Shankai Yan - RankMe

35 papers Misc 2Journal 22Unranked 11

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	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. Jinwei Wang, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Zilong Zhang, Qingchen Zhang, Quan Zou, Feifei Cui
2026	J	`jnl`	FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome. IEEE Trans. Comput. Biol. Bioinform. Buchao Zhan, Dongmei He, Xin Yang, Zilong Zhang, Shankai Yan
2026	J	`jnl`	Het2Gene: a phenotype-driven model for gene prioritization by heterogeneous graph embedding. Comput. Biol. Medicine Buchao Zhan, Xin Yang, Dongmei He, Zilong Zhang, Feifei Cui, Qingchen Zhang, Shankai Yan
2025	J	`jnl`	PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. Comput. Biol. Chem. Ruiqi Liu, Shankai Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Qingchen Zhang, Leyi Wei, Quan Zou, Feifei Cui
2025	J	`jnl`	RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction. BMC Bioinform. Jiangbo Zhang, Yunhui Peng, Feifei Cui, Zilong Zhang, Shankai Yan, Qingchen Zhang
2025	J	`jnl`	m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites. J. Chem. Inf. Model. Xinyu Li, Zhenjie Luo, Jingwei Lv, Chao Yang, Shankai Yan, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Feifei Cui
2025	—	`conf`	scCAVAE: Modeling Synergistic Interactions in Perturbation Responses via Attention and Hierarchical Supervised Contrastive Learning. BIBM Xin Li, Buchao Zhan, Jiangbo Zhang, Shankai Yan
2024	—	`conf`	Attention-aware Rare Disease Diagnosis via Graph Attention Neural Network. ICCBB Xin Yang, Dongmei He, Buchao Zhan, Qingchen Zhang, Shankai Yan
2024	—	`conf`	Augmented Mycobiome-Based Cancer Detection by an Interpretable Large Model. BIBM Dongmei He, Xin Yang, Buchao Zhan, Zilong Zhang, Qingchen Zhang, Shankai Yan
2024	—	`conf`	BMPCD: A Pan-Cancer Detection Method Base on Learning Cross-Domain Feature. ICCBB Dongmei He, Xin Yang, Zilong Zhang, Feifei Cui, Shankai Yan
2024	Misc	`conf`	Backbone Feature Hierarchy Selection Strategy and Verification in Small Object Detection. ICMLC Bin Zhang, Meizhen Luo, Shankai Yan, Juan Hu, Ling Peng, Liangshun Wu, Yujuan Wang
2024	—	`conf`	BiCalBERT: An Efficient Transformer-based Model for Chinese Question Answering. ISMSI Yanbo Han, Buchao Zhan, Bin Zhang, Chao Zhao, Shankai Yan
2024	—	`conf`	Food Named Entity Recognition with BERT and Adversarial Training. MLNLP Siqi Dong, Buchao Zhan, Shankai Yan
2024	J	`jnl`	MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm. Comput. Biol. Medicine Zhe Liu, Hiu-Man Wong, Xingjian Chen, Jiecong Lin, Shixiong Zhang, Shankai Yan, Fuzhou Wang, Xiangtao Li, Ka-Chun Wong
2024	—	`conf`	RARoK: Retrieval-Augmented Reasoning on Knowledge for Medical Question Answering. BIBM Buchao Zhan, Anqi Li, Xin Yang, Dongmei He, Yucong Duan, Shankai Yan
2024	—	`conf`	Text2SPARQL: Grammar Pre-training for Text-to-QDMR Semantic Parsers from Intermediate Question Decompositions. ICONIP (9) Buchao Zhan, Yucong Duan, Xin Yang, Dongmei He, Shankai Yan
2023	—	`conf`	AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies. BIBM Ruiqi Liu, Zilong Zhang, Xiuhao Fu, Shankai Yan, Feifei Cui
2022	Misc	`conf`	PhenoGene: Disease-gene prioritization using graph embedding on patient phenotypic profiles. AMIA Shankai Yan, Ling Luo, Li Fang, Daniel Veltri, Andrew J. Oler, Rajarshi Ghosh, Chih-Hsuan Wei, Morgan Similuk, Kai Wang, Zhiyong Lu
2022	J	`jnl`	PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. J. Biomed. Informatics Shankai Yan, Ling Luo, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
2021	—	`conf`	Feature Selection and Feature Extraction: Highlights. ISMSI Hiu-Man Wong, Xingjian Chen, Hiu-Hin Tam, Jiecong Lin, Shixiong Zhang, Shankai Yan, Xiangtao Li, Ka-Chun Wong
2021	J	`jnl`	Future DNA computing device and accompanied tool stack: Towards high-throughput computation. Future Gener. Comput. Syst. Shankai Yan, Ka-Chun Wong
2021	J	`jnl`	PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology. Bioinform. Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
2020	J	`jnl`	Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP). CoRR Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2020	J	`jnl`	BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale. PLoS Comput. Biol. Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2020	J	`jnl`	Context awareness and embedding for biomedical event extraction. Bioinform. Shankai Yan, Ka-Chun Wong
2020	J	`jnl`	Deleterious Non-Synonymous Single Nucleotide Polymorphism Predictions on Human Transcription Factors. IEEE ACM Trans. Comput. Biol. Bioinform. Ka-Chun Wong, Shankai Yan, Qiuzhen Lin, Xiangtao Li, Chengbin Peng
2020	J	`jnl`	GESgnExt: Gene Expression Signature Extraction and Meta-Analysis on Gene Expression Omnibus. IEEE J. Biomed. Health Informatics Shankai Yan, Ka-Chun Wong
2020	J	`jnl`	PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology. CoRR Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew J. Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N. Robinson, Zhiyong Lu
2020	J	`jnl`	Verbal aggression detection on Twitter comments: convolutional neural network for short-text sentiment analysis. Neural Comput. Appl. Junyi Chen, Shankai Yan, Ka-Chun Wong
2019	J	`jnl`	BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale. CoRR Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu
2019	J	`jnl`	Context awareness and embedding for biomedical event extraction. CoRR Shankai Yan, Ka-Chun Wong
2019	J	`jnl`	DNA Sequencing Technologies: Sequencing Data Protocols and Bioinformatics Tools. ACM Comput. Surv. Ka-Chun Wong, Jiao Zhang, Shankai Yan, Xiangtao Li, Qiuzhen Lin, Sam Kwong, Cheng Liang
2019	—	`conf`	Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. BioNLP@ACL Yifan Peng, Shankai Yan, Zhiyong Lu
2019	J	`jnl`	Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets. CoRR Yifan Peng, Shankai Yan, Zhiyong Lu
2017	J	`jnl`	Elucidating high-dimensional cancer hallmark annotation via enriched ontology. J. Biomed. Informatics Shankai Yan, Ka-Chun Wong