[1] Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, and Zhiyong Lu*. PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. AMIA 2022 Annual Symposium, Nov. 2022

[2] Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N Robinson, and Zhiyong Lu*. PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. Journal of Biomedical Informatics (SCI, IF=6.317, 中科院大类三区小类三区), Vol. 129, PP. 104059, May. 2022

[3] Shankai Yan and Ka-Chun WONG*. Future DNA Computing Device and Accompanied Tool Stack: Towards Highthroughput Computation. Future Generation Computer Systems (SCI, IF=7.187, 中科院大类二区小类二区), Vol. 117, PP. 111-124, Nov. 2020

[4] Shankai Yan and Ka-Chun WONG*. Context awareness and embedding for biomedical event extraction. Oxford Bioinformatics (SCI, IF=6.937, 中科院大类二区小类一区), Vol. 36-2, PP. 637-643, Aug. 2019

[5] Shankai Yan and Ka-Chun WONG*. GESgnExt: Gene Expression Signature Extraction and Meta-analysis on Gene Expression Omnibus. IEEE Journal of Biomedical and Health Informatics (SCI, IF=5.223, 中科院大类二区小类一区), Vol. 24-1, PP. 311-318, Jan. 2019

[6] Shankai Yan and Ka-Chun WONG*. Elucidating high-dimensional cancer hallmark annotation via enriched ontology. Journal of Biomedical Informatics (SCI, IF=6.317, 中科院大类三区小类三区), Vol. 73, PP. 84-94, Sep. 2017

[7] Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N Robinson, Zhiyong Lu*. PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology. Oxford Bioinformatics (SCI, IF=6.937, 中科院大类二区小类一区), Vol. 37-13, PP. 1884-1890, Jan. 2021

[8] Yifan Peng, Shankai Yan and Zhiyong Lu*. Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. ACL BioNLP Workshop (Highly Cited) 2019

[9] Ka-Chun WONG*, Shankai Yan, Qiuzhen Lin, Xiangtao Li and Chengbin Peng. Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors. IEEE/ACM Transactions on Computational Biology and Bioinformatics (SCI, IF=3.71, 中科院大类三区小类二区), Vol. 17-1, PP. 327-333, Nov. 2018

[10] Junyi Chen, Shankai Yan and Ka-Chun WONG*. Verbal aggression detection on Twitter comments: convolutional neural network for short-text sentiment analysis. Neural Computing and Applications (SCI, IF=5.858, 中科院大类二区小类二区), PP. 1-10, 2018

[11] Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu*. Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). Annual Review of Biomedical Data Science (SCI), Vol. 4, PP. 313-339, Jan. 2021

[12] Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, and Zhiyong Lu*. BioConceptVec: creating and evaluating literature based biomedical concept embeddings on a large scale. PLOS Computational Biology (SCI, IF=4.428, 中科院大类二区小类二区), Vol. 16-4, Apr. 2020

[13] Ka-Chun WONG*, Junyi Chen, Jiao Zhang, Jiecong Lin, Shankai Yan, Shxiong Zhang, Xiangtao Li, Cheng Liang, Chengbin Peng, Qiuzhen Lin, Sam KWONG, Jun Yu. Early cancer detection from multianalyte blood test results. iScience (SCI, IF=5.458, 中科院大类二区小类二区), Vol. 15, PP. 332-341, May. 2019

[14] Ka-Chun WONG*, Jiao Zhang, Shankai Yan, Xiangtao Li, Qiuzhen Lin, Sam KWONG, Cheng Liang. DNA Sequencing Technologies: Sequencing Data Protocols and Bioinformatics Tools. ACM Computing Surveys (SCI, IF=7.990, 中科院大类二区小类二区), Vol. 52-5, PP. 1-30, Sep. 2017

[15] Ka-Chun WONG*, Chengbin Peng, Shankai Yan and Cheng Liang. Probabilistic Inference on Multiple Normalized Genome-Wide Signal Profiles with Model Regularization. IEEE transactions on nano bioscience (SCI, IF=2.791, 中科院大类二区小类二区), Vol. 16(1), PP. 43-50, Jan. 2017

[16] Junyi Chen, Shankai Yan and Ka-Chun WONG. Aggressivity Detection on Social Network Comments. Proceedings of the 2017 International Conference on Intelligent Systems, Metaheuristics & Swarm Intelligence (EI), PP. 103–107, March 2017