30. Jiyun Han, Shizhuo, Zhang, Mingming Guan, Qiuyu Li, Xin Gao*, Juntao Liu*(通讯作者 2024.11), GeoNet enables the accurate prediction of protein-ligand binding sites through interpretable geometric deep learning. Structure. (SCI, 中科院1区，IF: 4.4)
29. Shizhuo Zhang, Jiyun Han, Juntao Liu1*(通讯作者 2024.11), Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning. GigaScience. (SCI, JCR 1区，IF: 11.8)
28. Jiyun Han, Tongxin Kong, Juntao Liu*(通讯作者 2024.9), PepNet: an interpretable neural network for anti-inflammatory and antimicrobial peptides prediction using a pre-trained protein language model. Communications Biology. (SCI, 中科院1区TOP，IF: 5.2)
27. Sheng Long, Xiaoran Tang, Xinyi Si, Tongxin Kong, Yanhao Zhu, Chuanzhi Wang, Chenqing Qi, Zengchao Mu*, Juntao Liu*(通讯作者 2024.8), TriFusion enables accurate prediction of miRNA-disease association by a tri-channel fusion neural network. Communications Biology. (SCI, 中科院1区TOP，IF: 5.2)
26. Jiyun Han, Qixuan Chen, Jiaying Su, Tongxin Kong, Yongchao Song, Sheng Long, Juntao Liu* (通讯作者 2024.7), TriStack enables accurate identification of antimicrobial and anti-inflammatory peptides by combining machine learning and deep learning approaches. Future Generations Computer Systems. (SCI, 中科院1区，IF: 6.2)
25. Yangyang Liu, Jiyun Han, Tongxin Kong, Nannan Xiao, Qinglin Mei, Juntao Liu* (通讯作者 2023.12), DriverMP enables improved identification of cancer driver genes. GigaScience. (SCI, JCR 1区，IF: 9.2)
24. Haonan Wu, Jiyun Han, Shizhuo Zhang, Gaojia Xin, Chaozhou Mou, Juntao Liu* (通讯作者 2023.11), Spatom: a graph neural network for structure-based protein–protein interaction site prediction. Briefings in Bioinformatics. (SCI, 中科院1区Top，IF: 9.5)
23. Dengyi Zhao, Juntao Liu* (通讯作者 2023.11.01), Ting Yu*, Protocol for transcriptome assembly by the TransBorrow algorithm. Biology Methods & Protocols. (ESCI, IF: 3.6)
22. Jiyun Han, Shizhuo Zhang, Juntao Liu* (通讯作者 2023.09.15), Protocol for predicting peptides with anticancer and antimicrobial properties by a tri-fusion neural network. Star Protocols. (Cell子刊 新)
21. Yilin Yu, Juntao Liu* (通讯作者 2023.09.03), SCM enables improved single-cell clustering by scoring consensus matrices. Mathematics. (SCI, JCR 1区，IF: 2.4)
20. Wanyun Zhou#, Yufei Liu#, Yingxin Li, Siqi Kong, Weilin Wang, Boyun Ding, Jiyun Han, Chaozhou Mou, Xin Gao*, Juntao Liu* (通讯作者 2023.03.10), TriNet: A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides. Patterns. (Cell子刊，IF: 6.5)
19. Pengfei Ding, Zhenhua Ming, Juntao Liu, Ivan Erill, Zheng Zhang (2022.10.19), Editorial: Microbiome and microbial informatics. Frontiers in Microbiology. (SCI, 中科院2区Top，IF: 6.064)
18. Chunxiang Wang#, Zengchao Mu#, Chaozhou Mou#, Hongyu Zheng, Juntao Liu* (通讯作者 2022.01), Consensus-based clustering of single cells by reconstructing cell-to-cell dissimilarity. Briefings in Bioinformatics. (SCI, 中科院1区Top，IF: 13.994)
17. Ting Yu, Renmin Han, Zhaoyuan Fang, Zengchao Mu, Hongyu Zheng, Juntao Liu* (通讯作者 2021.07.13), TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs. Briefings in Bioinformatics. (SCI, 中科院1区Top，IF: 11.622)
16. Zengchao Mu, Ting Yu, Xiaoping Liu, Hongyu Zheng, Leyi Wei*, Juntao Liu* (通讯作者 2021.06), FEGS: A novel feature extraction model for protein sequences and its applications. BMC Bioinformatics, 22:297. (SCI, 中科院2区，IF：3.242)
15. Chunxiang Wang, Xin Gao* and Juntao Liu* (通讯作者 2020.10.7), Impact of data preprocessing on cell‑type clustering based on single‑cell RNA‑seq data. BMC Bioinformatics, 21:440. (SCI, 中科院2区，IF：3.242)
14. Ting Yu, Zengchao Mu, Zhaoyuan Fang, Xiaoping Liu, Xin Gao*, Juntao Liu* (通讯作者 2020.8.17), TransBorrow: Genome-guided transcriptome assembly by borrowing assemblies from different assemblers. Genome Research, 30(8). (SCI, 中科院1区Top，IF：11.093)
13. Xiangyu Liu, Di Li, Juntao Liu, Zhengchang Su, Guojun Li (2020.7.11), RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters. Bioinformatics. (SCI, 中科院1区Top，IF：5.61)
12.Ting Yu#, Juntao Liu# (共同一作), Xin Gao*, Guojun Li* (2020.1.27) iPAC: a genome-guided assembler of isoforms via phasing and combing paths. Bioinformatics, doi: 10.1093/bioinformatics/btaa052. (SCI, 中科院1区Top，IF：4.531)
11.Zengchao Mu, Ting Yu, Enfeng Qi, Juntao Liu* (通讯作者), Guojun Li* (2019.06) DCGR: Feature extractions from protein sequences based on CGR via remodeling multiple information. BMC Bioinformatics, 20:351. (SCI, 中科院2区，IF：2.511)
10. Juntao Liu, Ting Yu, Zengchao Mu, Guojun Li* (2019.4.9), TransLiG: a de novo transcriptome assembler that uses line graph iteration. Genome Biology, 28(81). (SCI, 中科院1区Top, IF：14.028)
9. Juntao Liu, Xiangyu Liu, Xianwen Ren*, Guojun Li* (2019.3.31), scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions. Bioinformatics. (SCI, 中科院1区Top，IF：4.531)
8. Juntao Liu, Ting Yu, Tao Jiang*, Guojun Li* (2016.10.19), TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs. Genome Biology, 17(213). (SCI, 中科院1区Top, IF：14.028)
7. Juntao Liu, Guojun Li*, Zheng Chang, Ting Yu, Bingqiang Liu, Rick McMullen, Pengyin Cheng, Xiuzhen Huang* (2016.2.19), BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data. Plos Computational Biology, 12(2): e1004772. (SCI, 中科院1区Top, IF：4.428)
6. Juntao Liu, Jianyang Sun, Xiuzhen Huang, Guojun Li, Bingqiang Liu* (2015.7), Goldindec: A Novel Algorithm for Raman Spectrum Baseline Correction. Applied Spectroscopy, 69(7): 834. (SCI, 2区, IF：1.872)
5. Juntao Liu, Xiaoyun Duan, Jianyang Sun, Yanbin Yin, Guojun Li, Lushan Wang, Bingqiang Liu* (2013.11.20), Bi-Factor Analysis Based on Noise-Reduction (BIFANR): A New Algorithm for Detecting Coevolving Amino Acid Sites in Proteins. Plos One, 8(11):e79764. (SCI, 2区, IF：2.766)
4. Bo Gao, Yue Zhao, Yang Li, Juntao Liu, Lushan Wang, Guojun Li*, Zhengchang Su* (2018.12), Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples. Advanced Science. (SCI, 中科院1区Top，IF：15.804)
3. Ashraful Arefeen, Juntao Liu, Xinshu Xiao, Tao Jiang* (2018.2.23), TAPAS: Tool for Alternative Polyadenylation Site Analysis. Bioinformatics. (SCI, 中科院1区Top，IF：4.531)
2. Bo Gao, Guojun Li*, Juntao Liu, Yang Li, Xiuzhen Huang* (2017.3.21), Identification of driver modules in pan-cancer via coordinating coverage and exclusivity. Oncotarget, doi: 10.18632/oncotarget.16433. (SCI, 1区，IF：5.168)
1. Zheng Chang, Guojun Li*, Juntao Liu, Yu Zhang, Cody Ashby, Deli Liu, Carole L. Cramer, Xiuzhen Huang* (2015.2), Bridger: A new framework for de novo transcriptome assembly using RNA-seq data. Genome Biology. (SCI, 中科院1区Top, IF：14.028)
