Rui Yin

Rui Yin,

Assistant Professor

Department: MD-HOBI-GENERAL
Business Email: ruiyin@ufl.edu

About Rui Yin

My research mainly focuses on applying and developing machine learning approaches (CNN, RNN, GNN, Transformer, etc.) and protein language models to address biomedical problems, especially in (1) RNA virus and infectious diseases, e.g., mutation and variant identification, viral antigenicity and virulence prediction; (2) rare disease study, e.g., variant pathogenicity prediction and gene prioritization; (3) cancer study, e.g., miRNA-mRNA target identification in colorectal cancer patients and renal tumor classification, (4) Alzheimer’s disease and related dementias (AD/ADRD), e.g., computational drug repurposing for AD/ADRD; and (5) Health equity, e.g., identify social determinants of health that impact healthy aging people.

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Teaching Profile

Courses Taught
2024
GMS6805 Information Modeling in Biomedicine

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0002-1403-0396

Areas of Interest
  • Biomedical informatics
  • Genomics and precision medicine
  • Health Equity
  • Machine learning and applications
  • Protein language model

Publications

2024
EF-Net: Mental State Recognition by Analyzing Multimodal EEG-fNIRS via CNN
Sensors. 24(6) [DOI] 10.3390/s24061889. [PMID] 38544152.
2023
A review of enzyme design in catalytic stability by artificial intelligence
Briefings in Bioinformatics. 24(3) [DOI] 10.1093/bib/bbad065.
2023
COMET: Convolutional Dimension Interaction for Collaborative Filtering
ACM Transactions on Intelligent Systems and Technology. 14(4):1-18 [DOI] 10.1145/3588576.
2023
Developing Ethics and Equity Principles, Terms, and Engagement Tools to Advance Health Equity and Researcher Diversity in AI and Machine Learning: Modified Delphi Approach
JMIR AI. 2 [DOI] 10.2196/52888.
2023
Identification of Outcome-Oriented Progression Subtypes from Mild Cognitive Impairment to Alzheimer’s Disease Using Electronic Health Records.
AMIA … Annual Symposium proceedings. AMIA Symposium. 2023:764-773 [PMID] 38222396.
2023
ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences
Journal of Biomedical Informatics. 142 [DOI] 10.1016/j.jbi.2023.104388. [PMID] 37178781.
2022
A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods
Briefings in Bioinformatics. 23(5) [DOI] 10.1093/bib/bbac281.
2022
GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation
Briefings in Bioinformatics. [DOI] 10.1093/bib/bbac565.
2022
Mendelian Randomization Analysis Suggests No Associations of Herpes Simplex Virus Infections With Multiple Sclerosis
Frontiers in Neuroscience. 16 [DOI] 10.3389/fnins.2022.817067. [PMID] 35299622.
2021
Exploring the Lethality of Human-Adapted Coronavirus Through Alignment-Free Machine Learning Approaches Using Genomic Sequences
Current Genomics. 22(8):583-595 [DOI] 10.2174/1389202923666211221110857. [PMID] 35386190.
2021
GLIMG: Global and local item graphs for top-N recommender systems
Information Sciences. 580:1-14 [DOI] 10.1016/j.ins.2021.08.018.
2021
Growth Differentiation Factor 15 Is Associated With Alzheimer’s Disease Risk
Frontiers in Genetics. 12 [DOI] 10.3389/fgene.2021.700371. [PMID] 34484296.
2021
IAV-CNN: a 2D convolutional neural network model to predict antigenic variants of influenza A virus
IEEE/ACM Transactions on Computational Biology and Bioinformatics. 1-1 [DOI] 10.1109/tcbb.2021.3108971.
2021
Joint Analysis of Genome-Wide Association Data Reveals No Genetic Correlations Between Low Back Pain and Neurodegenerative Diseases
Frontiers in Genetics. 12 [DOI] 10.3389/fgene.2021.744299. [PMID] 34630533.
2021
VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments 
Bioinformatics. 37(6):737-743 [DOI] 10.1093/bioinformatics/btaa901.
2020
DL-CRISPR: A Deep Learning Method for Off-Target Activity Prediction in CRISPR/Cas9 With Data Augmentation
IEEE Access. 8:76610-76617 [DOI] 10.1109/access.2020.2989454.
2020
HopPER: an adaptive model for probability estimation of influenza reassortment through host prediction
BMC Medical Genomics. 13(1) [DOI] 10.1186/s12920-019-0656-7. [PMID] 31973709.
2020
Tempel: time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks
Bioinformatics. 36(9):2697-2704 [DOI] 10.1093/bioinformatics/btaa050.
2020
Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks
Journal of Bioinformatics and Computational Biology. 18(01) [DOI] 10.1142/s0219720020400028.
2019
An Encoding Scheme Capturing Generic Priors and Properties of Amino Acids Improves Protein Classification
IEEE Access. 7:7348-7356 [DOI] 10.1109/access.2018.2890096.
2019
Ensemble Prediction of Synergistic Drug Combinations Incorporating Biological, Chemical, Pharmacological, and Network Knowledge
IEEE Journal of Biomedical and Health Informatics. 23(3):1336-1345 [DOI] 10.1109/jbhi.2018.2852274.
2018
A context-free encoding scheme of protein sequences for predicting antigenicity of diverse influenza A viruses
BMC Genomics. 19(S10) [DOI] 10.1186/s12864-018-5282-9. [PMID] 30598102.
2018
Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses
BMC Genomics. 19(S2) [DOI] 10.1186/s12864-018-4461-z. [PMID] 29764421.
2018
Computational identification of physicochemical signatures for host tropism of influenza A virus
Journal of Bioinformatics and Computational Biology. 16(06) [DOI] 10.1142/s0219720018400231.
2018
Inference of Sequence Homology by BLAST visualization of Influenza Genome set
Proceedings of the 9th International Conference on Computational Systems-Biology and Bioinformatics. [DOI] 10.1145/3291757.3291769.
2018
Predicting antigenic variants of H1N1 influenza virus based on epidemics and pandemics using a stacking model
PLOS ONE. 13(12) [DOI] 10.1371/journal.pone.0207777. [PMID] 30576319.
2017
Identification of Potential Critical Virulent Sites Based on Hemagglutinin of Influenza a Virus in Past Pandemic Strains
Proceedings of the 6th International Conference on Bioinformatics and Biomedical Science. [DOI] 10.1145/3121138.3121166.
2017
Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics. [DOI] 10.1145/3107411.3107479.
ViPal: A Framework for Virulence Prediction of Influenza Viruses with Prior Viral Knowledge Using Genomic Sequences
. [DOI] 10.1101/2022.03.24.485635.

Grants

Sep 2022 ACTIVE
UF HEALTH CANCER CENTER PILOT PROJECTS GRANTS FUNDED THROUGHTHE FLORIDA CONSORTIUM OF NATIONAL CANCER INSTITUTE CENTER
Role: Project Manager
Funding: UF HEALTH SHANDS HOSPITAL

Education

Postdoc
2022 · Harvard Medical School
Ph.D.
2020 · Nanyang Technological University
Master
2015 · Central South University
Bachelor
2013 · Shandong University

Contact Details

Emails:
Business:
ruiyin@ufl.edu
Addresses:
Business Mailing:
PO Box 100147
Gainesville FL 32610
Business Street:
1889 Museum Rd, Suite 7000
GAINESVILLE FL 32611