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ORCIDShankai Yan
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2020 – today
- 2026
[j17]Buchao Zhan
, Xin Yang, Dongmei He, Zilong Zhang, Feifei Cui, Qingchen Zhang, Shankai Yan:
Het2Gene: a phenotype-driven model for gene prioritization by heterogeneous graph embedding. Comput. Biol. Medicine 205: 111543 (2026)- [j16]Buchao Zhan, Dongmei He, Xin Yang, Zilong Zhang, Shankai Yan:
FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome. IEEE Trans. Comput. Biol. Bioinform. 23(1): 247-258 (2026) - [j15]Jinwei Wang, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Zilong Zhang, Qingchen Zhang, Quan Zou, Feifei Cui:
DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model. IEEE Trans. Comput. Biol. Bioinform. 23(1): 326-340 (2026) - [c14]Chengye Hu, Buchao Zhan, Li Yuan, Wenqi Fan, Shankai Yan:
Consensus-on-Graph: Plan-Driven Exploration and Consensus Decision-Making on Knowledge Graphs. DASFAA (3) 2026: 508-523 - 2025
- [j14]Jiangbo Zhang, Yunhui Peng, Feifei Cui, Zilong Zhang, Shankai Yan, Qingchen Zhang:
RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction. BMC Bioinform. 26(1): 176 (2025) - [j13]Ruiqi Liu, Shankai Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Qingchen Zhang, Leyi Wei, Quan Zou, Feifei Cui:
PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. Comput. Biol. Chem. 118: 108448 (2025) - [j12]Xinyu Li, Zhenjie Luo, Jingwei Lv, Chao Yang, Shankai Yan, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Feifei Cui:
m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites. J. Chem. Inf. Model. 65(15): 8079-8096 (2025) - [c13]Xin Li, Buchao Zhan, Jiangbo Zhang, Shankai Yan:
scCAVAE: Modeling Synergistic Interactions in Perturbation Responses via Attention and Hierarchical Supervised Contrastive Learning. BIBM 2025: 1070-1075 - 2024
- [j11]Zhe Liu, Hiu-Man Wong, Xingjian Chen, Jiecong Lin, Shixiong Zhang, Shankai Yan, Fuzhou Wang, Xiangtao Li, Ka-Chun Wong:
MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm. Comput. Biol. Medicine 168: 107753 (2024) - [c12]Dongmei He, Xin Yang, Buchao Zhan, Zilong Zhang, Qingchen Zhang, Shankai Yan:
Augmented Mycobiome-Based Cancer Detection by an Interpretable Large Model. BIBM 2024: 925-931 - [c11]Buchao Zhan, Anqi Li, Xin Yang, Dongmei He, Yucong Duan, Shankai Yan:
RARoK: Retrieval-Augmented Reasoning on Knowledge for Medical Question Answering. BIBM 2024: 2837-2843 - [c10]Dongmei He, Xin Yang, Zilong Zhang, Feifei Cui, Shankai Yan:
BMPCD: A Pan-Cancer Detection Method Base on Learning Cross-Domain Feature. ICCBB 2024: 126-130 - [c9]Xin Yang, Dongmei He, Buchao Zhan, Qingchen Zhang, Shankai Yan:
Attention-aware Rare Disease Diagnosis via Graph Attention Neural Network. ICCBB 2024: 151-156 - [c8]Bin Zhang, Meizhen Luo, Shankai Yan, Juan Hu, Ling Peng, Liangshun Wu, Yujuan Wang:
Backbone Feature Hierarchy Selection Strategy and Verification in Small Object Detection. ICMLC 2024: 304-310 - [c7]Buchao Zhan, Yucong Duan, Xin Yang, Dongmei He, Shankai Yan:
Text2SPARQL: Grammar Pre-training for Text-to-QDMR Semantic Parsers from Intermediate Question Decompositions. ICONIP (9) 2024: 123-137 - [c6]Yanbo Han, Buchao Zhan, Bin Zhang, Chao Zhao, Shankai Yan:
BiCalBERT: An Efficient Transformer-based Model for Chinese Question Answering. ISMSI 2024: 100-104 - [c5]Siqi Dong, Buchao Zhan, Shankai Yan:
Food Named Entity Recognition with BERT and Adversarial Training. MLNLP 2024: 1-6 - 2023
- [c4]Ruiqi Liu, Zilong Zhang, Xiuhao Fu, Shankai Yan, Feifei Cui:
AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies. BIBM 2023: 23-29 - 2022
- [j10]Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu:
PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. J. Biomed. Informatics 129: 104059 (2022) - [c3]Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu:
PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. AMIA 2022 - 2021
- [j9]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. Bioinform. 37(13): 1884-1890 (2021) - [j8]Shankai Yan, Ka-Chun Wong:
Future DNA computing device and accompanied tool stack: Towards high-throughput computation. Future Gener. Comput. Syst. 117: 111-124 (2021) - [c2]Hiu-Man Wong, Xingjian Chen, Hiu-Hin Tam, Jiecong Lin, Shixiong Zhang, Shankai Yan, Xiangtao Li, Ka-Chun Wong:
Feature Selection and Feature Extraction: Highlights. ISMSI 2021: 49-53 - 2020
- [j7]Shankai Yan, Ka-Chun Wong:
Context awareness and embedding for biomedical event extraction. Bioinform. 36(2): 637-643 (2020) - [j6]Junyi Chen, Shankai Yan, Ka-Chun Wong:
Verbal aggression detection on Twitter comments: convolutional neural network for short-text sentiment analysis. Neural Comput. Appl. 32(15): 10809-10818 (2020) - [j5]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. 16(4) (2020) - [j4]Ka-Chun Wong, Shankai Yan, Qiuzhen Lin, Xiangtao Li, Chengbin Peng:
Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors. IEEE ACM Trans. Comput. Biol. Bioinform. 17(1): 327-333 (2020) - [j3]Shankai Yan, Ka-Chun Wong:
GESgnExt: Gene Expression Signature Extraction and Meta-Analysis on Gene Expression Omnibus. IEEE J. Biomed. Health Informatics 24(1): 311-318 (2020) - [i5]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. CoRR abs/2009.08478 (2020) - [i4]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). CoRR abs/2010.16413 (2020)
2010 – 2019
- 2019
- [j2]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 Comput. Surv. 52(5): 98:1-98:30 (2019) - [c1]Yifan Peng, Shankai Yan, Zhiyong Lu:
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. BioNLP@ACL 2019: 58-65 - [i3]Shankai Yan, Ka-Chun Wong:
Context awareness and embedding for biomedical event extraction. CoRR abs/1905.00982 (2019) - [i2]Yifan Peng, Shankai Yan, Zhiyong Lu:
Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. CoRR abs/1906.05474 (2019) - [i1]Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu:
BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR abs/1912.10846 (2019) - 2017
- [j1]Shankai Yan, Ka-Chun Wong:
Elucidating high-dimensional cancer hallmark annotation via enriched ontology. J. Biomed. Informatics 73: 84-94 (2017)
Coauthor Index
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