Nonlinear PD Control for Trajectory Tracking with Consideration of the Design for Control Methodology. - Puren R. Ouyang; Wen-Jun Zhang 005; Fang-Xiang Wu (ICRA, 2002)

A Genetic K-means Clustering Algorithm Applied to Gene Expression Data. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (AI, 2003)

An Algorithm to Reconstruct a Target DNA Sequence from Its Spectrum Connected at a Given Level. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (BIBE, 2003)

Determination of the Minimum Sample Size in Microarray Experiments to Cluster Genes Using K-means Clustering. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (BIBE, 2003)

Model-Based Clustering with Genes Expression Dynamics for Time-Course Gene Expression Data. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (BIBE, 2004)

A. Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks. - Fang-Xiang Wu; Anthony J. Kusalik; Wen-Jun Zhang 005 (CSB, 2004)

State-Space Model for Gene Regulatory Networks with Time Delays. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (CSB, 2004)

Modeling Gene Expression from Microarray Expression Data with State-Space Equations. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (Pacific Symposium on Biocomputing, 2004)

Genetic Weighted K-means for Large-Scale Clustering Problems. - Fang-Xiang Wu; Anthony J. Kusalik; Wen-Jun Zhang 005 (FLAIRS, 2005)

Dynamic Model-based Clustering for Time-course Gene Expression Data. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (J. Bioinform. Comput. Biol., 2005)

Control of hybrid Machines with 2-DOF for trajectory tracking problems. - Fang-Xiang Wu; Wen-Jun Zhang 005; Q. Li; Puren R. Ouyang; Z. X. Zhou (IEEE Trans. Control. Syst. Technol., 2005)

On Determination of Minimum Sample Size for Discovery of Temporal Gene Expression Patterns. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (IMSCCS (1), 2006)

Determination of the minimum number of microarray experiments for discovery of gene expression patterns. - Fang-Xiang Wu; Wen-Jun Zhang 005; Anthony J. Kusalik (BMC Bioinform., 2006)

Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides. - Chenhong Zhang; Mikelis G. Bickis; Fang-Xiang Wu; Anthony J. Kusalik (J. Bioinform. Comput. Biol., 2006)

A Framework for Mass Spectral Quality Assessment without Prior Information. - Fang-Xiang Wu; Jiarui Ding; Guy G. Poirier (BIBE, 2007)

Mining and Dynamic Simulation of Sub-Networks from Large Biomolecular Networks. - Xiaohua Hu 001; Fang-Xiang Wu; Michael K. Ng 001; Bahrad A. Sokhansanj (IC-AI, 2007)

A Genetic Weighted K-means Algorithm for Clustering Gene Expression Data. - Fang-Xiang Wu (IMSCCS, 2007)

Significance Analysis of Time-Course Gene Expression Profiles. - Fang-Xiang Wu (ISBRA, 2007)

Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks. - Xiaohua Hu 001; Fang-Xiang Wu (BMC Bioinform., 2007)

Stability and oscillation of genetic regulatory networks with time delays. - Fang-Xiang Wu (BIBE, 2008)

Feature Selection for Tandem Mass Spectrum Quality Assessment. - Jiarui Ding; Jin-Hong Shi; An-Min Zou; Fang-Xiang Wu (BIBM, 2008)

Detecting Significantly Expressed Genes from Their Time-Course Expression Profiles and Its Validation. - Fang-Xiang Wu (BIBM, 2008)

Adaptive dynamic surface control of a class of uncertain nonlinear systems in pure-feedback form using fuzzy backstepping approach. - Zeng-Guang Hou; An-Min Zou; Fang-Xiang Wu; Long Cheng 001; Min Tan 001 (CASE, 2008)

Genetic weighted k-means algorithm for clustering large-scale gene expression data. - Fang-Xiang Wu (BMC Bioinform., 2008)

Quality assessment of peptide tandem mass spectra. - Fang-Xiang Wu; Pierre Gagné; Arnaud Droit; Guy G. Poirier (BMC Bioinform., 2008)

Gene Regulatory Network modelling: a state-space approach. - Fang-Xiang Wu (Int. J. Data Min. Bioinform., 2008)

An approach to assessing peptide mass spectral quality without prior information. - Fang-Xiang Wu; Jiarui Ding; Guy G. Poirier (Int. J. Funct. Informatics Pers. Medicine, 2008)

Subspace pursuit for gene profile classificaiton. - Xiyi Hang; Wei Dai; Fang-Xiang Wu (GENSiPS, 2009)

Delay-Independent Stability of Genetic Regulatory Networks with Time Delays. - Fang-Xiang Wu (Adv. Complex Syst., 2009)

Quality assessment of tandem mass spectra using support vector machine (SVM). - An-Min Zou; Fang-Xiang Wu; Jiarui Ding; Guy G. Poirier (BMC Bioinform., 2009)

Using a State-Space Model and Location Analysis to Infer Time-Delayed Regulatory Networks. - Chushin Koh; Fang-Xiang Wu; Gopalan Selvaraj; Anthony J. Kusalik (EURASIP J. Bioinform. Syst. Biol., 2009)

Finding Significantly Expressed genes from time-course expression profiles. - Fang-Xiang Wu; Zhonghang Xia; Lei Mu (Int. J. Bioinform. Res. Appl., 2009)

Mining, Modeling, and Evaluation of Subnetworks From Large Biomolecular Networks and Its Comparison Study. - Xiaohua Hu 001; Michael K. Ng 001; Fang-Xiang Wu; Bahrad A. Sokhansanj (IEEE Trans. Inf. Technol. Biomed., 2009)

An adaptive approach to denoising tandem mass spectra. - Wenjun Chris Lin; Fang-Xiang Wu; Jinhon Shi; Jiarui Ding; Wenjun Zhang 005 (BIBM Workshops, 2010)

Structure identification and parameter estimation of biological s-systems. - Li-Zhi Liu; Fang-Xiang Wu; Li-Li Han; Wen-Jun Zhang 005 (BIBM, 2010)

Peptide charge state determination of tandem mass spectra from low-resolution collision induced dissociation. - Jin-Hong Shi; Fang-Xiang Wu (BIBM, 2010)

Speed improvements of peptide-spectrum matching using SIMD instructions. - Jian Zhang; Ian McQuillan; Fang-Xiang Wu (BIBM Workshops, 2010)

Estimation of parameters in rational reaction rates of molecular biological systems via weighted least squares. - Fang-Xiang Wu; Lei Mu; Zhong-Ke Shi (Int. J. Syst. Sci., 2010)

Dynamic-model-based method for selecting significantly expressed genes from time-course expression profiles. - Fang-Xiang Wu; Wen-Jun Zhang 005 (IEEE Trans. Inf. Technol. Biomed., 2010)

Charge state determination of peptide tandem mass spectra using support vector machine (SVM). - An-Min Zou; Jin-Hong Shi; Jiarui Ding; Fang-Xiang Wu (IEEE Trans. Inf. Technol. Biomed., 2010)

An Improved Graph Entropy-based Method for Identifying Protein Complexes. - Bolin Chen; Yan Yan 029; Jin-Hong Shi; Shenggui Zhang; Fang-Xiang Wu (BIBM, 2011)

Modeling Gene Regulatory Subnetworks from Time Course Gene Expression Data. - Xijun Liang; Zhonghang Xia; Li-Wei Zhang; Fang-Xiang Wu (BIBM, 2011)

Improve Accuracy of Peptide Identification with Consistency between Peptides. - Jin-Hong Shi; Bolin Chen; Fang-Xiang Wu (BIBM, 2011)

Delay-Dependent Stability for Genetic Regulatory Networks. - Li-Ping Tian 001; Fang-Xiang Wu (BIBM, 2011)

Globally delay-independent stability of ring-structured genetic regulatory networks. - Li-Ping Tian 001; Fang-Xiang Wu (CCECE, 2011)

Estimating parameters in genetic regulatory networks with SUM logic. - Li-Ping Tian 001; Li-Zhi Liu; Fang-Xiang Wu (EMBC, 2011)

Parallelizing Peptide-Spectrum scoring using modern graphics processing units. - Jian Zhang; Ian McQuillan; Fang-Xiang Wu (ICCABS, 2011)

Features-Based Deisotoping Method for Tandem Mass Spectra. - Zheng Yuan; Jin-Hong Shi; Wenjun Lin; Bolin Chen; Fang-Xiang Wu (Adv. Bioinformatics, 2011)

SVM-RFE based feature selection for tandem mass spectrum quality assessment. - Jiarui Ding; Jin-Hong Shi; Fang-Xiang Wu (Int. J. Data Min. Bioinform., 2011)

Global and Robust Stability Analysis of Genetic Regulatory Networks With Time-Varying Delays and Parameter Uncertainties. - Fang-Xiang Wu (IEEE Trans. Biomed. Circuits Syst., 2011)

Guest Editorial: Special Focus on Bioinformatics and Systems Biology. - Fang-Xiang Wu; Jun Huan (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Recurrent Neural Network for Non-Smooth Convex Optimization Problems With Application to the Identification of Genetic Regulatory Networks. - Long Cheng 001; Zeng-Guang Hou; Yingzi Lin; Min Tan 001; Wenjun Chris Zhang; Fang-Xiang Wu (IEEE Trans. Neural Networks, 2011)

Delay-Independent Stability of Genetic Regulatory Networks. - Fang-Xiang Wu (IEEE Trans. Neural Networks, 2011)

Not AU protein complexes exhibit dense structures in S. cerevisiae PPI network. - Bolin Chen; Jin-Hong Shi; Fang-Xiang Wu (BIBM, 2012)

A hybrid approach of support vector machines with logistic regression for β-turn prediction. - Murtada Khalafallah Elbashir; Jianxin Wang 001; Fang-Xiang Wu (BIBM Workshops, 2012)

A fuzzy cluster-based algorithm for peptide identification. - Xijun Liang; Zhonghang Xia; Xinnan Niu; Andrew J. Link; Liping Pang; Fang-Xiang Wu; Hongwei Zhang (BIBM Workshops, 2012)

Sparse kernel logistic regression for β-turns prediction. - Murtada Khalafallah Elbashir; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (ISB, 2012)

Alternating weighted least squares parameter estimation for biological S-systems. - Li-Zhi Liu; Fang-Xiang Wu; Wen-Jun Zhang 005 (ISB, 2012)

New global stability conditions for genetic regulatory networks with time-varying delays. - Li-Ping Tian 001; Zhong-Ke Shi; Fang-Xiang Wu (ISB, 2012)

Dynamic miRNA-TF-mRNA circuits in mouse lung development. - Xinghuo Ye; Juan Liu; Fang-Xiang Wu (ISB, 2012)

Inference of gene regulatory subnetworks from time course gene expression data. - Xijun Liang; Zhonghang Xia; Li-Wei Zhang; Fang-Xiang Wu (BMC Bioinform., 2012)

Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. - Wei Peng 004; Jianxin Wang 001; Weiping Wang 003; Qing Liu 003; Fang-Xiang Wu; Yi Pan 001 (BMC Syst. Biol., 2012)

Two recursive least squares parameter estimation algorithms for multirate multiple-input systems by using the auxiliary model. - Lili Han; Fang-Xiang Wu; Jie Sheng; Feng Ding 001 (Math. Comput. Simul., 2012)

Stability and Bifurcation of Ring-Structured Genetic Regulatory Networks With Time Delays. - Fang-Xiang Wu (IEEE Trans. Circuits Syst. I Regul. Pap., 2012)

Inference of Biological S-System Using the Separable Estimation Method and the Genetic Algorithm. - Li-Zhi Liu; Fang-Xiang Wu; Wen-Jun Zhang 005 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Symmetry Compression Method for Discovering Network Motifs. - Jianxin Wang 001; Yuannan Huang; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Reverse engineering of gene regulatory networks from biological data. - Li-Zhi Liu; Fang-Xiang Wu; Wen-Jun Zhang 005 (WIREs Data Mining Knowl. Discov., 2012)

Prioritizing human disease genes by multiple data integration. - Bolin Chen; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2013)

Prioritization of candidate genes based on disease similarity and protein's proximity in PPI networks. - Gamage Upeksha Ganegoda; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (BIBM, 2013)

PPI modules detection method through ABC-IFC algorithm. - Xiujuan Lei; Jianfang Tian; Fang-Xiang Wu (BIBM, 2013)

Identifying dynamic protein complexes based on gene expression profiles and PPI networks. - Min Li 007; Weijie Chen; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2013)

Robust inference of gene regulatory networks from multiple microarray datasets. - Li-Zhi Liu; Fang-Xiang Wu; Wen-Jun Zhang 005 (BIBM, 2013)

A dividing-and-matching algorithm to detect conserved protein complexes via local network alignment. - Wei Peng 004; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2013)

A multi-edge graph based de novo peptide sequencing method for HCD spectra. - Yan Yan 029; Anthony J. Kusalik; Fang-Xiang Wu (BIBM, 2013)

Construction of Uncertain Protein-Protein Interaction Networks and Its Applications. - Bihai Zhao; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (ISBRA, 2013)

Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits. - Juan Liu; Xinghuo Ye; Fang-Xiang Wu (BMC Syst. Biol., 2013)

Complexity Analysis and Parameter Estimation of Dynamic Metabolic Systems. - Li-Ping Tian 001; Zhong-Ke Shi; Fang-Xiang Wu (Comput. Math. Methods Medicine, 2013)

Robust identification method for nonlinear model structures and its application to high-performance aircraft. - Zhong-Ke Shi; Fang-Xiang Wu (Int. J. Syst. Sci., 2013)

A logistic regression based algorithm for identifying human disease genes. - Bolin Chen; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2014)

Detecting functional modules in dynamic protein-protein interaction networks using Markov Clustering and Firefly Algorithm. - Xiujuan Lei; Fang-Xiang Wu; Fei Wang 095; Aidong Zhang (BIBM, 2014)

NovoPair: De novo peptide sequencing for tandem mass spectra pair. - Yan Yan 029; Anthony J. Kusalik; Fang-Xiang Wu (BIBM, 2014)

Searching SNP Combinations Related to Evolutionary Information of Human Populations on HapMap Data. - Xiaojun Ding; Haihua Gu; Zhen Zhang 024; Min Li 007; Fang-Xiang Wu (ISBRA, 2014)

Identification of Essential Proteins by Using Complexes and Interaction Network. - Min Li 007; Yu Lu; Zhibei Niu; Fang-Xiang Wu; Yi Pan 001 (ISBRA, 2014)

Drug Target Identification Based on Structural Output Controllability of Complex Networks. - Lin Wu; Yichao Shen; Min Li 007; Fang-Xiang Wu (ISBRA, 2014)

NovoGMET: De Novo Peptide Sequencing Using Graphs with Multiple Edge Types (GMET) for ETD/ECD Spectra. - Yan Yan 029; Anthony J. Kusalik; Fang-Xiang Wu (ISBRA, 2014)

Identifying protein complexes and functional modules - from static PPI networks to dynamic PPI networks. - Bolin Chen; Weiwei Fan; Juan Liu; Fang-Xiang Wu (Briefings Bioinform., 2014)

Prediction of disease genes using tissue-specified gene-gene network. - Gamage Upeksha Ganegoda; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (BMC Syst. Biol., 2014)

A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets. - Li-Zhi Liu; Fang-Xiang Wu; Wen-Jun Zhang 005 (BMC Syst. Biol., 2014)

Improving protein function prediction using domain and protein complexes in PPI networks. - Wei Peng 004; Jianxin Wang 001; Juan Cai; Lu Chen; Min Li 007; Fang-Xiang Wu (BMC Syst. Biol., 2014)

State Observer Design for Delayed Genetic Regulatory Networks. - Li-Ping Tian 001; Zhi-Jun Wang; Amin Mohammadbagheri; Fang-Xiang Wu (Comput. Math. Methods Medicine, 2014)

Discovering biological patterns from short time-series gene expression profiles with integrating PPI data. - Weiwei Fan; Bolin Chen; Gopalan Selvaraj; Fang-Xiang Wu (Neurocomputing, 2014)

Detecting Protein Complexes Basedon Uncertain Graph Model. - Bihai Zhao; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

A Fast Algorithm for Nonnegative Matrix Factorization and Its Convergence. - Li-Xin Li; Lin Wu; Hui-Sheng Zhang; Fang-Xiang Wu (IEEE Trans. Neural Networks Learn. Syst., 2014)

A two-step logistic regression algorithm for identifying individual-cancer-related genes. - Bolin Chen; Xuequn Shang 001; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2015)

Predicting Protein Functions Based on Dynamic Protein Interaction Networks. - Bihai Zhao; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (ISBRA, 2015)

Estimation of control Energy and control Strategies for Complex Networks. - Dingjie Wang; Suoqin Jin; Fang-Xiang Wu; Xiufen Zou (Adv. Complex Syst., 2015)

Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison. - Wei Peng 004; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (Algorithms Mol. Biol., 2015)

EPGA2: memory-efficient de novo assembler. - Junwei Luo; Jianxin Wang 001; Weilong Li; Zhen Zhang 024; Fang-Xiang Wu; Min Li 007; Yi Pan 001 (Bioinform., 2015)

EPGA: de novo assembly using the distributions of reads and insert size. - Junwei Luo; Jianxin Wang 001; Zhen Zhang 024; Fang-Xiang Wu; Min Li 007; Yi Pan 001 (Bioinform., 2015)

CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks. - Yu Tang; Min Li 007; Jianxin Wang 001; Yi Pan 001; Fang-Xiang Wu (Biosyst., 2015)

Discovering essential proteins based on PPI network and protein complex. - Jun Ren; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu (Int. J. Data Min. Bioinform., 2015)

A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks. - Min Li 007; Yu Lu; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

UDoNC: An Algorithm for Identifying Essential Proteins Based on Protein Domains and Protein-Protein Interaction Networks. - Wei Peng 004; Jianxin Wang 001; Yingjiao Cheng; Yu Lu; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network. - Jianxin Wang 001; Jiancheng Zhong; Gang Chen 010; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Predicting microRNA-environmental factor interactions based on bi-random walk and multi-label learning. - Wei Lan; Jianxin Wang 001; Min Li 007; Chengqian Lu; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2016)

Detecting protein complexes from DPINs by OPTICS based on particle swarm optimization. - Xiujuan Lei; Huan Li; Fang-Xiang Wu (BIBM, 2016)

Mining protein complexes based on topology potential from weighted dynamic PPI network. - Xiujuan Lei; Yuchen Zhang 003; Fang-Xiang Wu; Aidong Zhang (BIBM, 2016)

Identifying disease genes from PPI networks weighted by gene expression under different conditions. - Ping Luo 003; Li-Ping Tian 001; Jishou Ruan; Fang-Xiang Wu (BIBM, 2016)

Construction of the spatial and temporal active protein interaction network for identifying protein complexes. - Xiangmao Meng; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2016)

The MSS of complex networks with centrality based preference and its application to biomolecular networks. - Lin Wu; Lingkai Tang; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (BIBM, 2016)

Identifying protein complexes in dynamic protein-protein interaction networks based on Cuckoo Search algorithm. - Jie Zhao 012; Xiujuan Lei; Fang-Xiang Wu (BIBM, 2016)

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm. - Huimin Luo; Jianxin Wang 001; Min Li 007; Junwei Luo; Xiaoqing Peng; Fang-Xiang Wu; Yi Pan 001 (Bioinform., 2016)

Sprites: detection of deletions from sequencing data by re-aligning split reads. - Zhen Zhang 024; Jianxin Wang 001; Junwei Luo; Xiaojun Ding; Jiancheng Zhong; Jun Wang 153; Fang-Xiang Wu; Yi Pan 001 (Bioinform., 2016)

C-DEVA: Detection, evaluation, visualization and annotation of clusters from biological networks. - Min Li 007; Yu Tang; Xuehong Wu; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (Biosyst., 2016)

Predicting essential proteins based on subcellular localization, orthology and PPI networks. - Gaoshi Li; Min Li 007; Jianxin Wang 001; Jingli Wu; Fang-Xiang Wu; Yi Pan 001 (BMC Bioinform., 2016)

Detecting protein complexes from DPINs by density based clustering with Pigeon-Inspired Optimization Algorithm. - Xiujuan Lei; Yulian Ding; Fang-Xiang Wu (Sci. China Inf. Sci., 2016)

Predicting drug-target interaction using positive-unlabeled learning. - Wei Lan; Jianxin Wang 001; Min Li 007; Jin Liu 012; Yaohang Li; Fang-Xiang Wu; Yi Pan 001 (Neurocomputing, 2016)

Protein complex identification through Markov clustering with firefly algorithm on dynamic protein-protein interaction networks. - Xiujuan Lei; Fei Wang 095; Fang-Xiang Wu; Aidong Zhang; Witold Pedrycz (Inf. Sci., 2016)

An interpretable model for predicting side effects of analgesics for osteoarthritis. - Liangliang Liu 001; Jianxin Wang 001; Min Li 007; Fang-Xiang Wu; Hong-Dong Li; Ying Yu; Zhihui Fei (BIBM, 2017)

MEC: Misassembly error correction in contigs using a combination of paired-end reads and GC-contents. - Binbin Wu; Jianxin Wang 001; Junwei Luo; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (BIBM, 2017)

LSLS: A Novel Scaffolding Method Based on Path Extension. - Min Li 007; Li Tang; Zhongxiang Liao; Junwei Luo; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (ICIC (2), 2017)

Relating Diseases Based on Disease Module Theory. - Peng Ni; Min Li 007; Ping Zhong 002; Guihua Duan; Jianxin Wang 001; Yaohang Li; Fang-Xiang Wu (ISBRA, 2017)

Protein-protein interactions: detection, reliability assessment and applications. - Xiaoqing Peng; Jianxin Wang 001; Wei Peng 004; Fang-Xiang Wu; Yi Pan 001 (Briefings Bioinform., 2017)

LDAP: a web server for lncRNA-disease association prediction. - Wei Lan; Min Li 007; Kaijie Zhao; Jin Liu 012; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2017)

BOSS: a novel scaffolding algorithm based on an optimized scaffold graph. - Junwei Luo; Jianxin Wang 001; Zhen Zhang 024; Min Li 007; Fang-Xiang Wu (Bioinform., 2017)

VAliBS: a visual aligner for bisulfite sequences. - Min Li 007; Ping Huang; Xiaodong Yan; Jianxin Wang 001; Yi Pan 001; Fang-Xiang Wu (BMC Bioinform., 2017)

PECC: Correcting contigs based on paired-end read distribution. - Min Li 007; Binbin Wu; Xiaodong Yan; Junwei Luo; Yi Pan 001; Fang-Xiang Wu; Jianxin Wang 001 (Comput. Biol. Chem., 2017)

Complex Brain Network Analysis and Its Applications to Brain Disorders: A Survey. - Jin Liu 012; Min Li 007; Yi Pan 001; Wei Lan; Ruiqing Zheng; Fang-Xiang Wu; Jianxin Wang 001 (Complex., 2017)

SDTRLS: Predicting Drug-Target Interactions for Complex Diseases Based on Chemical Substructures. - Cheng Yan; Jianxin Wang 001; Wei Lan; Fang-Xiang Wu; Yi Pan 001 (Complex., 2017)

Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC. - Jie Zhao 012; Xiujuan Lei; Fang-Xiang Wu (Complex., 2017)

United Complex Centrality for Identification of Essential Proteins from PPI Networks. - Min Li 007; Yu Lu; Zhibei Niu; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

NovoExD: De novo Peptide Sequencing for ETD/ECD Spectra. - Yan Yan 029; Anthony J. Kusalik; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Protein Inference from the Integration of Tandem MS Data and Interactome Networks. - Jiancheng Zhong; Jianxin Wang 001; Xiaojun Ding; Zhen Zhang 024; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Disease Inference with Symptom Extraction and Bidirectional Recurrent Neural Network. - Donglin Guo; Min Li 007; Ying Yu; Yaohang Li; Guihua Duan; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2018)

A Deep Learning Framework for Identifying Essential Proteins Based on Protein-Protein Interaction Network and Gene Expression Data. - Min Zeng; Min Li 007; Zhihui Fei; Fang-Xiang Wu; Yaohang Li; Yi Pan 001 (BIBM, 2018)

Using Deep Neural Network to Predict Drug Sensitivity of Cancer Cell Lines. - Yake Wang; Min Li 007; Ruiqing Zheng; Xinghua Shi; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (ICIC (2), 2018)

Predicting Gene-Disease Associations with Manifold Learning. - Ping Luo 003; Li-Ping Tian 001; Bolin Chen; Qianghua Xiao; Fang-Xiang Wu (ISBRA, 2018)

Sprites2: Detection of Deletions Based on an Accurate Alignment Strategy. - Zhen Zhang 024; Jianxin Wang 001; Junwei Luo; Juan Shang; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (ISBRA, 2018)

PBMarsNet: A Multivariate Adaptive Regression Splines Based Method to Reconstruct Gene Regulatory Networks. - Siyu Zhao; Ruiqing Zheng; Xiang Chen; Yaohang Li; Fang-Xiang Wu; Min Li 007 (ISBRA, 2018)

Predicting Disease Genes from Clinical Single Sample-Based PPI Networks. - Ping Luo 003; Li-Ping Tian 001; Bolin Chen; Qianghua Xiao; Fang-Xiang Wu (IWBBIO (1), 2018)

A review on machine learning principles for multi-view biological data integration. - Yifeng Li 001; Fang-Xiang Wu; Alioune Ngom (Briefings Bioinform., 2018)

CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases. - Chunyan Fan; Xiujuan Lei; Zengqiang Fang; Qinghua Jiang; Fang-Xiang Wu (Database J. Biol. Databases Curation, 2018)

DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization. - Min Li 007; Jie Yang 057; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2018)

Prediction of lncRNA-disease associations based on inductive matrix completion. - Chengqian Lu; Mengyun Yang; Feng Luo 001; Fang-Xiang Wu; Min Li 007; Yi Pan 001; Yaohang Li; Jianxin Wang 001 (Bioinform., 2018)

CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis. - Lin Wu; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (Bioinform., 2018)

DWNN-RLS: regularized least squares method for predicting circRNA-disease associations. - Cheng Yan; Jianxin Wang 001; Fang-Xiang Wu (BMC Bioinform., 2018)

Improved flower pollination algorithm for identifying essential proteins. - Xiujuan Lei; Ming Fang; Fang-Xiang Wu; Luonan Chen (BMC Syst. Biol., 2018)

Biomolecular Networks for Complex Diseases. - Fang-Xiang Wu; Jianxin Wang 001; Min Li 007; Haiying Wang 001 (Complex., 2018)

CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization. - Li-Ping Tian 001; Ping Luo 003; Haiying Wang 001; Huiru Zheng; Fang-Xiang Wu (Neurocomputing, 2018)

Topology potential based seed-growth method to identify protein complexes on dynamic PPI data. - Xiujuan Lei; Yuchen Zhang 003; Shi Cheng; Fang-Xiang Wu; Witold Pedrycz (Inf. Sci., 2018)

M-Matrix-Based State Observer Design for Genetic Regulatory Networks With Mixed Delays. - Li-Ping Tian 001; Venkat Palgat; Fang-Xiang Wu (IEEE Trans. Circuits Syst. II Express Briefs, 2018)

Predicting MicroRNA-Disease Associations Based on Improved MicroRNA and Disease Similarities. - Wei Lan; Jianxin Wang 001; Min Li 007; Jin Liu 012; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Classification of Alzheimer's Disease Using Whole Brain Hierarchical Network. - Jin Liu 012; Min Li 007; Wei Lan; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Improving Alzheimer's Disease Classification by Combining Multiple Measures. - Jin Liu 012; Jianxin Wang 001; Zhenjun Tang; Bin Hu 001; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Human Protein Complex Signatures for Drug Repositioning. - Fei Wang 095; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (BCB, 2019)

DoRC: Discovery of rare cells from ultra-large scRNA-seq data. - Xiang Chen; Fang-Xiang Wu; Jin Chen 004; Min Li 007 (BIBM, 2019)

Classification of Schizophrenia by Iterative Random Forest Feature Selection Based on DNA Methylation Array Data. - Xinyu Hu; Min Li 007; Linconghua Wang; Xingyi Li; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

Drug and disease similarity calculation platform for drug repositioning. - Lan Huang; Huimin Luo; Mengyun Yang; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

DualRank: multiplex network-based dual ranking for heterogeneous complex disease analysis. - Xingyi Li; Ju Xiang; Xinyu Hu; Fang-Xiang Wu; Min Li 007 (BIBM, 2019)

de novo repeat detection based on the third generation sequencing reads. - Xingyu Liao; Xiankai Zhang; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

Detecting protein complex based on hierarchical compressing network embedding. - Xiangmao Meng; Xiaoqing Peng; Fang-Xiang Wu; Min Li 007 (BIBM, 2019)

Tentative diagnosis prediction via deep understanding of patient narratives. - Ying Yu; Min Li 007; Liangliang Liu 001; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2019)

LncRNA-disease association prediction through combining linear and non-linear features with matrix factorization and deep learning techniques. - Min Zeng; Chengqian Lu; Fuhao Zhang; Zhangli Lu; Fang-Xiang Wu; Yaohang Li; Min Li 007 (BIBM, 2019)

A Global Similarity Learning for Clustering of Single-Cell RNA-Seq Data. - Xiaoshu Zhu; Lilu Guo; Yunpei Xu; Hong-Dong Li; Xingyu Liao; Fang-Xiang Wu; Xiaoqing Peng (BIBM, 2019)

Autoencoder Based Methods for Diagnosis of Autism Spectrum Disorder. - Sakib Mostafa; Wutao Yin; Fang-Xiang Wu (ICCABS, 2019)

Improved Spectral Clustering Method for Identifying Cell Types from Single-Cell Data. - Yuanyuan Li; Ping Luo 003; Yi Lu; Fang-Xiang Wu (ICIC (2), 2019)

Identification of Prognostic and Heterogeneous Breast Cancer Biomarkers Based on Fusion Network and Multiple Scoring Strategies. - Xingyi Li; Ju Xiang; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (ICIC (2), 2019)

IDNDDI: An Integrated Drug Similarity Network Method for Predicting Drug-Drug Interactions. - Cheng Yan; Guihua Duan; Yayan Zhang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (ISBRA, 2019)

Diagnosis of Autism Spectrum Disorder Based on Eigenvalues of Brain Networks. - Sakib Mostafa; Lingkai Tang; Fang-Xiang Wu (IEEE Access, 2019)

Control principles for complex biological networks. - Min Li 007; Hao Gao; Jianxin Wang 001; Fang-Xiang Wu (Briefings Bioinform., 2019)

SCOP: a novel scaffolding algorithm based on contig classification and optimization. - Min Li 007; Li Tang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

Enhancing the prediction of disease-gene associations with multimodal deep learning. - Ping Luo 003; Yuanyuan Li; Li-Ping Tian 001; Fang-Xiang Wu (Bioinform., 2019)

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks. - Ruiqing Zheng; Min Li 007; Xiang Chen; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation. - Ruiqing Zheng; Min Li 007; Zhenlan Liang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Bioinform., 2019)

Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks. - Xiujuan Lei; Ming Fang; Ling Guo; Fang-Xiang Wu (BMC Bioinform., 2019)

IILLS: predicting virus-receptor interactions based on similarity and semi-supervised learning. - Cheng Yan; Guihua Duan; Fang-Xiang Wu; Jianxin Wang 001 (BMC Bioinform., 2019)

DeepEP: a deep learning framework for identifying essential proteins. - Min Zeng; Min Li 007; Fang-Xiang Wu; Yaohang Li; Yi Pan 001 (BMC Bioinform., 2019)

Efficient multi-kernel DCNN with pixel dropout for stroke MRI segmentation. - Liangliang Liu 001; Fang-Xiang Wu; Jianxin Wang 001 (Neurocomputing, 2019)

Deep learning for biological/clinical data. - Fang-Xiang Wu; Min Li 007 (Neurocomputing, 2019)

Automatic ICD code assignment of Chinese clinical notes based on multilayer attention BiRNN. - Ying Yu; Min Li 007; Liangliang Liu 001; Zhihui Fei; Fang-Xiang Wu; Jianxin Wang 001 (J. Biomed. Informatics, 2019)

Controllability and Its Applications to Biological Networks. - Lin Wu; Min Li 007; Jianxin Wang 001; Fang-Xiang Wu (J. Comput. Sci. Technol., 2019)

Overlap matrix completion for predicting drug-associated indications. - Mengyun Yang; Huimin Luo; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (PLoS Comput. Biol., 2019)

Current challenges and solutions of de novo assembly. - Xingyu Liao; Min Li 007; You Zou; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Quant. Biol., 2019)

Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data. - Ping Luo 003; Li-Ping Tian 001; Jishou Ruan; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Automated ICD-9 Coding via A Deep Learning Approach. - Min Li 007; Zhihui Fei; Min Zeng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Construction of Refined Protein Interaction Network for Predicting Essential Proteins. - Min Li 007; Peng Ni; Xiaopei Chen; Jianxin Wang 001; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A Novel Scaffolding Algorithm Based on Contig Error Correction and Path Extension. - Min Li 007; Li Tang; Zhongxiang Liao; Junwei Luo; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

MGT-SM: A Method for Constructing Cellular Signal Transduction Networks. - Min Li 007; Ruiqing Zheng; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Computational Drug Repositioning with Random Walk on a Heterogeneous Network. - Huimin Luo; Jianxin Wang 001; Min Li 007; Junwei Luo; Peng Ni; Kaijie Zhao; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

DNRLMF-MDA: Predicting microRNA-Disease Associations Based on Similarities of microRNAs and Diseases. - Cheng Yan; Jianxin Wang 001; Peng Ni; Wei Lan; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

CSA: a web service for the complete process of ChIP-Seq analysis. - Min Li 007; Li Tang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (BMC Bioinform., 2019)

DDIGIP: predicting drug-drug interactions based on Gaussian interaction profile kernels. - Cheng Yan; Guihua Duan; Yi Pan 001; Fang-Xiang Wu; Jianxin Wang 001 (BMC Bioinform., 2019)

A topological AUC-based biomarker ensemble method for the complex disease analysis. - Xingyi Li; Ju Xiang; Fang-Xiang Wu; Min Li 007 (BIBM, 2020)

SPOC: Identification of Drug Targets in Biological Networks via Set Preference Output Control. - Hao Gao; Min Li 007; Fang-Xiang Wu (ISBRA, 2020)

Diagnosis of ASD from rs-fMRI Images Based on Brain Dynamic Networks. - Hongyu Guo; Wutao Yin; Sakib Mostafa; Fang-Xiang Wu (ISBRA, 2020)

MiRNA-Disease Associations Prediction Based on Negative Sample Selection and Multi-layer Perceptron. - Na Li; Guihua Duan; Cheng Yan; Fang-Xiang Wu; Jianxin Wang 001 (ISBRA, 2020)

ALSBMF: Predicting lncRNA-Disease Associations by Alternating Least Squares Based on Matrix Factorization. - Wen Zhu; Kaimei Huang; Xiaofang Xiao; Bo Liao; Yuhua Yao; Fang-Xiang Wu (IEEE Access, 2020)

MDIPA: a microRNA-drug interaction prediction approach based on non-negative matrix factorization. - Ali Akbar Jamali; Anthony J. Kusalik; Fang-Xiang Wu (Bioinform., 2020)

MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries. - Tao Li 033; Shaokai Wang; Feng Luo 001; Fang-Xiang Wu; Jianxin Wang 001 (Bioinform., 2020)

Protein-protein interaction site prediction through combining local and global features with deep neural networks. - Min Zeng; Fuhao Zhang; Fang-Xiang Wu; Yaohang Li; Jianxin Wang 001; Min Li 007 (Bioinform., 2020)

MADA: a web service for analysing DNA methylation array data. - Xinyu Hu; Li Tang; Linconghua Wang; Fang-Xiang Wu; Min Li 007 (BMC Bioinform., 2020)

RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads. - Xingyu Liao; Xin Gao 001; Xiankai Zhang; Fang-Xiang Wu; Jianxin Wang 001 (BMC Bioinform., 2020)

PESM: predicting the essentiality of miRNAs based on gradient boosting machines and sequences. - Cheng Yan; Fang-Xiang Wu; Jianxin Wang 001; Guihua Duan (BMC Bioinform., 2020)

Predicting novel CircRNA-disease associations based on random walk and logistic regression model. - Yulian Ding; Bolin Chen; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (Comput. Biol. Chem., 2020)

A network enhancement-based method for clustering of single cell RNA-seq data. - Xiaoshu Zhu; Lilu Guo; Rongyuan Li; Yunpei Xu; Fang-Xiang Wu; Xiaoqing Peng; Hong-Dong Li (Int. J. Data Min. Bioinform., 2020)

A survey on U-shaped networks in medical image segmentations. - Liangliang Liu 001; Jianhong Cheng; Quan Quan; Fang-Xiang Wu; Yu-Ping Wang 002; Jianxin Wang 001 (Neurocomputing, 2020)

Deep convolutional neural network for accurate segmentation and quantification of white matter hyperintensities. - Liangliang Liu 001; Shaowu Chen; Xiaofeng Zhu 001; Xing-Ming Zhao; Fang-Xiang Wu; Jianxin Wang 001 (Neurocomputing, 2020)

Enhancing the feature representation of multi-modal MRI data by combining multi-view information for MCI classification. - Jin Liu 012; Yi Pan 001; Fang-Xiang Wu; Jianxin Wang 001 (Neurocomputing, 2020)

Attention convolutional neural network for accurate segmentation and quantification of lesions in ischemic stroke disease. - Liangliang Liu 001; Lukasz A. Kurgan; Fang-Xiang Wu; Jianxin Wang 001 (Medical Image Anal., 2020)

Deep convolutional neural network for automatically segmenting acute ischemic stroke lesion in multi-modality MRI. - Liangliang Liu 001; Shaowu Chen; Fuhao Zhang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (Neural Comput. Appl., 2020)

miRTRS: A Recommendation Algorithm for Predicting miRNA Targets. - Hui Jiang 008; Jianxin Wang 001; Min Li 007; Wei Lan; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Artificial Fish Swarm Optimization Based Method to Identify Essential Proteins. - Xiujuan Lei; Xiaoqin Yang; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network. - Min Li 007; Xiangmao Meng; Ruiqing Zheng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

MultiMotifMaker: A Multi-Thread Tool for Identifying DNA Methylation Motifs from Pacbio Reads. - Tao Li 033; Xiankai Zhang; Feng Luo 001; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Improving de novo Assembly Based on Read Classification. - Xingyu Liao; Min Li 007; Junwei Luo; You Zou; Fang-Xiang Wu; Yi Pan 001; Feng Luo 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

An Efficient Trimming Algorithm based on Multi-Feature Fusion Scoring Model for NGS Data. - Xingyu Liao; Min Li 007; You Zou; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

GapReduce: A Gap Filling Algorithm Based on Partitioned Read Sets. - Junwei Luo; Jianxin Wang 001; Juan Shang; Huimin Luo; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Constructing Disease Similarity Networks Based on Disease Module Theory. - Peng Ni; Jianxin Wang 001; Ping Zhong 002; Yaohang Li; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

MEC: Misassembly Error Correction in Contigs based on Distribution of Paired-End Reads and Statistics of GC-contents. - Binbin Wu; Min Li 007; Xingyu Liao; Junwei Luo; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

BRWMDA: Predicting Microbe-Disease Associations Based on Similarities and Bi-Random Walk on Disease and Microbe Networks. - Cheng Yan; Guihua Duan; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Multi-Receptive-Field CNN for Semantic Segmentation of Medical Images. - Liangliang Liu 001; Fang-Xiang Wu; Yu-Ping Wang 002; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2020)

Predicting Human lncRNA-Disease Associations Based on Geometric Matrix Completion. - Chengqian Lu; Mengyun Yang; Min Li 007; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2020)

Ensemble disease gene prediction by clinical sample-based networks. - Ping Luo 003; Li-Ping Tian 001; Bolin Chen; Qianghua Xiao; Fang-Xiang Wu (BMC Bioinform., 2020)

EFCA: An Extended Formal Concept Analysis Method for Aspect Extraction in Healthcare Informatics. - Zohair Ahmed; Junwen Duan; Fang-Xiang Wu; Jianxin Wang 001 (BIBM, 2021)

A Graph Attention Neural Network for Diagnosing ASD with fMRI Data. - Wutao Yin; Longhai Li; Fang-Xiang Wu (BIBM, 2021)

Improving human essential protein prediction using only protein sequences via ensemble learning. - Min Zeng; Nian Wang; Yifan Wu 008; Yiming Li; Fang-Xiang Wu; Min Li 007 (BIBM, 2021)

Single Cell Clustering with Sparse Similarity Matrix Learning. - Wenjing Zhang; Yuting Tan 001; Fang-Xiang Wu (BIBM, 2021)

Biomedical data and computational models for drug repositioning: a comprehensive review. - Huimin Luo; Min Li 007; Mengyun Yang; Fang-Xiang Wu; Yaohang Li; Jianxin Wang 001 (Briefings Bioinform., 2021)

Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics. - Xiaoqing Peng; Hong-Dong Li; Fang-Xiang Wu; Jianxin Wang 001 (Briefings Bioinform., 2021)

A survey on predicting microbe-disease associations: biological data and computational methods. - Zhongqi Wen; Cheng Yan; Guihua Duan; Suning Li; Fang-Xiang Wu; Jianxin Wang 001 (Briefings Bioinform., 2021)

Proteoform characterization based on top-down mass spectrometry. - Jiancheng Zhong; Yusui Sun; Minzhu Xie; Wei Peng 004; Chushu Zhang; Fang-Xiang Wu; Jianxin Wang 001 (Briefings Bioinform., 2021)

Parallel computing for genome sequence processing. - You Zou; Yuejie Zhu; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (Briefings Bioinform., 2021)

IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation. - Hong-Dong Li; Changhuo Yang; Zhimin Zhang; Mengyun Yang; Fang-Xiang Wu; Gilbert S. Omenn; Jianxin Wang 001 (Bioinform., 2021)

Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks. - Chengqian Lu; Min Zeng; Fang-Xiang Wu; Min Li 007; Jianxin Wang 001 (Bioinform., 2021)

Identifying cell types from single-cell data based on similarities and dissimilarities between cells. - Yuanyuan Li; Ping Luo 003; Yi Lu; Fang-Xiang Wu (BMC Bioinform., 2021)

MMHGE: detecting mild cognitive impairment based on multi-atlas multi-view hybrid graph convolutional networks and ensemble learning. - Jin Liu 012; Dejiao Zeng; Rui Guo; Mingming Lu; Fang-Xiang Wu; Jianxin Wang 001 (Clust. Comput., 2021)

A dynamic predictor selection algorithm for predicting stock market movement. - Shuting Dong; Jianxin Wang 001; Hongze Luo; Haodong Wang; Fang-Xiang Wu (Expert Syst. Appl., 2021)

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. - Zhenlan Liang; Min Li 007; Ruiqing Zheng; Yu Tian; Xuhua Yan; Jin Chen 004; Fang-Xiang Wu; Jianxin Wang 001 (Genom. Proteom. Bioinform., 2021)

Essential Protein Prediction Based on node2vec and XGBoost. - Nian Wang; Min Zeng; Yiming Li; Fang-Xiang Wu; Min Li 007 (J. Comput. Biol., 2021)

Diagnosis of Autism Spectrum Disorder Based on Functional Brain Networks with Deep Learning. - Wutao Yin; Sakib Mostafa; Fang-Xiang Wu (J. Comput. Biol., 2021)

High-Risk Prediction of Cardiovascular Diseases via Attention-Based Deep Neural Networks. - Ying An; Nengjun Huang; Xianlai Chen; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

DeepDSC: A Deep Learning Method to Predict Drug Sensitivity of Cancer Cell Lines. - Min Li 007; Yake Wang; Ruiqing Zheng; Xinghua Shi; Yaohang Li; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

FUNMarker: Fusion Network-Based Method to Identify Prognostic and Heterogeneous Breast Cancer Biomarkers. - Xingyi Li; Ju Xiang; Jianxin Wang 001; Jinyan Li 001; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

EPGA-SC : A Framework for de novo Assembly of Single-Cell Sequencing Reads. - Xingyu Liao; Min Li 007; Junwei Luo; You Zou; Fang-Xiang Wu; Yi Pan 001; Feng Luo 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Novel Drug Repositioning Approach Based on Collaborative Metric Learning. - Huimin Luo; Jianxin Wang 001; Cheng Yan; Min Li 007; Fang-Xiang Wu; Yi Pan 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering. - Yunpei Xu; Hong-Dong Li; Yi Pan 001; Feng Luo 001; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

MCHMDA: Predicting Microbe-Disease Associations Based on Similarities and Low-Rank Matrix Completion. - Cheng Yan; Guihua Duan; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Deep Learning Framework for Identifying Essential Proteins by Integrating Multiple Types of Biological Information. - Min Zeng; Min Li 007; Zhihui Fei; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

DMFLDA: A Deep Learning Framework for Predicting lncRNA-Disease Associations. - Min Zeng; Chengqian Lu; Zhihui Fei; Fang-Xiang Wu; Yaohang Li; Jianxin Wang 001; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Deletion Detection Method Using the Distribution of Insert Size and a Precise Alignment Strategy. - Zhen Zhang 024; Junwei Luo; Juan Shang; Min Li 007; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information. - Fuhao Zhang; Hong Song; Min Zeng; Fang-Xiang Wu; Yaohang Li; Yi Pan 001; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

An Ensemble Method to Reconstruct Gene Regulatory Networks Based on Multivariate Adaptive Regression Splines. - Ruiqing Zheng; Min Li 007; Xiang Chen; Siyu Zhao; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

scASK: A Novel Ensemble Framework for Classifying Cell Types Based on Single-cell RNA-seq Data. - Bo Liu 084; Fang-Xiang Wu; Xiufen Zou (IEEE J. Biomed. Health Informatics, 2021)

Deep Matrix Factorization Improves Prediction of Human CircRNA-Disease Associations. - Chengqian Lu; Min Zeng; Fuhao Zhang; Fang-Xiang Wu; Min Li 007; Jianxin Wang 001 (IEEE J. Biomed. Health Informatics, 2021)

Human Protein Complex-Based Drug Signatures for Personalized Cancer Medicine. - Fei Wang 095; Yulian Ding; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (IEEE J. Biomed. Health Informatics, 2021)

Predicting disease-associated genes: Computational methods, databases, and evaluations. - Ping Luo 003; Bolin Chen; Bo Liao; Fang-Xiang Wu (WIREs Data Mining Knowl. Discov., 2021)

BayesImpute: a Bayesian imputation method for single-cell RNA-seq data. - Siqi Chen; Ruiqing Zheng; Luyi Tian; Fang-Xiang Wu; Min Li 007 (BIBM, 2022)

Prediction of exosomal piRNAs based on deep learning for sequence embedding with attention mechanism. - Yajun Liu; Yulian Ding; Aimin Li; Rong Fei; Guo Xie; Fang-Xiang Wu (BIBM, 2022)

Unseen Epitope-TCR Interaction Prediction based on Amino Acid Physicochemical Properties. - Rawshon Raha; Yulian Ding; Qiang Liu; Fang-Xiang Wu (BIBM, 2022)

EMDS: predicting essential miRNAs based on deep learning and sequences. - Cheng Yan; Guihua Duan; Fang-Xiang Wu (BIBM, 2022)

A Deep Neural Network for Cervical Cell Classification Based on Cytology Images. - Ming Fang; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (IEEE Access, 2022)

Chinese clinical named entity recognition via multi-head self-attention based BiLSTM-CRF. - Ying An; Xianyun Xia; Xianlai Chen; Fang-Xiang Wu; Jianxin Wang 001 (Artif. Intell. Medicine, 2022)

RMS-UNet: Residual multi-scale UNet for liver and lesion segmentation. - Rayyan Azam Khan; Yigang Luo; Fang-Xiang Wu (Artif. Intell. Medicine, 2022)

MLRDFM: a multi-view Laplacian regularized DeepFM model for predicting miRNA-disease associations. - Yulian Ding; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (Briefings Bioinform., 2022)

An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. - Cui-Xiang Lin; Hong-Dong Li; Chao Deng; Weisheng Liu; Shannon Erhardt; Fang-Xiang Wu; Xing-Ming Zhao; Yuanfang Guan; Jun Wang 153; Daifeng Wang; Bin Hu 001; Jianxin Wang 001 (Briefings Bioinform., 2022)

Predicting drug-drug interactions by graph convolutional network with multi-kernel. - Fei Wang 095; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (Briefings Bioinform., 2022)

HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure. - Ju Xiang; Xiangmao Meng; Yichao Zhao; Fang-Xiang Wu; Min Li 007 (Briefings Bioinform., 2022)

Biomedical data, computational methods and tools for evaluating disease-disease associations. - Ju Xiang; Jiashuai Zhang; Yichao Zhao; Fang-Xiang Wu; Min Li 007 (Briefings Bioinform., 2022)

DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding. - Min Zeng; Yifan Wu 008; Chengqian Lu; Fuhao Zhang; Fang-Xiang Wu; Min Li 007 (Briefings Bioinform., 2022)

ACP_MS: prediction of anticancer peptides based on feature extraction. - Caimao Zhou; Dejun Peng; Bo Liao; Ranran Jia; Fang-Xiang Wu (Briefings Bioinform., 2022)

PDMDA: predicting deep-level miRNA-disease associations with graph neural networks and sequence features. - Cheng Yan; Guihua Duan; Na Li; Lishen Zhang; Fang-Xiang Wu; Jianxin Wang 001 (Bioinform., 2022)

CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA-disease Associations and Its Application. - Chunyan Fan; Xiujuan Lei; Jiaojiao Tie; Yuchen Zhang 003; Fang-Xiang Wu; Yi Pan 001 (Genom. Proteom. Bioinform., 2022)

Multi-scale GAN with residual image learning for removing heterogeneous blur. - Rayyan Azam Khan; Yigang Luo; Fang-Xiang Wu (IET Image Process., 2022)

Machine learning based liver disease diagnosis: A systematic review. - Rayyan Azam Khan; Yigang Luo; Fang-Xiang Wu (Neurocomputing, 2022)

Guest editorial: Deep neural networks for precision medicine. - Fang-Xiang Wu; Min Li 007; Lukasz A. Kurgan; Luis Rueda 001 (Neurocomputing, 2022)

KAICD: A knowledge attention-based deep learning framework for automatic ICD coding. - Yifan Wu 008; Min Zeng; Zhihui Fei; Ying Yu; Fang-Xiang Wu; Min Li 007 (Neurocomputing, 2022)

Deep learning for brain disorder diagnosis based on fMRI images. - Wutao Yin; Longhai Li; Fang-Xiang Wu (Neurocomputing, 2022)

A semi-supervised autoencoder for autism disease diagnosis. - Wutao Yin; Longhai Li; Fang-Xiang Wu (Neurocomputing, 2022)

Corrigendum to "Deep learning for brain disorder diagnosis based on fMRI images" [Neurocomputing 469 (2022) 332-345]. - Wutao Yin; Longhai Li; Fang-Xiang Wu (Neurocomputing, 2022)

Drug-Target Interaction Prediction Using Multi-Head Self-Attention and Graph Attention Network. - Zhongjian Cheng; Cheng Yan; Fang-Xiang Wu; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy. - Haonan Feng; Ruiqing Zheng; Jianxin Wang 001; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

A Dual Ranking Algorithm Based on the Multiplex Network for Heterogeneous Complex Disease Analysis. - Xingyi Li; Ju Xiang; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

An Ensemble Hybrid Feature Selection Method for Neuropsychiatric Disorder Classification. - Liangliang Liu 001; Shaojie Tang 002; Fang-Xiang Wu; Yu-Ping Wang 002; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DPCMNE: Detecting Protein Complexes From Protein-Protein Interaction Networks Via Multi-Level Network Embedding. - Xiangmao Meng; Ju Xiang; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering. - Fei Wang 095; Yulian Ding; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning. - Cheng Yan; Guihua Duan; Yayan Zhang; Fang-Xiang Wu; Yi Pan 001; Jianxin Wang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Predicting miRNA-Disease Associations Based On Multi-View Variational Graph Auto-Encoder With Matrix Factorization. - Yulian Ding; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (IEEE J. Biomed. Health Informatics, 2022)

Temporal-Spatial Analysis of the Essentiality of Hub Proteins in Protein-Protein Interaction Networks. - Xiangmao Meng; Wenkai Li; Ju Xiang; Hayat Dino Bedru; Wenkang Wang; Fang-Xiang Wu; Min Li 007 (IEEE Trans. Netw. Sci. Eng., 2022)

Imputing single-cell RNA-seq data by graph autoencoder with multi-kernel. - Kang Jiang; Bo Liao; Petros Papagerakis; Fang-Xiang Wu (BIBM, 2023)

Prediction of piRNA-mRNA interactions based on an interactive inference network. - Yajun Liu; Ru Li; Aimin Li; Rong Fei; Guo Xie; Fang-Xiang Wu (BIBM, 2023)

MIPI 2023 Challenge on Nighttime Flare Removal: Methods and Results. - Yuekun Dai; Chongyi Li; Shangchen Zhou; Ruicheng Feng; Qingpeng Zhu; Qianhui Sun 002; Wenxiu Sun; Chen Change Loy; Jinwei Gu; Shuai Liu 009; Hao Wang 073; Chaoyu Feng; et al. (CVPR Workshops, 2023)

QLAB: Quadratic Loss Approximation-Based Optimal Learning Rate for Deep Learning. - Minghan Fu; Fang-Xiang Wu (CoRR, 2023)

Biomarker Identification via a Factorization Machine-Based Neural Network With Binary Pairwise Encoding. - Yulian Ding; Xiujuan Lei; Bo Liao; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction. - Ali Akbar Jamali; Anthony J. Kusalik; Fang-Xiang Wu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning. - Yiming Li; Min Zeng; Fuhao Zhang; Fang-Xiang Wu; Min Li 007 (Bioinform., 2023)

CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. - Xuhua Yan; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (Bioinform., 2023)

Multi-level GAN based enhanced CT scans for liver cancer diagnosis. - Rayyan Azam Khan; Yigang Luo; Fang-Xiang Wu (Biomed. Signal Process. Control., 2023)

A Two-Branch Neural Network for Short-Axis PET Image Quality Enhancement. - Minghan Fu; Meiyun Wang; Yaping Wu; Na Zhang 001; Yongfeng Yang; Haining Wang; Yun Zhou; Yue Shang; Fang-Xiang Wu; Hairong Zheng; Dong Liang 001; Zhanli Hu (IEEE J. Biomed. Health Informatics, 2023)

A multi-modal deep neural network for multi-class liver cancer diagnosis. - Rayyan Azam Khan; Minghan Fu; Brent Burbridge; Yigang Luo; Fang-Xiang Wu (Neural Networks, 2023)

Sparse2Noise: Low-dose synchrotron X-ray tomography without high-quality reference data. - Xiaoman Duan; Xiao Fan Ding; Naitao Li; Fang-Xiang Wu; Xiongbiao Chen; Ning Zhu (Comput. Biol. Medicine, 2023)

Identify potential circRNA-disease associations through a multi-objective evolutionary algorithm. - Yuchen Zhang 003; Xiujuan Lei; Cai Dai; Yi Pan 001; Fang-Xiang Wu (Inf. Sci., 2023)

invMap: a sensitive mapping tool for long noisy reads with inversion structural variants. - Ze-Gang Wei; Peng-Yu Bu; Xiao-Dan Zhang 011; Fei Liu; Yu Qian; Fang-Xiang Wu (Bioinform., 2023)

QLABGrad: A Hyperparameter-Free and Convergence-Guaranteed Scheme for Deep Learning. - Minghan Fu; Fang-Xiang Wu (AAAI, 2024)

Deciphering Bladder Cancer-Related circRNA Biomarkers: An Ensemble Model Integrating Deep Learning and Statistics for circRNA Analysis. - Yulian Ding; Yi Pan 001; Ronald C. Geyer; Franco J. Vizeacoumar; Frederick S. Vizeacoumar; Fang-Xiang Wu (BCB, 2024)

DrugEL: Ensemble Learning Model for Identification of Druggable Proteins. - Md Mamun Ali; Kawsar Ahmed; Francis M. Bui; Fang-Xiang Wu (BIBM, 2024)

Prediction of miRNA family based on class-incremental learning. - Yajun Liu; Lulu Qiu; Aimin Li; Rong Fei; Junhuai Li; Fang-Xiang Wu (BIBM, 2024)

HCCL: Hierarchical Channels and Contrastive Learning for Drug-Gene Multi-Relation Prediction. - Yizhe Shang; Jianrui Chen; Xiujuan Lei; Fang-Xiang Wu (BIBM, 2024)

Drug Combination Side Effect Prediction Based on Polypharmacy Network and GraphSAGE Algorithm. - Haiqiang Xiao; Xiujuan Lei; Yuchen Zhang 003; Fang-Xiang Wu (BIBM, 2024)

An Ensemble Learning Model for Predicting Unseen TCR-Epitope Interactions. - Rawshon Raha; Qiang Liu; Fang-Xiang Wu (ISBRA (1), 2024)

SG-Fusion: A swin-transformer and graph convolution-based multi-modal deep neural network for glioma prognosis. - Minghan Fu; Ming Fang; Rayyan Azam Khan; Bo Liao; Zhanli Hu; Fang-Xiang Wu (Artif. Intell. Medicine, 2024)

pathMap: a path-based mapping tool for long noisy reads with high sensitivity. - Ze-Gang Wei; Xiao-Dan Zhang; Xing-Guo Fan; Yu Qian; Fei Liu; Fang-Xiang Wu (Briefings Bioinform., 2024)

Deep integrated fusion of local and global features for cervical cell classification. - Ming Fang; Minghan Fu; Bo Liao; Xiujuan Lei; Fang-Xiang Wu (Comput. Biol. Medicine, 2024)

A systematic review on deep learning based methods for cervical cell image analysis. - Ming Fang; Bo Liao; Xiujuan Lei; Fang-Xiang Wu (Neurocomputing, 2024)

OIF-Net: An Optical Flow Registration-Based PET/MR Cross-Modal Interactive Fusion Network for Low-Count Brain PET Image Denoising. - Minghan Fu; Na Zhang 001; Zhenxing Huang; Chao Zhou; Xu Zhang; Jianmin Yuan; Qiang He; Yongfeng Yang; Hairong Zheng; Dong Liang 001; Fang-Xiang Wu; Wei Fan; et al. (IEEE Trans. Medical Imaging, 2024)

Identifying Associations Between Small Nucleolar RNAs and Diseases via Graph Convolutional Network and Attention Mechanism. - Shuchen Liu; Wen Zhu; Peng Wang; Shaoyou Yu; Fang-Xiang Wu (IEEE J. Biomed. Health Informatics, 2024)

An Adaptive Multi-view Feature Fusion Framework Based on Multiple Graphs for Predicting Drug-Drug Interactions. - Fei Wang 095; Zefan Cheng; Xiujuan Lei; Fang-Xiang Wu; Chun-Hou Zheng 001; Yansen Su (ICIC (26), 2025)

Joint Sparse Precision Matrix Estimation for Cancer Diagnosis. - Rwan Ahmed; Kang Jiang; Fang-Xiang Wu (ISBRA (2), 2025)

Traditional Chinese medicine studies for AD based on Logistic Matrix Factorization and Similarity Network Fusion. - Rui Ding; Shujuan Cao; Binying Cai; Yongming Zou; Fang-Xiang Wu (Appl. Math. Comput., 2025)

Nucleotide-level circRNA-RBP binding sites prediction based on hybrid encoding scheme and enhanced feature extraction. - Yajing Guo; Xiujuan Lei; Zhengfeng Wang; Ling Guo; Fang-Xiang Wu; Yi Pan 001 (Neural Networks, 2025)

Unraveling bladder cancer-related circRNA biomarkers: a hybrid model combining deep learning and statistics. - Yulian Ding; Yi Pan 001; Ronald C. Geyer; Franco J. Vizeacoumar; Frederick S. Vizeacoumar; Fang-Xiang Wu (Health Inf. Sci. Syst., 2025)