Hao Lin Hui Ding Research Scientist Students Postdoc Visiting Scholars Alumni Position

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


55. Xueqin Xie, Changchun Wu, Ziru Huang, Yuwei Zhou, Jian Huang, Fuying Dao, Dan Yan, Kejun Deng, Hao Lyu*, Caiyi Ma*, Hao Lin*. (2026) Artificial intelligence-powered prediction of diabetic complications: from clinical data to molecular omics. Briefings in Bioinformatics, Accepted. (2024 IF: 7.7)

54. Yuduo Hao, Sijia Xie, Yijie Wei, Xiaoshuo Sun, Yu Xiao, Xueqin Xie, Kaiyuan Han, Ting Wang, Zhepeng Wang, Luqiang Zhang*, Hao Lyu*, Hao Lin*. (2026) Single-cell Aging Clocks: A Precision Tool for Dissecting and Targeting the Aging Process. Ageing Research Reviews, 115: 103040. (2024 IF: 12.4)(中科院一区Top)

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, doi: 10.1016/j.xplc.2025.101625. (2024 IF: 11.6)(中科院一区Top)

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, 14: 3. (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, 26(22): 11005. (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 5-Year IF: 16.3)(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, 26(5): bbaf520. (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)