4.Univ Chinese Acad Sci, Beijing, Peoples R China
5.Chinese Acad Sci, Inst Automat, State Key Laboratoryof Multimodal Artificial Intel, Beijing, Peoples R China
6.Univ Chinese Acad Sci, Sch Artificial Intelligence, Beijing, Peoples R China
7.Chinese Acad Sci, Inst Stem Cell & Regenerat Med, Beijing, Peoples R China
8.Beijing Inst Stem Cell & Regenerat Med, Beijing, Peoples R China
9.Chinese Acad Sci, Res Ctr Ubiquitous Comp Syst, Inst Comp Technol, Beijing, Peoples R China
10.Chinese Acad Sci, Comp Network Informat Ctr, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Yang, Xiaodong,Liu, Guole,Feng, Guihai,et al. GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model[J]. CELL RESEARCH,2024:16.
APA Yang, Xiaodong.,Liu, Guole.,Feng, Guihai.,Bu, Dechao.,Wang, Pengfei.,...&Li, Xin.(2024).GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model.CELL RESEARCH,16.
MLA Yang, Xiaodong,et al."GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model".CELL RESEARCH (2024):16.

入库方式： OAI收割

来源：计算技术研究所

浏览0
下载0
收藏0
其他版本

除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。