Special Topic: AI for Biology
SCIS Selected Articles on Large Language Models (LLM)
生物信息 RESEARCH PAPER Supplementary Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 39

From intention to implementation: automating biomedical research via LLMs
Luo, Yi; Shi, Linghang; Li, Yihao; Zhuang, Aobo; Gong, Yeyun; Liu, Ling; Lin, Chen
Sci China Inf Sci, 2025, 68(7): 170105
Keywords: biomedical research; AI for research; large language models; multi-agent systems; automation
Cite as: Luo Y, Shi L H, Li Y H, et al. From intention to implementation: automating biomedical research via LLMs. Sci China Inf Sci, 2025, 68: 170105, doi: 10.1007/s11432-024-4485-0

Special Topic: AI for Biology
生物信息 REVIEW Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 32

Self-supervised learning in drug discovery
Chen, Yangyang; Wang, Zixu; Wang, Jianmin; Chu, Yanyi; Zhang, Qingpeng; Li, Zhong Alan; Zeng, Xiangxiang
Sci China Inf Sci, 2025, 68(7): 170103
Keywords: drug discovery; self-supervised learning; drug representation
Cite as: Chen Y Y, Wang Z X, Wang J M, et al. Self-supervised learning in drug discovery. Sci China Inf Sci, 2025, 68: 170103, doi: 10.1007/s11432-024-4453-4

Special Topic: AI for Biology
生物信息 REVIEW Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 23

AI in drug development: advances in response, combination therapy, repositioning, and molecular design
Qi, Ren; Liu, Shujia; Hui, Xingqi; Shaytan, Alexey K.; Liu, Bin
Sci China Inf Sci, 2025, 68(7): 170102
Keywords: artificial intelligence; deep learning; drug research; drug repositioning; genomic data
Cite as: Qi R, Liu S J, Hui X Q, et al. AI in drug development: advances in response, combination therapy, repositioning, and molecular design. Sci China Inf Sci, 2025, 68: 170102, doi: 10.1007/s11432-024-4461-0

Special Topic: AI for Biology
生物信息 REVIEW Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 15

Molecular pretraining models towards molecular property prediction
Qiao, Jianbo; Gao, Wenjia; Jin, Junru; Wang, Ding; Guo, Xu; Manavalan, Balachandran; Wei, Leyi
Sci China Inf Sci, 2025, 68(7): 170104
Keywords: molecular pretraining models; molecular property prediction; graph neural network; GNN; graph Transformer; PubChem; MoleculeNet
Cite as: Qiao J B, Gao W J, Jin J R, et al. Molecular pretraining models towards molecular property prediction. Sci China Inf Sci, 2025, 68: 170104, doi: 10.1007/s11432-024-4457-2

Special Topic: AI for Biology
SCIS Selected Articles on Large Language Models (LLM)
生物信息 REVIEW Supplementary Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 13

Large language models transform biological research: from architecture to utilization
Wang, Tao; Luo, Zeyu
Sci China Inf Sci, 2025, 68(7): 170101
Keywords: biological sequence and multimodal data; large language model; genome; transcriptome; proteome
Cite as: Wang T, Luo Z Y. Large language models transform biological research: from architecture to utilization. Sci China Inf Sci, 2025, 68: 170101, doi: 10.1007/s11432-024-4466-3

生物信息 LETTER Supplementary Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 5

Prediction of Budd-Chiari syndrome based on attention mechanisms of high-risk factors in multi-hop graph learning
Wang, Lei; Li, Shengli; Su, Xiaorui; Li, Zhengwei; Wei, Mengmeng; Zhao, Bowei; Zu, Maoheng; Zhang, Qingqiao; You, Zhuhong
Sci China Inf Sci, 2025, 68(7): 179102
Keywords: Budd-Chiari syndrome; attention mechanism; multi-hop graph learning; high-risk factors; graph neural networks
Cite as: Wang L, Li S L, Su X R, et al. Prediction of Budd-Chiari syndrome based on attention mechanisms of high-risk factors in multi-hop graph learning. Sci China Inf Sci, 2025, 68: 179102, doi: 10.1007/s11432-024-4358-3

Special Topic: AI for Biology
生物信息 RESEARCH PAPER Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 2

OntoGene: knowledge-enhanced BERT for promoter identification
Li, Yang; Gao, Mengli; Bian, Jilong; Zhao, Kaiqi; Li, Dan; Wang, Guohua
Sci China Inf Sci, 2025, 68(7): 170106
Keywords: promoter identification; knowledge enhancement; knowledge graph; BERT
Cite as: Li Y, Gao M L, Bian J L, et al. OntoGene: knowledge-enhanced BERT for promoter identification. Sci China Inf Sci, 2025, 68: 170106, doi: 10.1007/s11432-024-4481-9

生物信息 LETTER Supplementary Webpage Webpage-cn SpringerLink Google Scholar Cited in SCI: 0

TaxDiff: taxonomic-guided diffusion model for protein sequence generation
Lin, Zongying; Li, Hao; Lv, Liuzhenghao; Wang, Yu; Lin, Bin; Zhang, Junwu; Chen, Zijun; Chen, Calvin Yu-Chian; Yuan, Li; Tian, Yonghong
Sci China Inf Sci, 2025, 68(4): 149101
Keywords: controlled protein sequence generation; protein sequence design; diffusion model; generative models; protein sequence generation
Cite as: Lin Z Y, Li H, Lv L Z H, et al. TaxDiff: taxonomic-guided diffusion model for protein sequence generation. Sci China Inf Sci, 2025, 68: 149101, doi: 10.1007/s11432-024-4296-6