Hao Lv Ph.D. Associate Professor

I am an associate professor of Center for Informational Biology and the Key Laboratory for NeuroInformation of Ministry of Education in UESTC (Supervisor: Hao Lin). I mainly focused on developing machine learning/deep learning tools for identifying DNA, RNA, and protein modification sites. Currently, I am interested in developing computational pipeline to generate embedding and identify cell types from single-cell Hi-C data.

Google Scholar:  Hao Lv

E-mail: hao.lyu(at)uestc.edu.cn

Education and Training

2019-2023 Ph.D. in Bioinformatics, University of Electronic Science and Technology, Sichuan, China

2021-2022 Visiting Ph.D. student in DMLS, University of Zurich, Zurich, Switzerland (Supervisor: Mark Robinson)

2017-2019 M.S in Bioinformatics, University of Electronic Science and Technology, Sichuan, China

2013-2017 B.S in Bioinformatics, Shanxi Agricultural University, Shanxi, China

Published Papers

53. Chengzhi Xie, Feitong Hong, Yijie Wei, Sijia Xie, Xinwei Luo, Xiaolong Li, Wei Su, Xueqin Xie, Yuduo Hao, Hao Lyu, Hui Ding*, Huan Yang*, Fuying Dao*. (2025) PlantAMP: A fine-tuned protein large language model for plant antimicrobial peptide prediction. Plant Communications, accepted. (2024 IF: 11.6)

52. Xinwei Luo, Sijia Xie, Feitong Hong, Xiaolong Li, Yijie Wei, Yuwei Zhou, Wei Su, Yuhe Yang, Lixia Tang, Fuying Dao, Peiling Cai, Hao Lin*, Hongyan Lai*, Hao Lyu*. (2025) From multi-omics to deep learning: advances in cfDNA-based liquid biopsy for multi-cancer screening. Biomarker Research, accepted. (2024 IF: 11.5)

51. Yijie Wei, Feitong Hong, Sijia Xie, Xinwei Luo, Xiaolong Li, Fuying Dao, Kejun Deng, Hao Lin*, Hao Lyu*. (2025) Single-cell multi-omics in type 2 diabetes mellitus: revealing cellular heterogeneity and mechanistic insights. International Journal of Molecular Sciences, accepted. (2024 IF: 4.9)

50. Wei Su, Yuhe Yang, Yafei Zhao, Shishi Yuan, Xueqin Xie, Yuduo Hao, Hongqi Zhang, Dongxin Ye, Hao Lyu*, Hao Lin*. (2025) iPro-MP: a BERT-based model for the prediction of multiple prokaryotic promoters. Genome Biology, 26(1): 353. (2024 IF: 9.4)(中科院一区Top)

49. Feitong Hong, Kaiyuan Han, Yuduo Hao, Wei Su, Xueqin Xie, Xiaolong Li, Qiuming Chen, Yijie Wei, Xinwei Luo, Sijia Xie, Benjamin Lebeau, Crystal Ling, Hao Lv, Li Liu*, Hao Lin*, Fuying Dao*. (2025) Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes. Briefings in Bioinformatics, accepted. (2024 IF: 7.7)

48. Feitong Hong, Qiuming Chen, Xinwei Luo, Sijia Xie, Yijie Wei, Xiaolong Li, Kexin Li, Benjamin Lebeau, Crystal Ling, Fuying Dao, Hao Lin, Lixia Tang, Mi Yang*, Hao Lv*. (2025) A Multi-Omics Integration Framework With Automated Machine Learning Identifies Peripheral Immune-Coagulation Biomarkers for Schizophrenia Risk Stratification. International Journal of Molecular Sciences, 26(15): 7640. (2024 IF: 4.9)

47. Xueqin Xie, Changchun Wu, Yuhe Yang, Wei Su, Fuying Dao, Jian Huang, Zheng Shi, Hao Lyu*, Hao Lin*. (2025) Interpretable machine learning-guided single-cell mapping deciphers multi-lineage pancreatic dysregulation in type 2 diabetes. Cardiovascular Diabetology, 24: 300. (2024 IF: 10.6)(中科院一区Top)

46. Chengzhi Xie, Yijie Wei, Xinwei Luo, Huan Yang, Hongyan Lai, Fuying Dao*, Juan Feng*, Hao Lv*. (2025) NeXtMD: A New Generation of Machine Learning and Deep Learning Stacked Hybrid Framework for Accurate Identification of Anti-Inflammatory Peptides. BMC Biology, 23(1): 212. (2024 IF: 4.5)(中科院二区Top)

45. Xueqin Xie, Changchun Wu, Yixuan Qi, Shang-Hua Liu, Jian Huang, Hao Lyu*, Fuying Dao*, Hao Lin*. (2025) BertADP: A fine-tuned protein language model for anti-diabetic peptide prediction. BMC Biology, 23: 210. (2024 IF: 4.5)(中科院二区Top)

44. Xueqin Xie, Changchun Wu, Fuying Dao, Kejun Deng, Dan Yan, Jian Huang*, Hao Lyu*, Hao Lin*. (2025) scRiskCell: A single-cell framework for quantifying pancreatic islet risk cells and unravelling their dynamic transcriptional and molecular adaptation in the progression of type 2 diabetes. iMeta, 2025: e70060. (2024 IF: 33.2)(中科院一区Top)

43. Fuying Dao, Benjamin Lebeau, Crystal Chia Yin Ling, Mi Yang, Xueqin Xie, Melissa Jane Fullwood*, Hao Lin*, Hao Lyu*. (2025) RepliChrom: Interpretable machine learning predicts cancer-associated enhancer-promoter interactions using DNA replication timing iMeta, 2025: e70052. (2024 IF: 33.2)(中科院一区Top)

42. Hongqi Zhang, Shanghua Liu, Wei Su, Xueqin Xie, Junwen Yu, Fuying Dao, Mi Yang*, Hao Lyu*, Hao Lin*. (2025) NeuroScale: Evolutional Scale-Based Protein Language Models Enable Prediction of Neuropeptides. BMC Biology, DOI:10.1186/s12915-025-02243-6. (2024 IF: 4.5)(中科院二区Top)

41. Sijia Xie, Xinwei Luo, Feitong Hong, Yijie Wei, Yuduo Hao, Xueqin Xie, Xiaolong Li, Guangbo Xie*, Fuying Dao*, Hao Lyu*. (2025) Towards Precision Aging Biology: Single-Cell Multi-Omics and Advanced AI-Driven Strategies. Aging and Disease, DOI: 10.14336/AD.2025.0218. (2024 IF: 6.9)

40. Hao Lin*, Hao Lv*, Fuying dao*. (2025) Editorial: Advances in machine learning for epigenetics and biomedical applications. Methods, 235: 53–54. (2024 IF: 4.3)

39. Fuying Dao &, Xueqin Xie &, Hongqi Zhang &, Zhengxing Guan, Changchun Wu, Wei Su, Hongyan Lai, Dong Gao, Yuhe Yang, Yang Zhang, Lin Ning, Shi-Hao Li, Yuduo Hao, Benjamin Lebeau, Crystal Ling Chia Yin, Jian Huang, Melissa Jane Fullwood*, Hao Lin*, Hao Lv*. (2025) PlantEMS: A Comprehensive Database of Epigenetic Modification Sites Across Multiple Plant Species. Plant Communications, 6(4). (2024 IF: 11.6)(中科院一区Top)

38. HongYan Lai, Tao Zhu, Sijia Xie, Xinwei Luo, Feitong Hong, Diyu Luo, Fuying Dao, Hao Lin, Kunxian Shu, Hao Lv*. (2024) Empirical comparison and analysis of artificial intelligence-based methods for identifying phosphorylation sites of SARS-CoV-2 infection. International Journal of Molecular Sciences, 25(24):13674. (2023 IF: 4.9)

37. Yong Li, Ru Gao, Liu Shan, Hongqi Zhang, Hao Lv*, Hongyan Lai. (2024) PhosBERT: A self-supervised learning model for identifying phosphorylation sites in SARS-CoV-2-infected human cells. Methods, 230: 140-146. (2023 IF: 4.2)

36. Zhi-Feng Gu, Yu-Duo Hao, Tian-Yu Wang, Pei-Ling Cai, Yang Zhang, Ke-Jun Deng, Hao Lin*, Hao Lv*. (2024) Prediction of blood-brain barrier penetrating peptides based on data augmentation with Augur. BMC Biology, 22(1): 86. (2022 IF: 5.4)(中科院一区Top)

35. Fu-Ying Dao, Meng-Lu Liu, Wei Su, Hao Lv, Zhao-Yue Zhang, Hao Lin*, Li Liu*. (2023) AcrPred: A hybrid optimization with enumerated machine learning algorithm to predict Anti-CRISPR proteins. International Journal of Biological Macromolecules, 228: 706-714. (2021 IF: 8.025)(中科院一区Top)

34. Fu-Ying Dao, Hao Lv, Melissa J. Fullwood*, Hao Lin*. (2022) Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information. Research, 2022: ID 9780293. (2021 IF: 11.036)

33. Zijie Sun&, Qinlai Huang&, Yuhe Yang, Shihao Li, Hao Lv, Yang Zhang, Hao Lin*, Lin Ning*. (2022) PSnoD: identifying potential snoRNA-disease associations based on bounded nuclear norm regularization. Briefings in Bioinformatics, 23(4): bbac240.(2021 IF: 13.994)

32. Hao Lv, Fu-Ying Dao, Hao Lin*. (2022) DeepKla: an attention mechanism-based deep neural network for protein lysine lactylation site prediction. iMeta, 1(1):e11. (IF: 23.8)

31. Hao Lv&, Yang Zhang&, Jia-Shu Wang, Shi-Shi Yuan, Zi-Jie Sun, Fu-Ying Dao, Zheng-Xing Guan, Hao Lin*, Ke-Jun Deng*. (2022) iRice-MS: an integrated XGBoost model for detecting multi-type post-translational modification sites in rice. Briefings in Bioinformatics, doi: 10.1093/bib/bbab486. (2021 IF: 13.994)

30. Hao Lv, Lei Shi, Joshua William Berkenpas, Fu-Ying Dao, Hasan Zulfiqar, Hui Ding, Yang Zhang*, Liming Yang*, Renzhi Cao*. (2022) Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design. Briefings in Bioinformatics, doi.org/10.1093/bib/bbab320. (2021 IF: 13.994)

29. Hao Lv, Fu-Ying Dao, Hasan Zulfiqar, Hao Lin*. (2022) DeepIPs: comprehensive assessment and computational identification of phosphorylation site of SARS-CoV-2 infection using a deep learning-based approach. Briefings in Bioinformatics, DOI:10.1093/bib/bbab244. (2021 IF: 13.994)

28. Hao Lv&, Fu-Ying Dao&, Hasan Zulfiqar, Wei Su, Hui Ding, Li Liu*, Hao Lin* (2022) A sequence-based deep learning approach to predict CTCF-mediated chromatin loop. Briefings in Bioinformatics, DOI:10.1093/bib/bbab031. (2021 IF: 13.994)

27. Hasan Zulfiqar, Zi-Jie Sun, Qin-Lai Huang, Shi-Shi Yuan, Hao Lv, Fu-Ying Dao, Hao Lin*, Yan-Wen Li*. (2022) Deep-4mCW2V: A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli. Methods, 203: 558-563. (2021 IF: 4.647) (ESI Highly Cited)

26. Fu-Ying Dao, Hao Lv, Zhao-Yue Zhang, Hao Lin*. (2022) BDselect: a package for k-mer selection based on binomial distribution. Current Bioinformatics, 17(3): 238-244(7). (2022 IF: 4.850)

25. Hao Lv, Fu-Ying Dao, Zheng-Xing Guan, Hui Yang, Yan-Wen Li*, and Hao Lin*. (2021) Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method. Briefings in Bioinformatics, Doi:10.1093/bib/bbaa255. (2020 IF: 11.622) (ESI Highly Cited; ESI Hot)

24. Hao Lv, Fu-Ying Dao, Dan Zhang, Hui Yang, Hao Lin*. (2021) Advances in mapping the epigenetic modifications of 5-methylcytosine (5mC), N6-methyladenine (6mA), and N4-methylcytosine (4mC). Biotechnology and Bioengineering, doi: 10.1002/bit.27911. (2020 IF: 4.530) (Top 10 Highly Cited Papers of the Journal)

23. Hasan Zulfiqar, Qin-Lai Huang, Hao Lv, Zi-Jie Sun, Fu-Ying Dao, Hao Lin*. (2021) Deep-4mCGP: A Deep Learning Approach to Predict 4mC Sites in Geobacter pickeringii by Using Correlation-Based Feature Selection Technique. International Journal of Molecular Sciences, 23(3), 1251. (2021 IF: 6.208)

22. Fu-Ying Dao, Hao Lv, Wei Su, Zi-Jie Sun, Qin-Lai Huang, Hao Lin* (2021) iDHS-Deep: An integrated tool for predicting DNase I hypersensitive sites by deep neural network. Briefings in Bioinformatics, DOI:10.1093/bib/bbab047. (2020 IF: 11.622)

21. Fu-Ying Dao, Hao Lv, Dan Zhang, Zi-Mei Zhang, Li Liu*, Hao Lin*. (2021) DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops. Briefings in Bioinformatics, DOI:10.1093/bib/bbaa356. (2020 IF: 11.622) (ESI Highly Cited)

20. Wei Su, Meng-Lu Liu, Yu-He Yang, Jia-Shu Wang, Shi-Hao Li, Hao Lv, Fu-Ying Dao, Hui Yang, Hao Lin* (2021) PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters. Journal of Molecular Biology, 433: 166860. (2019 IF: 5.469)

19. Fu-Ying Dao, Hao Lv, Hasan Zulfiqar, Hui Yang, Wei Su, Hui Gao, Hui Ding, Hao Lin*. (2021) A computational platform to identify origins of replication sites in eukaryotes. Briefings in Bioinformatics, DOI: 10.1093/bib/bbaa017. (2020 IF: 11.622) (ESI Highly Cited)

18. Dan Zhang&, Zhao-Chun Xu&, Wei Su, Yu-He Yang, Hao Lv, Hui Yang, Hao Lin*. (2021) iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features. Bioinformatics, 37(2): 171-177. (2019 IF: 5.610) (ESI Highly Cited)

17. Hasan Zulfiqar, Fu-Ying Dao, Hui Yang, Hao Lv, Peng Zhou, Wei Chen*, Hao Lin* (2021) Identification of Potent Inhibitors against SARS-Cov-2 through Computational Drug Repurposing Study. Current Bioinformatics, 16(10): 1320-1327(8). (2020 IF: 3.543)

16. Hao Lv, Zi-Mei Zhang, Shi-Hao Li, Jiu-Xin Tan, Wei Chen*, Hao Lin*. (2020) Evaluation of different computational methods on 5-methylcytosine sites identification. Briefings in Bioinformatics, DOI: 10.1093/bib/bbz048. (2019 IF: 8.990) (ESI Highly Cited; Top 10 Highly Cited Papers of the Journal)

15. Hao Lv, Fu-Ying Dao, Dan Zhang, Zheng-Xing Guan, Hui Yang, Wei Su, Meng-Lu Liu, Hui Ding, Wei Chen, Hao Lin*. (2020) iDNA-MS: an integrated computational tool for detecting DNA modification sites in multiple genomes. iScience, DOI: 10.1016/j.isci.2020.100991. (2019 IF: 4.447) (ESI Highly Cited)

14. Fu-Ying Dao &, Hao Lv &, Yu-He Yang, Hasan Zulfiqar, Hui Gao, Hao Lin*. (2020) Computational identification of N6-Methyladenosine sites in multiple tissues of mammals. Computational and Structural Biotechnology Journal, DOI: 10.1016/j.csbj.2020.04.015. (2019 IF: 6.018)

13. Zi-Mei Zhang, Jia-Shu Wang, Hasan Zulfiqar, Hao Lv, Fu-Ying Dao, Hao Lin*. (2020) Early Diagnosis of Pancreatic Ductal Adenocarcinoma by Combining Relative Expression Orderings with Machine Learning Method. Frontiers in Cell and Developmental Biology, 8: 582864. (2019 IF: 5.201)

12. Hao Lv, Fu-Ying Dao, Zheng-Xing Guan, Dan Zhang, Jiu-Xin Tan, Yong Zhang*, Wei Chen*, Hao Lin*. (2019) iDNA6mA-Rice: a computational tool for detecting N6-methyladenine sites in rice. Frontiers in Genetics, DOI: 10.3389/fgene.2019.00793. (2018 IF: 3.517)

11. Fu-Ying Dao, Hao Lv, Fang Wang, Chao-Qin Feng, Hui Ding*, Wei Chen*, Hao Lin*. (2019) Identify origin of replication in Sccharomyces cerevisiae using two-step feature selection technique. Bioinformatics, 35(12):2075-2083. (2018 IF: 4.531) (ESI Highly Cited; ESI Hot)

10. Wei Chen*, Hao Lv, Fulei Nie, Hao Lin*. (2018) i6mA-Pred:Identifying DNA N6-methyladenine sites in the rice genome. Bioinformatics, DOI: 10.1093/bioinformatics/btz015. (2018 IF: 4.531) (ESI Highly Cited; ESI Hot)

9. Wei Chen*, Pengmian Feng, Xiaoming Song, Hao Lv, Hao Lin*. (2019) iRNA-m7G: identifying N7-methylguanosine sites by fusing multiple features. Molecular Therapy - Nucleic Acids, 18: 269-274. (2018 IF: 5.919)

8. Wei Chen*, Xiaoming Song, Hao Lv, Hao Lin*. (2019) iRNA-m2G: identifying N2-methylguanosine sites based on sequence derived information. Molecular Therapy - Nucleic Acids, 18: 253-258. (2018 IF: 5.919)

7. Jiu-Xin Tan, Hao Lv, Fang Wang, Fu-Ying Dao, Wei Chen*, Hui Ding*. (2019) A survey for predicting enzyme family classes using machine learning methods. Current Drug Targets, 20(5): 540-550. (2018 IF: 2.642)

6. Fu-Ying Dao, Hao Lv, Fang Wang, Hui Ding*. (2018) Recent advances on the machine learning methods in identifying DNA replication origins in eukaryotic genomics. Frontiers in Genetics, 9: 613. (2017 IF: 4.151)

5. Hui Yang, Hao Lv, Hui Ding, Wei Chen*, Hao Lin*. (2018) iRNA-2OM: A sequence-based predictor for identifying 2’-O-methylation sites in Homo sapiens. Journal of Computational Biology, 25(11): 1266-1277. (2017 IF: 1.191) (ESI Highly Cited; ESI Hot)

4. Hui Yang, Wuritu Yang, Fu-Ying Dao, Hao Lv, Hui Ding*, Wei Chen*, Hao Lin*. (2020) A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae. Briefings in Bioinformatics, 21(5): 1568-1580. (2020 IF: 11.622) (ESI Highly Cited; ESI Hot)

3. Li Liu*, Qian-Zhong Li*, Wen Jin, Hao Lv, Hao Lin*. (2019) Revealing gene function and transcription relationship by reconstructing gene-level chromatin interaction. Computational and Structural Biotechnology Journal, 17: 195-205. (2018 IF: 4.72)

2. Jiu-Xin Tan, Fu-Ying Dao, Hao Lv, Peng-Mian Feng *, Hui Ding * (2018) Identifying Phage Virion Proteins by Using Two-Step Feature Selection Methods. Molecules, 23(8): 2000. (2017 IF: 3.098)

1. Pengmian Feng*, Zhaochun Xu, Hui Yang, Hao Lv, Hui Ding, Li Liu*. (2018) Identification of D-modification sites by integrating heterogeneous features in Saccharomyces cerevisiae. Molecules, 24(3). (2017 IF: 3.098)