Rui Yin

Rui Yin

Assistant Professor at Department of Health Outcomes and Biomedical Informatics, University of Florida

You can also find my articles on my Google Scholar profile

2023
  • Zhou, Z., Glanz, Z., Liu, M., Bian, J., Yin, R.*, Gao, H.* (2023). HSELDA: Heterogeneous Sub-Graph Learning for lncRNA-Disease Associations Prediction. 2023 IEEE International Conference on Bioinformatics and Biomedicine. (Accepted)
  • Wan, Z., Lin, Z., Rashida, S., Nga, S., Yin, R., Senthilnath, J., Kwoh*, C. (2023). PESI: Paratope-Epitope Set Interaction for SARS-CoV-2 Neutralization Prediction. 2023 IEEE International Conference on Bioinformatics and Biomedicine. (Accepted)
  • Ye, B., Li, J., Chen, X., Yin, C., Subramaniam, A., Zhang, X., Bian, J., Yin*, R. (2023). MTLNFM: Multi-task Learning to Predict Patient Clinical Outcomes with Neural Factorization Machine, 2023 AMIA Annual Symposium. (Accepted)
  • Ding, P., Zeng, M., Yin, R.* (2023). Editorial: Computational Methods to Analyze RNA Data for Human Diseases. Frontiers in Genetics.
  • Xu, J., Yin, R., Smith, G., DeKosky, S., & Bian, J. (2023). Identification of Outcome-Oriented Progression Subtypes from Mild Cognitive Impairment to Alzheimer’s Disease Using Electronic Health Records. AMIA 2023 Annual Symposium. (Accepted)
  • Yin, R., Luo, Z., Zhuang, P., Zeng, M., Li, M., Lin, Z., Kwoh, C. K. (2023). ViPal: a framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences. Journal of Biomedical Informatics, 142, 104388.
  • Yin, R., Ye, B., Bian J. (2023). CLCAP: Contrastive Learning Improves Antigenicity Prediction for Influenza A Virus Using Convolutional Neural Networks. Methods
  • Ming, Y., Wang, W., Yin, R., et al. (2023). A review of the enzyme design in catalytic stability by artificial intelligence. Briefings in Bioinformatics
  • Lin, Z., Feng, L., Guo, X., Zhang, Y., Yin, R., Kwoh, C. K., Xu, C. (2023). Comet: Convolutional dimension interaction for collaborative filtering. ACM Transactions on Intelligent Systems and Technology, 14(4), 1-18.
2022
  • Li M, Zhao B, Yin R, et al. GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence-to-graph transformation. Briefings in Bioinformatics (2022)
  • Yin R, Zhu X, Kwoh CK, et al. “A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods.” Briefings in Bioinformatics (2022)
  • Zhang W, Wu P, Yin R, Sun M, Zhang R, Liao X, Lin Y, Lu H. Mendelian Randomization Analysis Suggests No Associations of Herpes Simplex Virus Infections With Multiple Sclerosis. Frontiers in neuroscience. 2022;16. (pdf)
2021
  • Yin R, Luo Z, Kwoh CK. Exploring the Lethality of Human-Adapted Coronavirus Through Alignment-Free Machine Learning Approaches Using Genomic Sequences. Current Genomics. 2021 Dec 1;22(8):583-95. (pdf)
  • Wu P, Du B, Wang B, Yin R, Lv X, Dai Y, Zhang W, Xia K. Joint Analysis of Genome-Wide Association Data Reveals No Genetic Correlations Between Low Back Pain and Neurodegenerative Diseases. Frontiers in genetics. 2021:1717. (pdf)
  • Yin R, Luo Z, Zhuang P, Zhuoyi Lin, et al. VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza a virus using all 8 segments[J]. Bioinformatics. (pdf)
  • Lin Z, Feng L, Yin R, Xu C, Kwoh CK. GLIMG: Global and local item graphs for top-N recommender systems. Information Sciences. 2021 Nov 1;580:1-4. (pdf)
  • Yin R, Yin R, Thwin N N, Zhuang P, Zhuoyi Lin, et al. IAV-CNN: a 2D convolutional neural network model to predict antigenic variants of influenza A virus[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021. (pdf)
  • Wu PF, Zhang X, Zhou P, Yin R, Zhou XT, Zhang W. Growth differentiation factor 15 is associated with Alzheimer’s disease risk. Frontiers in Genetics. 2021 Aug 13:1500. (pdf)
2020
  • Yin R, Luusua E, Dabrowski J, et al. Tempel: Time-series Mutation Prediction of Influenza A Viruses via Attention-based Recurrent Neural Networks[J]. Bioinformatics, 2020. (pdf)
  • Zhang Y, Long Y, Yin R, et al. DL-CRISPR: A Deep Learning Method for Off-Target Activity Prediction in CRISPR/Cas9 With Data Augmentation[J]. IEEE Access, 2020, 8: 76610-76617. (pdf)
  • Yin R, Zhang Y, Zhou X, et al. Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks[J]. Journal of Bioinformatics and Computational Biology, 2020. (pdf)
  • Yin R,, Zhou X, Rashid S, et al. HopPER: an adaptive model for probability estimation of influenza reassortment through host prediction[J]. BMC Medical Genomics, 2020, 13(1): 9. (pdf)
2019
  • Zhou X, Yin R, Zheng J, et al. An encoding scheme capturing generic priors and properties of amino acids improves protein classification[J]. IEEE Access, 2019, 7: 7348-7356. (pdf)
  • Yin R, Chee Keong Kwoh, and Jie Zheng. Whole Genome Sequencing Analysis: Computational Pipelines and Workflows in Bioinformatics, Encyclopedia of Bioinformatics and Computational Biology, 176-183, 2019. (pdf)
2018
  • Yin R, Tran V H, Zhou X, et al. Predicting antigenic variants of H1N1 influenza virus based on epidemics and pandemics using a stacking model[J]. PloS one, 2018, 13(12): e0207777. (pdf)
  • Zhou X, Yin R, Kwoh C K, et al. A context-free encoding scheme of protein sequences for predicting antigenicity of diverse influenza A viruses[J]. BMC genomics, 2018, 19(10): 936. (pdf)
  • Yin R, Zhou X, Zheng J, et al. Computational identification of physicochemical signatures for host tropism of influenza A virus[J]. Journal of bioinformatics and computational biology, 2018: 1840023- 1840023. (pdf)
  • Ding P, Yin R, Luo J, et al. Ensemble Prediction of Synergistic Drug Combinations Incorporating Biological, Chemical, Pharmacological and Network Knowledge[J]. IEEE journal of biomedical and health informatics, 2018. (pdf)
  • Yin R, Tan J, Akhila D, et al. Inference of Sequence Homology by BLAST visualization of Influenza Genome set[C]//Proceedings of the 9th International Conference on Computational Systems-Biology and Bioinformatics. ACM, 2018: 5. (pdf)
2017
  • Ivan F X, Zhou X, Deshpande A, Yin R, et al. Phylogenetic tree based method for uncovering co- mutational site-pairs in influenza viruses[C]//Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2017: 21-26. (pdf)
  • Yin R, Zhou X, Ivan F X, et al. Identification of Potential Critical Virulent Sites Based on Hemagglu- tinin of Influenza a Virus in Past Pandemic Strains[C]//Proceedings of the 6th International Conference on Bioinformatics and Biomedical Science. ACM, 2017: 30-36. (Best presentation) (pdf)
Prior to 2016
  • The device of matrix sedimentation, China, 2014
  • The device and method of Linear sweep polarographic wave model, China, 2013