Fang-Xiang Wu

According to our database1, Fang-Xiang Wu authored at least 169 papers between 2002 and 2019.

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Bibliography

2019
DNRLMF-MDA: Predicting microRNA-Disease Associations Based on Similarities of microRNAs and Diseases.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

MGT-SM: A Method for Constructing Cellular Signal Transduction Networks.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

A Novel Scaffolding Algorithm Based on Contig Error Correction and Path Extension.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

Construction of Refined Protein Interaction Network for Predicting Essential Proteins.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

Automated ICD-9 Coding via A Deep Learning Approach.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data.
IEEE/ACM Trans. Comput. Biology Bioinform., 2019

Controllability and Its Applications to Biological Networks.
J. Comput. Sci. Technol., 2019

Automatic ICD code assignment of Chinese clinical notes based on multilayer attention BiRNN.
Journal of Biomedical Informatics, 2019

Deep learning for biological/clinical data.
Neurocomputing, 2019

Efficient multi-kernel DCNN with pixel dropout for stroke MRI segmentation.
Neurocomputing, 2019

Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks.
BMC Bioinformatics, 2019

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks.
Bioinformatics, 2019

SCOP: a novel scaffolding algorithm based on contig classification and optimization.
Bioinformatics, 2019

IDNDDI: An Integrated Drug Similarity Network Method for Predicting Drug-Drug Interactions.
Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

Identification of Prognostic and Heterogeneous Breast Cancer Biomarkers Based on Fusion Network and Multiple Scoring Strategies.
Proceedings of the Intelligent Computing Theories and Application, 2019

Improved Spectral Clustering Method for Identifying Cell Types from Single-Cell Data.
Proceedings of the Intelligent Computing Theories and Application, 2019

2018
Improving Alzheimer's Disease Classification by Combining Multiple Measures.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

Classification of Alzheimer's Disease Using Whole Brain Hierarchical Network.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

Predicting MicroRNA-Disease Associations Based on Improved MicroRNA and Disease Similarities.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

M-Matrix-Based State Observer Design for Genetic Regulatory Networks With Mixed Delays.
IEEE Trans. on Circuits and Systems, 2018

Topology potential based seed-growth method to identify protein complexes on dynamic PPI data.
Inf. Sci., 2018

CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization.
Neurocomputing, 2018

Biomolecular Networks for Complex Diseases.
Complexity, 2018

Improved flower pollination algorithm for identifying essential proteins.
BMC Systems Biology, 2018

DWNN-RLS: regularized least squares method for predicting circRNA-disease associations.
BMC Bioinformatics, 2018

CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis.
Bioinformatics, 2018

Prediction of lncRNA-disease associations based on inductive matrix completion.
Bioinformatics, 2018

DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization.
Bioinformatics, 2018

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases.
Database, 2018

A review on machine learning principles for multi-view biological data integration.
Briefings in Bioinformatics, 2018

Predicting Disease Genes from Clinical Single Sample-Based PPI Networks.
Proceedings of the Bioinformatics and Biomedical Engineering, 2018

PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks.
Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

Sprites2: Detection of Deletions Based on an Accurate Alignment Strategy.
Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

Predicting Gene-Disease Associations with Manifold Learning.
Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines.
Proceedings of the Intelligent Computing Theories and Application, 2018

A Deep Learning Framework for Identifying Essential Proteins Based on Protein-Protein Interaction Network and Gene Expression Data.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Disease Inference with Symptom Extraction and Bidirectional Recurrent Neural Network.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017
Protein Inference from the Integration of Tandem MS Data and Interactome Networks.
IEEE/ACM Trans. Comput. Biology Bioinform., 2017

NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra.
IEEE/ACM Trans. Comput. Biology Bioinform., 2017

United Complex Centrality for Identification of Essential Proteins from PPI Networks.
IEEE/ACM Trans. Comput. Biology Bioinform., 2017

Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC.
Complexity, 2017

SDTRLS: Predicting Drug-Target Interactions for Complex Diseases Based on Chemical Substructures.
Complexity, 2017

Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey.
Complexity, 2017

PECC: Correcting contigs based on paired-end read distribution.
Computational Biology and Chemistry, 2017

VAliBS: a visual aligner for bisulfite sequences.
BMC Bioinformatics, 2017

BOSS: a novel scaffolding algorithm based on an optimized scaffold graph.
Bioinformatics, 2017

LDAP: a web server for lncRNA-disease association prediction.
Bioinformatics, 2017

Protein-protein interactions: detection, reliability assessment and applications.
Briefings in Bioinformatics, 2017

Relating Diseases Based on Disease Module Theory.
Proceedings of the Bioinformatics Research and Applications - 13th International Symposium, 2017

LSLS: A Novel Scaffolding Method Based on Path Extension.
Proceedings of the Intelligent Computing Theories and Application, 2017

MEC: Misassembly error correction in contigs using a combination of paired-end reads and GC-contents.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

An interpretable model for predicting side effects of analgesics for osteoarthritis.
Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016
Protein complex identification through Markov clustering with firefly algorithm on dynamic protein-protein interaction networks.
Inf. Sci., 2016

Predicting drug-target interaction using positive-unlabeled learning.
Neurocomputing, 2016

Detecting protein complexes from DPINs by density based clustering with Pigeon-Inspired Optimization Algorithm.
SCIENCE CHINA Information Sciences, 2016

Predicting essential proteins based on subcellular localization, orthology and PPI networks.
BMC Bioinformatics, 2016

C-DEVA: Detection, evaluation, visualization and annotation of clusters from biological networks.
Biosystems, 2016

Sprites: detection of deletions from sequencing data by re-aligning split reads.
Bioinformatics, 2016

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm.
Bioinformatics, 2016

Identifying protein complexes in dynamic protein-protein interaction networks based on Cuckoo Search algorithm.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

The MSS of complex networks with centrality based preference and its application to biomolecular networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Construction of the spatial and temporal active protein interaction network for identifying protein complexes.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Identifying disease genes from PPI networks weighted by gene expression under different conditions.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Mining protein complexes based on topology potential from weighted dynamic PPI network.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Detecting protein complexes from DPINs by OPTICS based on particle swarm optimization.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Predicting microRNA-environmental factor interactions based on bi-random walk and multi-label learning.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

UDoNC: An Algorithm for Identifying Essential Proteins Based on Protein Domains and Protein-Protein Interaction Networks.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

Discovering essential proteins based on PPI network and protein complex.
IJDMB, 2015

CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks.
Biosystems, 2015

EPGA: de novo assembly using the distributions of reads and insert size.
Bioinformatics, 2015

EPGA2: memory-efficient de novo assembler.
Bioinformatics, 2015

Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison.
Algorithms for Molecular Biology, 2015

Estimation of control Energy and control Strategies for Complex Networks.
Advances in Complex Systems, 2015

Predicting Protein Functions Based on Dynamic Protein Interaction Networks.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

A two-step logistic regression algorithm for identifying individual-cancer-related genes.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
A Fast Algorithm for Nonnegative Matrix Factorization and Its Convergence.
IEEE Trans. Neural Netw. Learning Syst., 2014

Detecting Protein Complexes Basedon Uncertain Graph Model.
IEEE/ACM Trans. Comput. Biology Bioinform., 2014

Discovering biological patterns from short time-series gene expression profiles with integrating PPI data.
Neurocomputing, 2014

State Observer Design for Delayed Genetic Regulatory Networks.
Comp. Math. Methods in Medicine, 2014

Improving protein function prediction using domain and protein complexes in PPI networks.
BMC Systems Biology, 2014

A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets.
BMC Systems Biology, 2014

Prediction of disease genes using tissue-specified gene-gene network.
BMC Systems Biology, 2014

Identifying protein complexes and functional modules - from static PPI networks to dynamic PPI networks.
Briefings in Bioinformatics, 2014

NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra.
Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Drug Target Identification Based on Structural Output Controllability of Complex Networks.
Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Identification of Essential Proteins by Using Complexes and Interaction Network.
Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Searching SNP Combinations Related to Evolutionary Information of Human Populations on HapMap Data.
Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

NovoPair: De novo peptide sequencing for tandem mass spectra pair.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Detecting functional modules in dynamic protein-protein interaction networks using Markov Clustering and Firefly Algorithm.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

A logistic regression based algorithm for identifying human disease genes.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013
Robust identification method for nonlinear model structures and its application to high-performance aircraft.
Int. J. Systems Science, 2013

Complexity Analysis and Parameter Estimation of Dynamic Metabolic Systems.
Comp. Math. Methods in Medicine, 2013

Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits.
BMC Systems Biology, 2013

Construction of Uncertain Protein-Protein Interaction Networks and Its Applications.
Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

A multi-edge graph based de novo peptide sequencing method for HCD spectra.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

A dividing-and-matching algorithm to detect conserved protein complexes via local network alignment.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Robust inference of gene regulatory networks from multiple microarray datasets.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Identifying dynamic protein complexes based on gene expression profiles and PPI networks.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

PPI modules detection method through ABC-IFC algorithm.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Prioritization of candidate genes based on disease similarity and protein's proximity in PPI networks.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

Prioritizing human disease genes by multiple data integration.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012
Reverse engineering of gene regulatory networks from biological data.
Wiley Interdiscip. Rev. Data Min. Knowl. Discov., 2012

Symmetry Compression Method for Discovering Network Motifs.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Inference of Biological S-System Using the Separable Estimation Method and the Genetic Algorithm.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

Stability and Bifurcation of Ring-Structured Genetic Regulatory Networks With Time Delays.
IEEE Trans. on Circuits and Systems, 2012

Two recursive least squares parameter estimation algorithms for multirate multiple-input systems by using the auxiliary model.
Mathematics and Computers in Simulation, 2012

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks.
BMC Systems Biology, 2012

Inference of gene regulatory subnetworks from time course gene expression data.
BMC Bioinformatics, 2012

Dynamic miRNA-TF-mRNA circuits in mouse lung development.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

New global stability conditions for genetic regulatory networks with time-varying delays.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

Alternating weighted least squares parameter estimation for biological S-systems.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

Sparse kernel logistic regression for β-turns prediction.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

A fuzzy cluster-based algorithm for peptide identification.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

A hybrid approach of support vector machines with logistic regression for β-turn prediction.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Not AU protein complexes exhibit dense structures in S. cerevisiae PPI network.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
Delay-Independent Stability of Genetic Regulatory Networks.
IEEE Trans. Neural Networks, 2011

Recurrent Neural Network for Non-Smooth Convex Optimization Problems With Application to the Identification of Genetic Regulatory Networks.
IEEE Trans. Neural Networks, 2011

Guest Editorial: Special Focus on Bioinformatics and Systems Biology.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Global and Robust Stability Analysis of Genetic Regulatory Networks With Time-Varying Delays and Parameter Uncertainties.
IEEE Trans. Biomed. Circuits and Systems, 2011

SVM-RFE based feature selection for tandem mass spectrum quality assessment.
IJDMB, 2011

Features-Based Deisotoping Method for Tandem Mass Spectra.
Adv. Bioinformatics, 2011

Parallelizing Peptide-Spectrum scoring using modern graphics processing units.
Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

Estimating parameters in genetic regulatory networks with SUM logic.
Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

Globally delay-independent stability of ring-structured genetic regulatory networks.
Proceedings of the 24th Canadian Conference on Electrical and Computer Engineering, 2011

Delay-Dependent Stability for Genetic Regulatory Networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

Improve Accuracy of Peptide Identification with Consistency between Peptides.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

Modeling Gene Regulatory Subnetworks from Time Course Gene Expression Data.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

An Improved Graph Entropy-based Method for Identifying Protein Complexes.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010
Charge state determination of peptide tandem mass spectra using support vector machine (SVM).
IEEE Trans. Information Technology in Biomedicine, 2010

Dynamic-model-based method for selecting significantly expressed genes from time-course expression profiles.
IEEE Trans. Information Technology in Biomedicine, 2010

Estimation of parameters in rational reaction rates of molecular biological systems via weighted least squares.
Int. J. Systems Science, 2010

Peptide charge state determination of tandem mass spectra from low-resolution collision induced dissociation.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

Structure identification and parameter estimation of biological s-systems.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009
Mining, Modeling, and Evaluation of Subnetworks From Large Biomolecular Networks and Its Comparison Study.
IEEE Trans. Information Technology in Biomedicine, 2009

Finding Significantly Expressed genes from time-course expression profiles.
IJBRA, 2009

Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks.
EURASIP J. Bioinformatics and Systems Biology, 2009

Quality assessment of tandem mass spectra using support vector machine (SVM).
BMC Bioinformatics, 2009

Delay-Independent Stability of Genetic Regulatory Networks with Time Delays.
Advances in Complex Systems, 2009

Subspace pursuit for gene profile classificaiton.
Proceedings of the 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 2009

2008
An approach to assessing peptide mass spectral quality without prior information.
I. J. Functional Informatics and Personalised Medicine, 2008

Gene Regulatory Network modelling: a state-space approach.
IJDMB, 2008

Genetic weighted k-means algorithm for clustering large-scale gene expression data.
BMC Bioinformatics, 2008

Adaptive dynamic surface control of a class of uncertain nonlinear systems in pure-feedback form using fuzzy backstepping approach.
Proceedings of the 2008 IEEE International Conference on Automation Science and Engineering, 2008

Detecting Significantly Expressed Genes from Their Time-Course Expression Profiles and Its Validation.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

Feature Selection for Tandem Mass Spectrum Quality Assessment.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

Charge state determination of peptide tandem mass spectra using support vector machine (SVM).
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008

Stability and oscillation of genetic regulatory networks with time delays.
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008

2007
Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks.
BMC Bioinformatics, 2007

Significance Analysis of Time-Course Gene Expression Profiles.
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

A Genetic Weighted K-means Algorithm for Clustering Gene Expression Data.
Proceedings of the Proceeding of the Second International Multi-Symposium of Computer and Computational Sciences (IMSCCS 2007), 2007

Mining and Dynamic Simulation of Sub-Networks from Large Biomolecular Networks.
Proceedings of the 2007 International Conference on Artificial Intelligence, 2007

A Framework for Mass Spectral Quality Assessment without Prior Information.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides.
J. Bioinformatics and Computational Biology, 2006

Determination of the minimum number of microarray experiments for discovery of gene expression patterns.
BMC Bioinformatics, 2006

On Determination of Minimum Sample Size for Discovery of Temporal Gene Expression Patterns.
Proceedings of the Interdisciplinary and Multidisciplinary Research in Computer Science, 2006

Quality Assessment of Peptide Tandem Mass Spectra.
Proceedings of the Interdisciplinary and Multidisciplinary Research in Computer Science, 2006

2005
Control of hybrid Machines with 2-DOF for trajectory tracking problems.
IEEE Trans. Contr. Sys. Techn., 2005

Dynamic Model-based Clustering for Time-course Gene Expression Data.
J. Bioinformatics and Computational Biology, 2005

Genetic Weighted K-means for Large-Scale Clustering Problems.
Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference, 2005

2004
Modeling Gene Expression from Microarray Expression Data with State-Space Equations.
Proceedings of the Biocomputing 2004, 2004

State-Space Model for Gene Regulatory Networks with Time Delays.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

A. Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

Model-Based Clustering with Genes Expression Dynamics for Time-Course Gene Expression Data.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004

2003
Determination of the Minimum Sample Size in Microarray Experiments to Cluster Genes Using K-means Clustering.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

An Algorithm to Reconstruct a Target DNA Sequence from Its Spectrum Connected at a Given Level.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

A Genetic K-means Clustering Algorithm Applied to Gene Expression Data.
Proceedings of the Advances in Artificial Intelligence, 2003

2002
Nonlinear PD Control for Trajectory Tracking with Consideration of the Design for Control Methodology.
Proceedings of the 2002 IEEE International Conference on Robotics and Automation, 2002


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