A Novel Hybrid GA/SVM System for Protein Sequences Classification. - Xing-Ming Zhao; De-Shuang Huang; Yiu-ming Cheung; Hong-Qiang Wang; Xin Huang (IDEAL, 2004)

Representation of DNA sequences with multiple resolutions and BP neural network based classification. - Xin Huang; De-Shuang Huang; Hong-Qiang Wang; Xing-Ming Zhao (IJCNN, 2004)

A feature_core and SVM-based algorithm for identification of bioprocess-specific genome features. - Hong-Qiang Wang; Deshuang Huang; Guang-Zheng Zhang; Xing-Ming Zhao (IJCNN, 2004)

A Novel Clustering Analysis Based on PCA and SOMs for Gene Expression Patterns. - Hong-Qiang Wang; De-Shuang Huang; Xing-Ming Zhao; Xin Huang (ISNN (2), 2004)

A novel approach to extracting features from motif content and protein composition for protein sequence classification. - Xing-Ming Zhao; Yiu-ming Cheung; De-Shuang Huang (Neural Networks, 2005)

Classifying G-Protein Coupled Receptors with Hydropathy Blocks and Support Vector Machines. - Xing-Ming Zhao; De-Shuang Huang; Shiwu Zhang; Yiu-ming Cheung (ICIC (3), 2006)

A new technique for selecting features from protein sequences. - Xing-Ming Zhao; Ji-Xiang Du; Hong-Qiang Wang; Yunping Zhu; Yixue Li (Int. J. Pattern Recognit. Artif. Intell., 2006)

Classifying protein sequences using hydropathy blocks. - De-Shuang Huang; Xing-Ming Zhao; Guang-Bin Huang; Yiu-ming Cheung (Pattern Recognit., 2006)

Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks. - Xing-Ming Zhao; Rui-Sheng Wang; Luonan Chen; Kazuyuki Aihara (APBC, 2008)

Domain-Domain Interaction Identification with a Feature Selection Approach. - Xing-Ming Zhao; Luonan Chen (PRIB, 2008)

Gene function prediction using labeled and unlabeled data. - Xing-Ming Zhao; Yong Wang 001; Luonan Chen; Kazuyuki Aihara (BMC Bioinform., 2008)

Gene Expression Data Classification Using Consensus Independent Component Analysis. - Chun-Hou Zheng 001; De-Shuang Huang; Xiangzhen Kong; Xing-Ming Zhao (Genom. Proteom. Bioinform., 2008)

Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function. - Peng Chen 001; De-Shuang Huang; Xing-Ming Zhao; Xueling Li (Int. J. Bioinform. Res. Appl., 2008)

Protein function prediction with the shortest path in functional linkage graph and boosting. - Xing-Ming Zhao; Luonan Chen; Kazuyuki Aihara (Int. J. Bioinform. Res. Appl., 2008)

A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures. - Xing-Ming Zhao; Luonan Chen (BMEI, 2009)

Modeling and Dynamical Analysis of Molecular Networks. - Ruiqi Wang; Xing-Ming Zhao; Zengrong Liu (Complex (2), 2009)

Automatic Modeling of Signaling Pathways by Network Flow Model. - Xing-Ming Zhao; Rui-Sheng Wang; Luonan Chen; Kazuyuki Aihara (J. Bioinform. Comput. Biol., 2009)

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. - Junfeng Xia; Xing-Ming Zhao; Jiangning Song; De-Shuang Huang (BMC Bioinform., 2010)

FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures. - Chenglei Sun; Xing-Ming Zhao; Weihua Tang; Luonan Chen (BMC Syst. Biol., 2010)

A systems biology approach to identify effective cocktail drugs. - Zikai Wu; Xing-Ming Zhao; Luonan Chen (BMC Syst. Biol., 2010)

Analysis of Gene Expression Data Using Rpem Algorithm in Normal Mixture Model with Dynamic Adjustment of Learning Rate. - Xing-Ming Zhao; Yiu-ming Cheung; De-Shuang Huang (Int. J. Pattern Recognit. Artif. Intell., 2010)

Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data. - Xing-Ming Zhao; Murat Iskar; Georg Zeller; Michael Kuhn 004; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2011)

Drug-target network in myocardial infarction: A structural analysis. - Haiying Wang 001; Huiru Zheng; Francisco Azuaje; Xing-Ming Zhao (BIBM, 2012)

Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations. - Fu-Yan Hu; Xing-Ming Zhao; Nelson L. S. Tang; Yan Zhang; Luonan Chen (ISB, 2012)

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. - Xiujun Zhang; Xing-Ming Zhao; Kun He 007; Le Lu 001; Yongwei Cao; Jingdong Liu; Jin-Kao Hao; Zhi-Ping Liu; Luonan Chen (Bioinform., 2012)

Identifying dysregulated pathways in cancers from pathway interaction networks. - Keqin Liu; Zhi-Ping Liu; Jin-Kao Hao; Luonan Chen; Xing-Ming Zhao (BMC Bioinform., 2012)

Exploring drug combinations in genetic interaction network. - Yin-Ying Wang; Ke-Jia Xu; Jiangning Song; Xing-Ming Zhao (BMC Bioinform., 2012)

The drug cocktail network. - Ke-Jia Xu; Jiangning Song; Xing-Ming Zhao (BMC Syst. Biol., 2012)

Identifying disease genes and module biomarkers by differential interactions. - Xiaoping Liu 002; Zhi-Ping Liu; Xing-Ming Zhao; Luonan Chen (J. Am. Medical Informatics Assoc., 2012)

Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources. - Yan-Fen Dai; Yin-Ying Wang; Xing-Ming Zhao (PRIB, 2013)

eFG: an electronic resource for Fusarium graminearum. - Xiaoping Liu 002; Xiaodong Zhang; Weihua Tang; Luonan Chen; Xing-Ming Zhao (Database J. Biol. Databases Curation, 2013)

NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. - Xiujun Zhang; Keqin Liu; Zhi-Ping Liu; Béatrice Duval; Jean-Michel Richer; Xing-Ming Zhao; Jin-Kao Hao; Luonan Chen (Bioinform., 2013)

Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs. - Wei-Hua Chen; Xing-Ming Zhao; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2013)

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. - Mingjun Wang; Xing-Ming Zhao; Hao Tan; Tatsuya Akutsu; James C. Whisstock; Jiangning Song (Bioinform., 2014)

Pattern recognition in bioinformatics. - Xing-Ming Zhao; Alioune Ngom; Jin-Kao Hao (Neurocomputing, 2014)

Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication". - Wei-Hua Chen; Xing-Ming Zhao; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2014)

jNMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data. - Hong-Qiang Wang; Chun-Hou Zheng 001; Xing-Ming Zhao (Bioinform., 2015)

Identifying cancer-related microRNAs based on gene expression data. - Xing-Ming Zhao; Keqin Liu; Guanghui Zhu; Feng He 004; Béatrice Duval; Jean-Michel Richer; De-Shuang Huang; Changjun Jiang; Jin-Kao Hao; Luonan Chen (Bioinform., 2015)

Editorial - Data mining in bioinformatics. - Xing-Ming Zhao (J. Bioinform. Comput. Biol., 2015)

The exploration of functional divergence between human and macaque brains based on gene networks. - Peipei Xiao; Xing-Ming Zhao (BIBM, 2016)

A hybrid sequential feature selection approach for the diagnosis of Alzheimer's Disease. - Yang Han; Xing-Ming Zhao (IJCNN, 2016)

Understanding tissue-specificity with human tissue-specific regulatory networks. - Wei-Li Guo; Lin Zhu 008; Suping Deng; Xing-Ming Zhao; Deshuang Huang (Sci. China Inf. Sci., 2016)

Data mining in systems biology. - Ao Li 001; Xing-Ming Zhao; Shuigeng Zhou (Neurocomputing, 2016)

A systematic exploration of the associations between amino acid variants and post-translational modifications. - Gui-Min Qin; Yi-Bo Hou; Xing-Ming Zhao (Neurocomputing, 2016)

A survey on biomarker identification based on molecular networks. - Guanghui Zhu; Xing-Ming Zhao; Jun Wu 006 (Quant. Biol., 2016)

Identifying Disease Associated miRNAs Based on Protein Domains. - Gui-Min Qin; Rui-Yi Li; Xing-Ming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Data Mining in Systems Biology. - Xing-Ming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Exploring functional variant using a deep learning framework. - Tianyi Sun; Zhuo Liu; Xing-Ming Zhao; Rui Jiang 001 (CASE, 2017)

PPIM: A protein-protein interaction database for Maize. - Guanghui Zhu; Rui Jiang 001; Xing-Ming Zhao (CASE, 2017)

PhosD: inferring kinase-substrate interactions based on protein domains. - Gui-Min Qin; Rui-Yi Li; Xing-Ming Zhao (Bioinform., 2017)

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. - Wei-Hua Chen; Guanting Lu; Xiao Chen; Xing-Ming Zhao; Peer Bork (Nucleic Acids Res., 2017)

CSTEA: a webserver for the Cell State Transition Expression Atlas. - Guanghui Zhu; Hui Yang; Xiao Chen; Jun Wu; Yong Zhang 006; Xing-Ming Zhao (Nucleic Acids Res., 2017)

PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data. - Feng He 004; Guanghui Zhu; Yin-Ying Wang; Xing-Ming Zhao; De-Shuang Huang (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Prediction of Drug Response with a Topology Based Dual-Layer Network Model. - Suyun Huang; Xing-Ming Zhao (ISBRA, 2018)

MVP: a microbe-phage interaction database. - Na L. Gao; Chengwei Zhang; Zhanbing Zhang; Songnian Hu; Martin J. Lercher; Xing-Ming Zhao; Peer Bork; Zhi Liu; Wei-Hua Chen (Nucleic Acids Res., 2018)

DeepPhos: prediction of protein phosphorylation sites with deep learning. - Fenglin Luo; Minghui Wang; Yu Liu; Xing-Ming Zhao; Ao Li 001 (Bioinform., 2019)

EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning. - Xiao-Fei Zhang; Le Ou-Yang; Shuo Yang; Xing-Ming Zhao; Xiaohua Hu 001; Hong Yan 001 (Bioinform., 2019)

Victors: a web-based knowledge base of virulence factors in human and animal pathogens. - Samantha Sayers; Li Li; Edison Ong; Shunzhou Deng; Guanghua Fu; Yu Lin; Brian Yang; Shelley Zhang 002; Zhenzong Fa; Bin Zhao; Zuoshuang Xiang; Yongqing Li; et al. (Nucleic Acids Res., 2019)

DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets. - Yin-Ying Wang; Chunfeng Cui; Liqun Qi 001; Hong Yan 001; Xing-Ming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

EmDL: Extracting miRNA-Drug Interactions from Literature. - Wen-Bin Xie; Hong Yan 001; Xing-Ming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Joint Learning of Multiple Differential Networks With Latent Variables. - Le Ou-Yang; Xiao-Fei Zhang; Xing-Ming Zhao; Debby Dan Wang; Fu Lee Wang; Baiying Lei; Hong Yan 001 (IEEE Trans. Cybern., 2019)

GANcon: Protein Contact Map Prediction With Deep Generative Adversarial Network. - Hang Yang; Minghui Wang; Zhenhua Yu 002; Xing-Ming Zhao; Ao Li 001 (IEEE Access, 2020)

scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation. - Ke Jin; Le Ou-Yang; Xing-Ming Zhao; Hong Yan 001; Xiao-Fei Zhang (Bioinform., 2020)

A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks. - Zi-Chao Zhang 001; Xiao-Fei Zhang; Min Wu 008; Le Ou-Yang; Xing-Ming Zhao; Xiaoli Li 001 (Bioinform., 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)

GMrepo: a database of curated and consistently annotated human gut metagenomes. - Sicheng Wu; Chuqing Sun; Yanze Li; Teng Wang; Long-Hao Jia; Senying Lai; Yaling Yang; Pengyu Luo; Die Dai; Yong-Qing Yang; Qibin Luo; Na L. Gao; et al. (Nucleic Acids Res., 2020)

nMAGMA: a network-enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia. - Anyi Yang; Jingqi Chen; Xing-Ming Zhao (Briefings Bioinform., 2021)

PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information. - Hangyuan Yang; Minghui Wang; Xia Liu; Xing-Ming Zhao; Ao Li 001 (Bioinform., 2021)

MAT2: manifold alignment of single-cell transcriptomes with cell triplets. - Jinglong Zhang; Xu Zhang; Ying Wang 005; Feng Zeng; Xing-Ming Zhao (Bioinform., 2021)

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. - Sanathoi Gurumayum; Puzi Jiang; Xiaowen Hao; Tulio de Lima Campos; Neil D. Young; Pasi K. Korhonen; Robin B. Gasser; Peer Bork; Xing-Ming Zhao; Lijie He; Wei-Hua Chen (Nucleic Acids Res., 2021)

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. - Senying Lai; Long-Hao Jia; Balakrishnan Subramanian; Shaojun Pan; Jinglong Zhang; Yanqi Dong; Wei-Hua Chen; Xing-Ming Zhao (Nucleic Acids Res., 2021)

STAB: a spatio-temporal cell atlas of the human brain. - Liting Song; Shaojun Pan; Zichao Zhang 001; Long-Hao Jia; Wei-Hua Chen; Xing-Ming Zhao (Nucleic Acids Res., 2021)

Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. - Kai Shi 004; Wei Lin 003; Xing-Ming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network. - Guiying Dong; Zi-Chao Zhang 001; Jianfeng Feng; Xing-Ming Zhao (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)

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice. - Yanze Li; Wenming Cao 005; Na L. Gao; Xing-Ming Zhao; Wei-Hua Chen (Genom. Proteom. Bioinform., 2022)

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. - Die Dai; Jiaying Zhu; Chuqing Sun; Min Li; Jinxin Liu; Sicheng Wu; Ning Kang 001; Lijie He; Xing-Ming Zhao; Wei-Hua Chen (Nucleic Acids Res., 2022)

mBodyMap: a curated database for microbes across human body and their associations with health and diseases. - Hanbo Jin; Guoru Hu; Chuqing Sun; Yiqian Duan; Zhenmo Zhang; Zhi Liu; Xing-Ming Zhao; Wei-Hua Chen (Nucleic Acids Res., 2022)

Co-VAE: Drug-Target Binding Affinity Prediction by Co-Regularized Variational Autoencoders. - Tianjiao Li; Xing-Ming Zhao; Limin Li (IEEE Trans. Pattern Anal. Mach. Intell., 2022)

CITEdb: a manually curated database of cell-cell interactions in human. - Nayang Shan; Yao Lu; Hao Guo; Dongyu Li; Jitong Jiang; Linlin Yan; Jiudong Gao; Yong Ren; Xing-Ming Zhao; Lin Hou (Bioinform., 2022)

Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues. - Xingzhong Zhao; Yucheng T. Yang; Xing-Ming Zhao (BIBM, 2023)

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. - Shaojun Pan; Xing-Ming Zhao; Luís Pedro Coelho (Bioinform., 2023)

Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics. - Xingzhong Zhao; Anyi Yang; Zi-Chao Zhang 001; Yucheng T. Yang; Xing-Ming Zhao (Briefings Bioinform., 2023)

A survey on computational strategies for genome-resolved gut metagenomics. - Long-Hao Jia; Yingjian Wu; Yanqi Dong; Jingchao Chen; Wei-Hua Chen; Xing-Ming Zhao (Briefings Bioinform., 2023)

Improving Alzheimer's Disease Diagnosis With Multi-Modal PET Embedding Features by a 3D Multi-Task MLP-Mixer Neural Network. - Zi-Chao Zhang 001; Xingzhong Zhao; Guiying Dong; Xing-Ming Zhao (IEEE J. Biomed. Health Informatics, 2023)

MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework. - Kai Shi 004; Qiaohui Liu; Qingrong Ji; Qisheng He; Xing-Ming Zhao (Briefings Bioinform., 2024)

Enhancing Generalized Fetal Brain MRI Segmentation using A Cascade Network with Depth-wise Separable Convolution and Attention Mechanism. - Zhigao Cai; Xing-Ming Zhao (CoRR, 2024)