Shanfeng Zhu

发表

TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules

Hau-San Wong, Shuigeng Zhou, Hiroshi Mamitsuka, 2012, PloS one.

Proceedings of the Twenty-Fifth International Joint Conference on Artificial Intelligence (IJCAI-16)

Samuel Kaski, Shanfeng Zhu, Makoto Yamada, 2016, IJCAI 2016.

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu, 2017, bioRxiv.

Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach

Jung-Hsien Chiang, Devin C. Koestler, Celine Vens, 2018, bioRxiv.

Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC

Fengzhu Sun, Jianfeng Feng, Shanfeng Zhu, 2018, PLoS genetics.

DREAM Community. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial

Stephen R. Piccolo, Suleiman A. Khan, Luke N. Kumar, 2016 .

Phen2Disease: A Phenotype-driven Semantic Similarity-based Integrated Model for Disease and Gene Prioritization

Shanfeng Zhu, W. Zhai, Xiaodi Huang, 2022, bioRxiv.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Michael W. Weiner, Robert C. Green, Yen-Jen Oyang, 2016, Alzheimer's & Dementia.

MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities

Fengzhu Sun, Shanfeng Zhu, R. You, 2021, bioRxiv.

SolidBin: improving metagenome binning with semi-supervised normalized cut

Zhengyang Wang, Shanfeng Zhu, Fengzhu Sun, 2019, Bioinform..

A Robust Convex Formulation for Ensemble Clustering

Samuel Kaski, Makoto Yamada, Hiroshi Mamitsuka, 2016, IJCAI.

Enhanced clustering of biomedical documents using ensemble non-negative matrix factorization

Wei Yuan, Fei Wang, Xiaodi Huang, 2011, Inf. Sci..

Quasispecies pattern of hepatitis B virus predicts hepatocellular carcinoma using deep-sequencing and machine learning.

Yong Duan, Shanfeng Zhu, Xianzhang Huang, 2020, The Journal of infectious diseases.

Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma

Jianfeng Feng, D. Wong, Shanfeng Zhu, 2022, Virology journal.

Next-generation sequencing revealed divergence in deletions of the preS region in the HBV genome between different HBV-related liver diseases.

Fengzhu Sun, Shanfeng Zhu, Chunfang Gao, 2017, The Journal of general virology.

Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and Medline

Hiroshi Mamitsuka, Yasushi Okuno, Gozoh Tsujimoto, 2006, Cancer informatics.

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules

John Sidney, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka, 2006, Bioinform..

Computational Methods for Prediction of Human Protein-Phenotype Associations: A Review

Lizhi Liu, Shanfeng Zhu, Shanfeng Zhu, 2021, Phenomics.

HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank

Xiaodi Huang, Lizhi Liu, Hiroshi Mamitsuka, 2020, Bioinform..

Towards accurate human promoter recognition: a review of currently used sequence features and classification methods

Hong Yan, Jia Zeng, Shanfeng Zhu, 2009, Briefings Bioinform..

Hao Ding, Ichigaku Takigawa, Hiroshi Mamitsuka, 2014, Briefings Bioinform..

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences

Ying Wang, Shanfeng Zhu, Fengzhu Sun, 2019, Briefings Bioinform..

Collaborative matrix factorization with multiple similarities for predicting drug-target interactions

Hao Ding, Hiroshi Mamitsuka, Shanfeng Zhu, 2013, KDD.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction

Hiroshi Mamitsuka, Ronghui You, Shuwei Yao, 2021, Bioinform..

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information

Shanfeng Zhu, Y. Xiong, R. You, 2021, Nucleic Acids Res..

NetGO: improving large-scale protein function prediction with massive network information

Hiroshi Mamitsuka, Shanfeng Zhu, Yi Xiong, 2018, bioRxiv.

GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank

Yi Xiong, Hiroshi Mamitsuka, Shanfeng Zhu, 2017, bioRxiv.

DeepText2Go: Improving large-scale protein function prediction with deep semantic text representation

Shanfeng Zhu, Ronghui You, Shanfeng Zhu, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation.

Xiaodi Huang, Shanfeng Zhu, Ronghui You, 2018, Methods.

Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools

Hiroshi Mamitsuka, Shanfeng Zhu, Keiko Udaka, 2011, Briefings Bioinform..

MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction

Shanfeng Zhu, Shanfeng Zhu, Linyuan Guo, 2013, BMC Genomics.

MetaMHC: a meta approach to predict peptides binding to MHC molecules

Hiroshi Mamitsuka, Shanfeng Zhu, Keiko Udaka, 2010, Nucleic Acids Res..

Machine learning competition in immunology - Prediction of HLA class I binding peptides.

Harris Papadopoulos, Tomer Hertz, Vladimir Brusic, 2011, Journal of immunological methods.

ICH-LR2S2: a new risk score for predicting stroke-associated pneumonia from spontaneous intracerebral hemorrhage

Jianfeng Feng, Yilong Wang, Yongjun Wang, 2022, Journal of translational medicine.

Towardmore accurate pan-specific MHC-peptide binding prediction : a review of current methods and tools

Hiroshi Mamitsuka, Lianming Zhang, Shanfeng Zhu, 2012 .

MHC2MIL: a novel multiple instance learning based method for MHC-II peptide binding prediction by considering peptide flanking region and residue positions

Xiaodi Huang, Mingjie Qian, Yichang Xu, 2014, BMC Genomics.

Ensemble approaches for improving HLA class I-peptide binding prediction.

Hiroshi Mamitsuka, Shanfeng Zhu, Xihao Hu, 2011, Journal of immunological methods.

MetaMHCpan, A Meta Approach for Pan-Specific MHC Peptide Binding Prediction.

Hiroshi Mamitsuka, Shanfeng Zhu, Cheng Luo, 2016, Methods in molecular biology.

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.

Yan Zhang, Xihao Hu, Shanfeng Zhu, 2009, Journal of genetics and genomics = Yi chuan xue bao.

Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer

Hiroshi Mamitsuka, Lei Xie, Shanfeng Zhu, 2022, Bioinformatics.

DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information

Xiaodi Huang, Tao Huang, Ronghui You, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network

Fengzhu Sun, X. Zhou, Shanfeng Zhu, 2021, NAR genomics and bioinformatics.

DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

Shi-Hua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu, 2016, Bioinform..

HPOAnnotator: improving large-scale prediction of HPO annotations by low-rank approximation with HPO semantic similarities and multiple PPI networks

Xiaodi Huang, Lizhi Liu, Hiroshi Mamitsuka, 2019, BMC Medical Genomics.

AiProAnnotator: Low-rank Approximation with network side information for high-performance, large-scale human Protein abnormality Annotator

Hiroshi Mamitsuka, Shanfeng Zhu, Junning Gao, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations

Hiroshi Mamitsuka, Shanfeng Zhu, Lizhi Liu, 2021, Bioinform..

Enhancing quantitative intra-day stock return prediction by integrating both market news and stock prices information

Xiaotie Deng, Xiaodi Huang, Xiaodong Li, 2014, Neurocomputing.

FullMeSH: improving large-scale MeSH indexing with full text

Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, 2019, Bioinform..

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu, 2016, Bioinform..

MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence

ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu, 2015, Bioinform..

A probabilistic model for mining implicit 'chemical compound-gene' relations from literature

Hiroshi Mamitsuka, Shanfeng Zhu, Yasushi Okuno, 2005, ECCB/JBI.

AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification

Hiroshi Mamitsuka, Shanfeng Zhu, R. You, 2018, NeurIPS.

Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints

Jun Gu, Jia Zeng, Wei Feng, 2013, IEEE Transactions on Cybernetics.

GrantExtractor: Accurate Grant Support Information Extraction from Biomedical Fulltext Based on Bi-LSTM-CRF

Xiaodi Huang, Shanfeng Zhu, Suyang Dai, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Improving Stock Market Prediction by Integrating Both Market News and Stock Prices

Chao Wang, Xiaotie Deng, Xiaodong Li, 2011, DEXA.

MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents

Jing Zhou, Xuhui Li, Hiroshi Mamitsuka, 2015, 2015 34th Chinese Control Conference (CCC).

MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents

Zhou Jing, Shui Yuxuan, Peng Shengwen, 2015, CCC 2015.

Field independent probabilistic model for clustering multi-field documents

Jia Zeng, Ichigaku Takigawa, Hiroshi Mamitsuka, 2009, Inf. Process. Manag..

BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text.

Hiroshi Mamitsuka, Shanfeng Zhu, Yuxuan Liu, 2020, Bioinformatics.

BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text

Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu, 2020, bioRxiv.

Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity

Jia Zeng, Hiroshi Mamitsuka, Shanfeng Zhu, 2009, Bioinform..

The Fudan-UIUC Participation in the BioASQ Challenge Task 2a: The Antinomyra system

ChengXiang Zhai, Shanfeng Zhu, Ke Liu, 2014, CLEF.

On computational complexity of membership test in flow games and linear production games

Xiaotie Deng, Qizhi Fang, Shanfeng Zhu, 2002, Int. J. Game Theory.

GoSum: Extractive Summarization of Long Documents by Reinforcement Learning and Graph Organized discourse state

Shanfeng Zhu, Junyi Bian, Xiaodi Huang, 2022, ArXiv.

SVR-PAIRWISE method to predict MHC-II binding peptides

Juan Liu, Shanfeng Zhu, Lian Wang, 2010, Int. J. Bioinform. Res. Appl..

Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules

Hiroshi Mamitsuka, Shanfeng Zhu, Xiaodi Huang, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Application of a new probabilistic model for mining implicit associated cancer genes from OMIM and medline.

Hiroshi Mamitsuka, G. Tsujimoto, Y. Okuno, 2007, Cancer Informatics.

VACmap: an accurate long-read aligner for unraveling complex structural variations

Shanfeng Zhu, Hongyu Ding, Zhirui Liao, 2023, bioRxiv.

Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model

Hiroshi Mamitsuka, Shanfeng Zhu, Yasushi Okuno, 2007, BMC Systems Biology.

Top-d Rank Aggregation in Web Meta-search Engine - (Extended Abstract)

Qizhi Fang, Shanfeng Zhu, Han Xiao, 2010, FAW.

MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing.

Hiroshi Mamitsuka, Shanfeng Zhu, Shengwen Peng, 2018, Methods in molecular biology.

BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model

Xiaodong Chen, Hiroshi Mamitsuka, Shanfeng Zhu, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Instance-Wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters

Hiroshi Mamitsuka, Shanfeng Zhu, Xiaodong Zheng, 2015, IJCAI.

AttentionXML: Extreme Multi-Label Text Classification with Multi-Label Attention Based Recurrent Neural Networks pdf

Hiroshi Mamitsuka, Shanfeng Zhu, Ronghui You, 2018, ArXiv.

Application of a New Probabilistic Model for Mining Implicit Associated Cancer Genes from OMIM and Medline

Hiroshi Mamitsuka, G. Tsujimoto, Y. Okuno, 2009 .

Protein language model powers accurate and fast sequence search for remote homology

Shanfeng Zhu, Y. Xiong, R. You, 2023, bioRxiv.

Multiconstrained gene clustering based on generalized projections Multiconstrained gene clustering based on generalized projections

Alan Wee-Chung Liew, Shanfeng Zhu, Jia Zeng, 2010 .

DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank.

Hiroshi Mamitsuka, Shanfeng Zhu, Qingjun Yuan, 2018, Methods in molecular biology.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Satrajit S. Ghosh, Genevera I. Allen, Taylor J. Maxwell, 2016, Alzheimer's & Dementia.

Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools

Hiroshi Mamitsuka, Lianming Zhang, Shanfeng Zhu, 2011, Briefings Bioinform..

Towards accurate human promoter recognition: a review of currently used sequence features and classification methods

Shanfeng Zhu, Hong Yan, Jia Zeng, 2009, Briefings Bioinform..

Quasispecies pattern of hepatitis B virus predicts hepatocellular carcinoma using deep-sequencing and machine learning.

Yong Duan, Shanfeng Zhu, Xianzhang Huang, 2020, The Journal of infectious diseases.

NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations

Shanfeng Zhu, Y. Xiong, R. You, 2022, bioRxiv.

Does Summarization Help Stock Prediction? A News Impact Analysis

Haoran Xie, Fu Lee Wang, Qing Li, 2015, IEEE Intelligent Systems.

Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition

Shanfeng Zhu, Junyi Bian, Jiaxuan Zheng, 2023, ArXiv.

Constrained Multi-scale Dense Connections for Accurate Biomedical Image Segmentation

Yanchun Zhang, Xiaowei Xu, Jiawei Zhang, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

XTQ: A Declarative Functional XML Query Language pdf

Arif Ghafoor, Xuhui Li, Mengchi Liu, 2014, ArXiv.

Approximate and dynamic rank aggregation

Xiaotie Deng, Francis Y. L. Chin, Qizhi Fang, 2004, Theor. Comput. Sci..

Protein language model powers accurate and fast sequence search for remote homology

Shanfeng Zhu, Y. Xiong, R. You, 2024, bioRxiv.