Shankai Yan

According to our database, Shankai Yan authored at least 32 papers between 2017 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome.

Buchao Zhan, Dongmei He, Xin Yang, Zilong Zhang, Shankai Yan

IEEE Trans. Comput. Biol. Bioinform., 2026

DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model.

Jinwei Wang, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Zilong Zhang, Qingchen Zhang, Quan Zou, Feifei Cui

IEEE Trans. Comput. Biol. Bioinform., 2026

Het2Gene: a phenotype-driven model for gene prioritization by heterogeneous graph embedding.

Buchao Zhan, Xin Yang, Dongmei He, Zilong Zhang, Feifei Cui, Qingchen Zhang, Shankai Yan

Comput. Biol. Medicine, 2026

Consensus-on-Graph: Plan-Driven Exploration and Consensus Decision-Making on Knowledge Graphs.

Chengye Hu, Buchao Zhan, Li Yuan, Wenqi Fan, Shankai Yan

Proceedings of the Database Systems for Advanced Applications, 2026

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

BMC Bioinform., December, 2025

m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites.

Xinyu Li, Zhenjie Luo, Jingwei Lv, Chao Yang, Shankai Yan, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Feifei Cui

J. Chem. Inf. Model., 2025

PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model.

Ruiqi Liu, Shankai Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Qingchen Zhang, Leyi Wei, Quan Zou, Feifei Cui

Comput. Biol. Chem., 2025

scCAVAE: Modeling Synergistic Interactions in Perturbation Responses via Attention and Hierarchical Supervised Contrastive Learning.

Xin Li, Buchao Zhan, Jiangbo Zhang, Shankai Yan

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2025

2024

MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm.

Zhe Liu, Hiu-Man Wong, Xingjian Chen, Jiecong Lin, Shixiong Zhang, Shankai Yan, Fuzhou Wang, Xiangtao Li, Ka-Chun Wong

Comput. Biol. Medicine, January, 2024

Food Named Entity Recognition with BERT and Adversarial Training.

Siqi Dong, Buchao Zhan, Shankai Yan

Proceedings of the 7th International Conference on Machine Learning and Natural Language Processing, 2024

BiCalBERT: An Efficient Transformer-based Model for Chinese Question Answering.

Yanbo Han, Buchao Zhan, Bin Zhang, Chao Zhao, Shankai Yan

Proceedings of the 2024 8th International Conference on Intelligent Systems, 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

Proceedings of the Neural Information Processing - 31st International Conference, 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

Proceedings of the 2024 16th International Conference on Machine Learning and Computing, 2024

Attention-aware Rare Disease Diagnosis via Graph Attention Neural Network.

Xin Yang, Dongmei He, Buchao Zhan, Qingchen Zhang, Shankai Yan

Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics, 2024

BMPCD: A Pan-Cancer Detection Method Base on Learning Cross-Domain Feature.

Dongmei He, Xin Yang, Zilong Zhang, Feifei Cui, Shankai Yan

Proceedings of the 2024 8th International Conference on Computational Biology and Bioinformatics, 2024

RARoK: Retrieval-Augmented Reasoning on Knowledge for Medical Question Answering.

Buchao Zhan, Anqi Li, Xin Yang, Dongmei He, Yucong Duan, Shankai Yan

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2024

Augmented Mycobiome-Based Cancer Detection by an Interpretable Large Model.

Dongmei He, Xin Yang, Buchao Zhan, Zilong Zhang, Qingchen Zhang, Shankai Yan

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2024

2023

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

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology.

Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu

J. Biomed. Informatics, 2022

PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles.

Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu

Proceedings of the AMIA 2022, 2022

2021

Future DNA computing device and accompanied tool stack: Towards high-throughput computation.

Shankai Yan, Ka-Chun Wong

Future Gener. Comput. Syst., 2021

PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology.

Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu

Bioinform., 2021

Feature Selection and Feature Extraction: Highlights.

Hiu-Man Wong, Xingjian Chen, Hiu-Hin Tam, Jiecong Lin, Shixiong Zhang, Shankai Yan, Xiangtao Li, Ka-Chun Wong

Proceedings of the ISMSI 2021: 2021 5th International Conference on Intelligent Systems, 2021

2020

GESgnExt: Gene Expression Signature Extraction and Meta-Analysis on Gene Expression Omnibus.

Shankai Yan, Ka-Chun Wong

IEEE J. Biomed. Health Informatics, 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

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.

Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu

PLoS Comput. Biol., 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

Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP).

Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu

CoRR, 2020

Context awareness and embedding for biomedical event extraction.

Shankai Yan, Ka-Chun Wong

Bioinform., 2020

2019

DNA Sequencing Technologies: Sequencing Data Protocols and Bioinformatics Tools.

Ka-Chun Wong, Jiao Zhang, Shankai Yan, Xiangtao Li, Qiuzhen Lin, Sam Kwong, Cheng Liang

ACM Comput. Surv., 2019

Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets.

Yifan Peng, Shankai Yan, Zhiyong Lu

Proceedings of the 18th BioNLP Workshop and Shared Task, 2019

2017

Elucidating high-dimensional cancer hallmark annotation via enriched ontology.

Shankai Yan, Ka-Chun Wong

J. Biomed. Informatics, 2017