Hong Yan

发表

Gene expression profiling of 1200 pancreatic ductal adenocarcinoma reveals novel subtypes

Hongya Zhao, Hong Yan, Lan Zhao, 2018, BMC Cancer.

mTD: A database of microRNAs affecting therapeutic effects of drugs.

Xing-Ming Zhao, Hong Yan, Wen-Bin Xie, 2017, Journal of genetics and genomics = Yi chuan xue bao.

An Improved Position Weight Matrix Method Based on an Entropy Measure for the Recognition of Prokaryotic Promoters

Hong Yan, Qinqin Wu, Jiajun Wang, 2009 .

Identifying differential networks based on multi-platform gene expression data.

Le Ou-Yang, Hong Yan, Xiao-Fei Zhang, 2016, Molecular bioSystems.

Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences.

Hong Yan, Weiqiang Zhou, Qinqin Wu, 2011, Journal of theoretical biology.

Incorporating prior information into differential network analysis using nonparanormal graphical models : supplementary data

Le Ou-Yang, Xiao-Fei Zhang, Hong Yan, 2017 .

Characterization of Eukaryotic Core Promoters Based on Nonlinear Dimensionality Reduction

Xi Yang, Hong Yan, 2012 .

New Insights to Hydrogen Bonds to Provide Stability in the EGFR Related to Non-small Cell Lung Cancer

Hong Yan, Avirup Ghosh, 2019, Proceedings of the 2019 11th International Conference on Bioinformatics and Biomedical Technology.

Analysis of DNA deformation patterns in nucleosome core particles based on isometric feature mapping and continuous wavelet transform

Xi Yang, Hong Yan, 2012 .

SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition

Hong Yan, Jia Zeng, Xiaoyu Zhao, 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Prediction of Protein-Protein Interactions Based on Molecular Interface Features and the Support Vector Machine

Hong Yan, Xiaodan Fan, Weiqiang Zhou, 2013 .

Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks

Le Ou-Yang, Xiao-Fei Zhang, Hong Yan, 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values

Le Ou-Yang, Xiao-Fei Zhang, Dehan Cai, 2021, Briefings Bioinform..

Computational Analysis of Receptor-Binding Domains of SARS-CoV-2 to Reveal the Mechanism of Immune Escape

Kongyan Li, Hong Yan, Mengxu Zhu, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib

M. Wong, Hong Yan, D. D. Wang, 2015, BMC Bioinformatics.

A POCS-based method for estimating unobserved values in microarray time-series data

Hong Yan, Jia Zeng, 2008, 2008 International Conference on Machine Learning and Cybernetics.

scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning

Yuan Zhu, Le Ou-Yang, Xiao-Fei Zhang, 2021, Briefings Bioinform..

A Joint Graphical Model for Inferring Gene Networks Across Multiple Subpopulations and Data Types

Hong Yan, Ting Yan, Le Ou-Yang, 2019, IEEE Transactions on Cybernetics.

DiffGraph: an R package for identifying gene network rewiring using differential graphical models

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2018, Bioinform..

Detecting overlapping protein complexes based on a generative model with functional and topological properties

D. Dai, Le Ou-Yang, Xiao-Fei Zhang, 2014, BMC Bioinformatics.

Detecting overlapping protein complexes based on a generative model with functional and topological properties

Dao-Qing Dai, Hong Yan, Le Ou-Yang, 2014, BMC Bioinformatics.

A two-layer integration framework for protein complex detection

Min Wu, Xiaoli Li, Hong Yan, 2016, BMC Bioinformatics.

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning

Hong Yan, Xing-Ming Zhao, Le Ou-Yang, 2019, Bioinform..

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation

Hong Yan, Xing-Ming Zhao, Le Ou-Yang, 2020, Bioinform..

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning

Xiao-Fei Zhang, Hong Yan, Hui-Sheng Li, 2022, Bioinformatics.

Biclustering-based Iterative Segmentation of human face images for facial feature extraction

Hong Yan, Haoran Xie, Fu Lee Wang, 2016, 2016 IEEE Region 10 Conference (TENCON).

Molecular subtyping of cancer: current status and moving toward clinical applications

Hong Yan, Michael K Ng, Lan Zhao, 2019, Briefings Bioinform..

Hong Yan, Rizwan Qureshi, Avirup Ghosh, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Genotype-determined EGFR-RTK heterodimerization and its effects on drug resistance in lung Cancer treatment revealed by molecular dynamics simulations

Hong Yan, D. D. Wang, Mengxu Zhu, 2021, BMC molecular and cell biology.

Geometrical Features of Epidermal Growth Factor Receptor-Related Dimers Reveal the Mechanisms of Drug Resistance in Lung Cancer Patients

Hong Yan, Rizwan Qureshi, Mengxu Zhu, 2021, IEEE Access.

Computational Analysis of Structural Dynamics of EGFR and its Mutants

Hong Yan, Rizwan Qureshi, Avirup Ghosh, 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Parametric Models for Understanding Atomic Trajectories in Different Domains of Lung Cancer Causing Protein

Hong Yan, Rizwan Qureshi, Mehmood Nawaz, 2019, IEEE Access.

An Eigen-Binding Site Based Method for the Analysis of Anti-EGFR Drug Resistance in Lung Cancer Treatment

Hong Yan, Debby Dan Wang, Lichun Ma, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Identifying EGFR mutation-induced drug resistance based on alpha shape model analysis of the dynamics

Hong Yan, Lichun Ma, Bin Zou, 2016, Proteome Science.

Selectivity profile of afatinib for EGFR-mutated non-small-cell lung cancer.

Debby D Wang, Hong Yan, Guangyu Zhu, 2016, Molecular bioSystems.

Differential network analysis from cross-platform gene expression data

Hong Yan, Xing-Ming Zhao, Xiao-Fei Zhang, 2016, Scientific Reports.

Contribution of EGFR and ErbB-3 Heterodimerization to the EGFR Mutation-Induced Gefitinib- and Erlotinib-Resistance in Non-Small-Cell Lung Carcinoma Treatments

Hong Yan, Victor H. F. Lee, Debby D. Wang, 2015, PloS one.

MCNF: A Novel Method for Cancer Subtyping by Integrating Multi-Omics and Clinical Data

Hong Yan, Lan Zhao, Hong Yan, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Position-specific deformation pattern of the nucleosome DNA revealed by principal component analysis and sequence alignment-based statistics

Xi Yang, Hong Yan, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

Principal component analysis of nucleosome DNA conformational data

Hong Yan, Xi Yang, Xi Yang, 2010, 2010 International Conference on Machine Learning and Cybernetics.

Predicting new indications of compounds with a network pharmacology approach: Liuwei Dihuang Wan as a case study

Hong Yan, Xing-Ming Zhao, Kang Ning, 2017, Oncotarget.

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

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

Personalized prediction of EGFR mutation-induced drug resistance in lung cancer

Hong Yan, Weiqiang Zhou, Maria Wong, 2013, Scientific Reports.

Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis

Hong Yan, Bin Zou, Victor H. F. Lee, 2018, BMC Bioinformatics.

Deciphering mechanisms of acquired T790M mutation after EGFR inhibitors for NSCLC by computational simulations

Lijiang Chen, Hong Yan, D. D. Wang, 2017, Scientific Reports.

DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets

Hong Yan, Xing-Ming Zhao, Chunfeng Cui, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions

Debby D Wang, Hong Yan, Mengxu Zhu, 2020, Briefings Bioinform..

Decoding the EGFR mutation-induced drug resistance in lung cancer treatment by local surface geometric properties

Hong Yan, Debby Dan Wang, Maria P. Wong, 2015, Comput. Biol. Medicine.

Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity

Hong Yan, Le Ou-Yang, Xiao-Fei Zhang, 2020, Bioinform..

Structural properties of replication origins in yeast DNA sequences

Hong Yan, Xiao-Qin Cao, Hong Yan, 2008, Physical biology.

Sparse regularized low-rank tensor regression with applications in genomic data analysis

Hong Yan, Le Ou-Yang, Xiao-Fei Zhang, 2020, Pattern Recognit..

Regularized logistic regression with network-based pairwise interaction for biomarker identification in breast cancer

D. Dai, Yuan Zhu, Meng-Yun Wu, 2016, BMC Bioinformatics.

A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks

Hong Yan, Le Ou-Yang, Xiao-Fei Zhang, 2017, BMC Bioinformatics.

Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods

Hong Yan, Haoran Xie, Le Ou-Yang, 2020, Computational and structural biotechnology journal.

Hydrogen bond analysis of the EGFR-ErbB3 heterodimer related to non-small cell lung cancer and drug resistance.

Hong Yan, Avirup Ghosh, Hong Yan, 2019, Journal of theoretical biology.

Analysis of surface structures of hydrogen bonding in protein–ligand interactions using the alpha shape model

Hong Yan, Weiqiang Zhou, Hong Yan, 2012 .

Identifying Gene Network Rewiring Based on Partial Correlation

Xingpeng Jiang, Hong Yan, Le Ou-Yang, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Analysis of the relationship between lung cancer drug response level and atom connectivity dynamics based on trimmed Delaunay triangulation

Lijiang Chen, Hong Yan, Debby D. Wang, 2016 .

Alpha shape and Delaunay triangulation in studies of protein-related interactions

Hong Yan, Weiqiang Zhou, Hong Yan, 2014, Briefings Bioinform..

Prediction of DNA-binding protein based on statistical and geometric features and support vector machines

Hong Yan, Weiqiang Zhou, Hong Yan, 2011, Proteome Science.

Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression

Ting Xu, Hong Yan, Le Ou-Yang, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib

Hong Yan, Debby D Wang, Lichun Ma, 2015, BMC Bioinformatics.

A Novel CCK Receptor GPR173 Mediates Potentiation of GABAergic Inhibition

Y. Chan, D. Pei, Ge Zhang, 2023, The Journal of Neuroscience.

Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks

D. Dai, Yuan Zhu, Meng-Yun Wu, 2016, BMC Bioinformatics.

AI in drug discovery and its clinical relevance

Taimoor Muzaffar Gondal, T. Alam, X. Le, 2023, Heliyon.

Visualization of Protein-Drug Interactions for the Analysis of Drug Resistance in Lung Cancer

Hong Yan, Rizwan Qureshi, Mengxu Zhu, 2020, IEEE Journal of Biomedical and Health Informatics.

Proteo-chemometrics interaction fingerprints of protein-ligand complexes predict binding affinity

Debby Dan Wang, Hong Yan, Haoran Xie, 2021, Bioinform..

EmDL: Extracting miRNA-Drug Interactions from Literature

Hong Yan, Xing-Ming Zhao, Wenbin Xie, 2019, TCBB.

AI in drug discovery and its clinical relevance

Taimoor Muzaffar Gondal, T. Alam, X. Le, 2023, Heliyon.

Incorporating prior information into differential network analysis using non‐paranormal graphical models

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2017, Bioinform..

scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation

Le Ou-Yang, Xiao-Fei Zhang, Hong Yan, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Differential network analysis by simultaneously considering changes in gene interactions and gene expression

Le Ou-Yang, Hong Qin, Jia-Juan Tu, 2021, Bioinform..

Structural property of regulatory elements in human promoters.

Hong Yan, Xiao-Qin Cao, Hong Yan, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Physical signals for protein–DNA recognition

Hong Yan, Xiao-Qin Cao, Hong Yan, 2009, Physical biology.

Relationship between periodic dinucleotides and the nucleosome structure revealed by alpha shape modeling

Hong Yan, Weiqiang Zhou, Hong Yan, 2010 .

Protein complex detection based on partially shared multi-view clustering

D. Dai, Yuan Zhu, Meng-Yun Wu, 2016, BMC Bioinformatics.

Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Node-based differential network analysis in genomics

Hong Yan, Xiao-Fei Zhang, Le Ou-Yang, 2017, Comput. Biol. Chem..

Deciphering mechanisms of acquired T790M mutation after EGFR inhibitors for NSCLC by computational simulations

Lijiang Chen, Hong Yan, Victor H. F. Lee, 2017, Scientific Reports.

Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis

Hong Yan, V. Lee, Bin Zou, 2018, BMC Bioinformatics.

EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib

M. Wong, Hong Yan, D. D. Wang, 2015, BMC Bioinformatics.

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

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

SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition

Hong Yan, Xiao-Qin Cao, Hong Yan, 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Finding human promoter groups based on DNA physical properties.

Hongya Zhao, Hong Yan, Xiao-Qin Cao, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

PCA-HPR: A principle component analysis model for human promoter recognition

Hong Yan, Jia Zeng, Xiaomeng Li, 2008, Bioinformation.

Analysis of drug resistance in non-small-cell lung cancer based on singular value decomposition

Hong Yan, Xue-Rong Shi, Lichun Ma, 2016, 2016 International Conference on Machine Learning and Cybernetics (ICMLC).

Joint Learning of Multiple Differential Networks With Latent Variables

Hong Yan, Xing-Ming Zhao, Fu Lee Wang, 2019, IEEE Transactions on Cybernetics.

Computational Evaluation of EGFR Dynamic Characteristics in Mutation-Induced Drug Resistance Prediction

Hong Yan, Debby Dan Wang, Lixin Han, 2015, 2015 IEEE International Conference on Systems, Man, and Cybernetics.

Alpha shape and Delaunay triangulation in studies of protein-related interactions

Hong Yan, Weiqiang Zhou, 2014, Briefings Bioinform..

An Improved Position Weight Matrix Method Based on an Entropy Measure for the Recognition of Prokaryotic Promoters

Hong Yan, Jiajun Wang, Qinqin Wu, 2009, 2009 3rd International Conference on Bioinformatics and Biomedical Engineering.

The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

Debby D Wang, Hong Yan, Hong Yan, 2011, Physical biology.

EmDL: Extracting miRNA-Drug Interactions from Literature

Xingming Zhao, Hong Yan, Wen-Bin Xie, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Identifying EGFR mutation-induced drug resistance based on alpha shape model analysis of the dynamics

Hong Yan, Bin Zou, Lichun Ma, 2016, Proteome Science.