Elucidating high-dimensional cancer hallmark annotation via enriched ontology. - Shankai Yan; Ka-Chun Wong (J. Biomed. Informatics, 2017)

Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. - Yifan Peng 002; Shankai Yan; Zhiyong Lu (BioNLP@ACL, 2019)

DNA Sequencing Technologies: Sequencing Data Protocols and Bioinformatics Tools. - Ka-Chun Wong; Jiao Zhang 003; Shankai Yan; Xiangtao Li; Qiuzhen Lin; Sam Kwong; Cheng Liang 001 (ACM Comput. Surv., 2019)

Context awareness and embedding for biomedical event extraction. - Shankai Yan; Ka-Chun Wong (Bioinform., 2020)

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). - Qingyu Chen 001; Robert Leaman; Alexis Allot; Ling Luo 001; Chih-Hsuan Wei; Shankai Yan; Zhiyong Lu (CoRR, 2020)

Verbal aggression detection on Twitter comments: convolutional neural network for short-text sentiment analysis. - Junyi Chen; Shankai Yan; Ka-Chun Wong (Neural Comput. Appl., 2020)

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. - Qingyu Chen 001; Kyubum Lee; Shankai Yan; Sun Kim; Chih-Hsuan Wei; Zhiyong Lu (PLoS Comput. Biol., 2020)

Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors. - Ka-Chun Wong; Shankai Yan; Qiuzhen Lin; Xiangtao Li; Chengbin Peng (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

GESgnExt: Gene Expression Signature Extraction and Meta-Analysis on Gene Expression Omnibus. - Shankai Yan; Ka-Chun Wong (IEEE J. Biomed. Health Informatics, 2020)

Feature Selection and Feature Extraction: Highlights. - Hiu-Man Wong; Xingjian Chen; Hiu-Hin Tam; Jiecong Lin; Shixiong Zhang 002; Shankai Yan; Xiangtao Li; Ka-Chun Wong (ISMSI, 2021)

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. - Ling Luo 001; Shankai Yan; Po-Ting Lai; Daniel Veltri; Andrew J. Oler; Sandhya Xirasagar; Rajarshi Ghosh; Morgan Similuk; Peter N. Robinson; Zhiyong Lu (Bioinform., 2021)

Future DNA computing device and accompanied tool stack: Towards high-throughput computation. - Shankai Yan; Ka-Chun Wong (Future Gener. Comput. Syst., 2021)

PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. - Shankai Yan; Ling Luo 001; Li Fang; Daniel Veltri; Andrew J. Oler; Rajarshi Ghosh; Chih-Hsuan Wei; Morgan Similuk; Kai Wang; Zhiyong Lu (AMIA, 2022)

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. - Shankai Yan; Ling Luo 001; Po-Ting Lai; Daniel Veltri; Andrew J. Oler; Sandhya Xirasagar; Rajarshi Ghosh; Morgan Similuk; Peter N. Robinson; Zhiyong Lu (J. Biomed. Informatics, 2022)

AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies. - Ruiqi Liu; Zilong Zhang; Xiuhao Fu; Shankai Yan; Feifei Cui (BIBM, 2023)

Augmented Mycobiome-Based Cancer Detection by an Interpretable Large Model. - Dongmei He; Xin Yang; Buchao Zhan; Zilong Zhang; Qingchen Zhang 001; Shankai Yan (BIBM, 2024)

RARoK: Retrieval-Augmented Reasoning on Knowledge for Medical Question Answering. - Buchao Zhan; Anqi Li; Xin Yang; Dongmei He; Yucong Duan; Shankai Yan (BIBM, 2024)

BMPCD: A Pan-Cancer Detection Method Base on Learning Cross-Domain Feature. - Dongmei He; Xin Yang; Zilong Zhang; Feifei Cui; Shankai Yan (ICCBB, 2024)

Attention-aware Rare Disease Diagnosis via Graph Attention Neural Network. - Xin Yang; Dongmei He; Buchao Zhan; Qingchen Zhang 001; Shankai Yan (ICCBB, 2024)

Backbone Feature Hierarchy Selection Strategy and Verification in Small Object Detection. - Bin Zhang; Meizhen Luo; Shankai Yan; Juan Hu; Ling Peng; Liangshun Wu; Yujuan Wang (ICMLC, 2024)

Text2SPARQL: Grammar Pre-training for Text-to-QDMR Semantic Parsers from Intermediate Question Decompositions. - Buchao Zhan; Yucong Duan; Xin Yang; Dongmei He; Shankai Yan (ICONIP (9), 2024)

Food Named Entity Recognition with BERT and Adversarial Training. - Siqi Dong; Buchao Zhan; Shankai Yan (MLNLP, 2024)

MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm. - Zhe Liu; Hiu-Man Wong; Xingjian Chen; Jiecong Lin; Shixiong Zhang 002; Shankai Yan; Fuzhou Wang; Xiangtao Li; Ka-Chun Wong (Comput. Biol. Medicine, 2024)

PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. - Ruiqi Liu; Shankai Yan; Zilong Zhang; Junlin Xu; Yajie Meng; Qingchen Zhang 001; Leyi Wei; Quan Zou 001; Feifei Cui (Comput. Biol. Chem., 2025)

RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction. - Jiangbo Zhang; Yunhui Peng; Feifei Cui; Zilong Zhang; Shankai Yan; Qingchen Zhang 001 (BMC Bioinform., 2025)