Biomedical data and AI

Hao Xu^#^{1

2}, Shibo Zhou^#², Zefeng Zhu^{2

3}, Vincenzo Vitelli⁴, Liangyi Chen⁵, Ziwei Dai⁶, Ning Yang⁷, Luhua Lai^{8

9

10}, Shengyong Yang¹¹, Sergey Ovchinnikov¹², Zhuoran Qiao¹³, Sirui Liu¹⁴, Chen Song^{15

16}, Jianfeng Pei¹⁷, Han Wen¹⁸, Jianfeng Feng¹⁹, Yaoyao Zhang²⁰, Zhengwei Xie²¹, Yang-Yu Liu^{22

23}, Zhiyuan Li^{24

25}, Fulai Jin²⁶, Hao Li²⁷, Mohammad Lotfollahi²⁸, Xuegong Zhang²⁹, Ge Yang^{30

31}, Shihua Zhang³², Ge Gao³³, Pulin Li³⁴, Qi Liu³⁵, Jing-Dong Jackie Han^{36

37

38}

Affiliations

¹ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
² Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
³ Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
⁴ Department of Physics, University of Chicago, Chicago, IL, 60637, USA. vitelli@uchicago.edu.
⁵ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. lychen@pku.edu.cn.
⁶ School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. daizw@sustech.edu.cn.
⁷ Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, 610213, China. yn_biophy@pku.edu.cn.
⁸ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.
⁹ Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, 610213, China. lhlai@pku.edu.cn.
¹⁰ College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.
¹¹ Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China. yangsy@scu.edu.cn.
¹² Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. so3@mit.edu.
¹³ Lambic Therapeutics, Inc., San Diego, CA, 92121, USA. zrqiao0@gmail.com.
¹⁴ Changping Laboratory, Beijing, 102200, China. liusirui@cpl.ac.cn.
¹⁵ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. c.song@pku.edu.cn.
¹⁶ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. c.song@pku.edu.cn.
¹⁷ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. jfpei@pku.edu.cn.
¹⁸ Al for Science Institute, Beijing, 100083, China. wenh@aisi.ac.cn.
¹⁹ Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China. jffeng@fudan.edu.cn.
²⁰ Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China. yaoyaozhang@scu.edu.cn.
²¹ Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China. xiezhengwei@bjmu.edu.cn.
²² Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA. yyl@channing.harvard.edu.
²³ Center for Artificial Intelligence and Modeling, the Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA. yyl@channing.harvard.edu.
²⁴ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. zhiyuanli@pku.edu.cn.
²⁵ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. zhiyuanli@pku.edu.cn.
²⁶ Department of Genetics and Genome Sciences, School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA. fulai.jin@case.edu.
²⁷ Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94110, USA. haoli@genome.ucsf.edu.
²⁸ Sanger Institute, Cambridge, CB10 1SA, UK. ml19@sanger.ac.uk.
²⁹ Department of Automation, Tsinghua University, Beijing, 100084, China. zhangxg@tsinghua.edu.cn.
³⁰ State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China. ge.yang@ia.ac.cn.
³¹ School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China. ge.yang@ia.ac.cn.
³² Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing, 100190, China. zsh@amss.ac.cn.
³³ Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China. gaog@pku.edu.cn.
³⁴ Whitehead Institute and Eugene Bell Career Development and Tissue Engineering, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. pli@wi.mit.edu.
³⁵ State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China. qiliu@tongji.edu.cn.
³⁶ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. jackie.han@pku.edu.cn.
³⁷ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. jackie.han@pku.edu.cn.
³⁸ Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, 610213, China. jackie.han@pku.edu.cn.

^# Contributed equally.

PMID: 40100542
DOI: 10.1007/s11427-024-2859-1

Biomedical data and AI

Hao Xu et al. Sci China Life Sci. 2025 May.

. 2025 May;68(5):1536-1540.

doi: 10.1007/s11427-024-2859-1. Epub 2025 Mar 14.

Authors

Affiliations

¹ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
² Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
³ Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
⁴ Department of Physics, University of Chicago, Chicago, IL, 60637, USA. vitelli@uchicago.edu.
⁵ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. lychen@pku.edu.cn.
⁶ School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. daizw@sustech.edu.cn.
⁷ Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, 610213, China. yn_biophy@pku.edu.cn.
⁸ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.
⁹ Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, 610213, China. lhlai@pku.edu.cn.
¹⁰ College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. lhlai@pku.edu.cn.
¹¹ Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China. yangsy@scu.edu.cn.
¹² Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. so3@mit.edu.
¹³ Lambic Therapeutics, Inc., San Diego, CA, 92121, USA. zrqiao0@gmail.com.
¹⁴ Changping Laboratory, Beijing, 102200, China. liusirui@cpl.ac.cn.
¹⁵ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. c.song@pku.edu.cn.
¹⁶ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. c.song@pku.edu.cn.
¹⁷ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. jfpei@pku.edu.cn.
¹⁸ Al for Science Institute, Beijing, 100083, China. wenh@aisi.ac.cn.
¹⁹ Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China. jffeng@fudan.edu.cn.
²⁰ Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China. yaoyaozhang@scu.edu.cn.
²¹ Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, 100871, China. xiezhengwei@bjmu.edu.cn.
²² Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA. yyl@channing.harvard.edu.
²³ Center for Artificial Intelligence and Modeling, the Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA. yyl@channing.harvard.edu.
²⁴ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. zhiyuanli@pku.edu.cn.
²⁵ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. zhiyuanli@pku.edu.cn.
²⁶ Department of Genetics and Genome Sciences, School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA. fulai.jin@case.edu.
²⁷ Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94110, USA. haoli@genome.ucsf.edu.
²⁸ Sanger Institute, Cambridge, CB10 1SA, UK. ml19@sanger.ac.uk.
²⁹ Department of Automation, Tsinghua University, Beijing, 100084, China. zhangxg@tsinghua.edu.cn.
³⁰ State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China. ge.yang@ia.ac.cn.
³¹ School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China. ge.yang@ia.ac.cn.
³² Academy of Mathematics and System Science, Chinese Academy of Sciences, Beijing, 100190, China. zsh@amss.ac.cn.
³³ Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China. gaog@pku.edu.cn.
³⁴ Whitehead Institute and Eugene Bell Career Development and Tissue Engineering, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA. pli@wi.mit.edu.
³⁵ State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China. qiliu@tongji.edu.cn.
³⁶ Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. jackie.han@pku.edu.cn.
³⁷ Center for Quantitative Biology (CQB), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. jackie.han@pku.edu.cn.
³⁸ Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, 610213, China. jackie.han@pku.edu.cn.

^# Contributed equally.

PMID: 40100542
DOI: 10.1007/s11427-024-2859-1

No abstract available

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Conflict of interest statement

Compliance and ethics. The authors declare that they have no conflict of interest.

References

1. Chen, Z., Wei, L., and Gao, G. (2024). Foundation models for bioinformatics. Quant Biol 12, 339–344. - DOI
1. Hao, M., Wei, L., Yang, F., Yao, J., Theodoris, C.V., Wang, B., Li, X., Yang, G., and Zhang, X. (2024). Current opinions on large cellular models. Quant Biol 12, 433–443. - DOI
1. Zhang, Q., Ding, K., Lv, T., Wang, X., Yin, Q., Zhang, Y., Yu, J., Wang, Y., Li, X., Xiang, Z., et al. (2025). Scientific large language models: a survey on biological & chemical domains. ACM Comput Surv 57, 1–38. - DOI

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Biomedical data and AI

Affiliations

Biomedical data and AI

Authors

Affiliations

Conflict of interest statement

References

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