[1] Chengye Hu, Buchao Zhan, Li Yuan, Wenqi Fan, and Shankai Yan*. Consensus-on-Graph: Plan-Driven Exploration and Consensus Decision-Making on Knowledge Graphs. 31st International Conference on Database Systems for Advanced Applications (DASFAA), Apr. 2026 (CCF-B)

[2] Xin Li, Buchao Zhan, Jiangbo Zhang, and Shankai Yan*. scCAVAE: Predicting Perturbation Responses by Modeling Synergistic Interactions with Attention and Hierarchical Supervised Contrastive Learning. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Dec. 2025 (CCF-B)

[3] Buchao Zhan, Dongmei He, Xin Yang, Zilong Zhang, and Shankai Yan*. FNatPred: a data-driven approach for distinguishing between NAT and Tumor on the fungal microbiome. IEEE/ACM Transactions on Computational Biology and Bioinformatics. (SCI, IF=3.4, CCF-B), Vol. 23, PP. 247-258, Dec. 2025

[4] Jiangbo Zhang, Yunhui Peng, Feifei Cui, Zilong Zhang, Shankai Yan*, and Qingchen Zhang*. RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein. BMC Bioinformatics, Vol. 26, PP. 176, Jul. 2025

[5] Buchao Zhan, Anqi Li, Xin Yang, Dongmei He, Yucong Duan, and Shankai Yan*. RARoK:Retrieval-Augmented Reasoning on Knowledge for Medical Question Answering. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Dec. 2024 (CCF-B)

[6] Dongmei He, Xin Yang, Buchao Zhan, Zilong Zhang, Qingchen Zhang, and Shankai Yan*. Augmented Mycobiome-Based Cancer Detection by an Interpretable Large Model. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Dec. 2024 (CCF-B)

[7] Buchao Zhan, Yucong Duan, Xin Yang, Dongmei He, and Shankai Yan*. Text2SPARQL: Grammar Pre-training for Text-to-QDMR Semantic Parsers from Intermediate Question Decompositions. International Conference on Neural Information Processing (ICONIP), Dec. 2024 (CCF-C)

[8] 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 (CCF-C, Qualis-A2), Nov. 2022

[9] 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

[10] 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

[11] Shankai Yan and Ka-Chun WONG*. Context awareness and embedding for biomedical event extraction. Oxford Bioinformatics (SCI, IF=6.937, 中科院大类三区小类三区), Vol. 36-2, PP. 637-643, Aug. 2019

[12] 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

[13] 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

[14] Zhe Liu, Hiu-Man Wong, Xingjian Chen, Jiecong Lin, Shixiong Zhang, Shankai Yan, Fuzhou Wang, Xiangtao Li, Ka-Chun Wong*. (2023). MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm. Computers in Biology and Medicine (SCI, IF=7, 中科院大类二区小类一区), Vol. 168, PP. 107753, Jan. 2024

[15] 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

[16] 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

[17] 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

[18] 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

[19] 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

[20] 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

[21] 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

[22] 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

[23] 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

[24] Xin Yang, Dongmei He, Buchao Zhan, Zilong Zhang, Feifei Cui, Qingchen Zhang, and Shankai Yan*. Attention-aware rare disease diagnosis via Graph Attention Neural Network. ICCBB 2024 (EI)

[25] Dongmei He, Xin Yang, Zilong Zhang, Feifei Cui, Qingchen Zhang, and Shankai Yan*, BMPCD: A Pan-Cancer Detection Method Base on Learning Cross-Domain Feature. ICCBB 2024 (EI)

[26] Siqi Dong, Buchao Zhan and Shankai Yan*. Food Named Entity Recognition with BERT and Adversarial Training. MLNLP 2024 (EI)

[27] Yuchen Ma, Buchao Zhan, Jianhua Yu and Shankai Yan*. SACMR: Sentiment Analysis in Chinese Language using Modified RoBERTa. ICCIA 2024 (EI)

[28] Buchao Zhan, Yucong Duan and Shankai Yan*. IC-BERT: An Instruction Classifier Model Alleviates the Hallucination of Large Language Models in Traditional Chinese Medicine. ICCIA 2024 (EI)

[29] Yanbo Han, Buchao Zhan, Bin Zhang, Chao Zhao and Shankai Yan*.  BiCalBERT: An Efficient Transformer-based Model for Chinese Question Answering. Proceedings of the 2024 International Conference on Intelligent Systems, Metaheuristics & Swarm Intelligence (EI), PP. 100-104

[30] 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