机构：[1]Donghai County People’s Hospital (Affiliated Kangda College of Nanjing Medical University), Department of Oncology, Zhujiang Hospital, Southern Medical University, Lianyungang 222000, China 南方医科大学珠江医院[2]Institute of Logic and Computation, Vienna University of Technology, Vienna, Austria [3]Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China 南方医科大学珠江医院[4]Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China [5]Department of Joint Surgery and Sports Medicine, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Guangdong, China [6]Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China [7]Cancer Center, The Sixth Affiliated Hospital, School of Medicine, South China University of Technology, Foshan, 528000, China [8]Department of Radiation Oncology, Zhongshan Hospital Affiliated to Fudan University, Shanghai, China [9]Hepatobiliary Surgery Department, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, China [10]Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China [11]Department of Radiology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China 四川省人民医院[12]Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China [13]The School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3000, Australia [14]Suzhou Industrial Park Monash Research Institute of Science and Technology, Suzhou, Jiangsu 215000, China [15]College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, 230032, China [16]Department of Urology, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, China [17]Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China [18]Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai 200011, China [19]Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
Large language models (LLMs), representing a breakthrough advancement in artificial intelligence, have demonstrated substantial application value and development potential in bioinformatics research, particularly showing significant progress in the processing and analysis of complex biological data. This comprehensive review systematically examines the development and applications of LLMs in bioinformatics, with particular emphasis on their advancements in protein and nucleic acid structure prediction, omics analysis, drug design and screening, and biomedical literature mining. This work highlights the distinctive capabilities of LLMs in end-to-end learning and knowledge transfer paradigms. Additionally, this paper thoroughly discusses the major challenges confronting LLMs in current applications, including key issues such as model interpretability and data bias. Furthermore, this review comprehensively explores the potential of LLMs in cross-modal learning and interdisciplinary development. In conclusion, this paper aims to systematically summarize the current research status of LLMs in bioinformatics, objectively evaluate their advantages and limitations, and provide insights and recommendations for future research directions, thereby positioning LLMs as essential tools in bioinformatics research and fostering innovative developments in the biomedical field.
语种：
外文
被引次数：
WOS：
PubmedID：
中科院(CAS)分区：
出版当年[2025]版：
大类|2 区生物学
小类|1 区数学与计算生物学2 区生化研究方法
最新[2025]版：
大类|2 区生物学
小类|1 区数学与计算生物学2 区生化研究方法
JCR分区：
出版当年[2024]版：
Q1BIOCHEMICAL RESEARCH METHODSQ1MATHEMATICAL & COMPUTATIONAL BIOLOGY
最新[2024]版：
Q1BIOCHEMICAL RESEARCH METHODSQ1MATHEMATICAL & COMPUTATIONAL BIOLOGY
第一作者机构：[1]Donghai County People’s Hospital (Affiliated Kangda College of Nanjing Medical University), Department of Oncology, Zhujiang Hospital, Southern Medical University, Lianyungang 222000, China
共同第一作者：
通讯作者：
通讯机构：[1]Donghai County People’s Hospital (Affiliated Kangda College of Nanjing Medical University), Department of Oncology, Zhujiang Hospital, Southern Medical University, Lianyungang 222000, China [19]Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
推荐引用方式(GB/T 7714)：
Lin Anqi,Ye Junpu,Qi Chang,et al.Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics[J].BRIEFINGS IN BIOINFORMATICS.2025,26(4):doi:10.1093/bib/bbaf357.
APA：
Lin, Anqi,Ye, Junpu,Qi, Chang,Zhu, Lingxuan,Mou, Weiming...&Luo, Peng.(2025).Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics.BRIEFINGS IN BIOINFORMATICS,26,(4)
MLA：
Lin, Anqi,et al."Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics".BRIEFINGS IN BIOINFORMATICS 26..4(2025)
