Xing-Ming Zhao

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 47

Top Topics

Essential Genes

Protein Interaction

Top Venues

Nucleic Acids Res.

IEEE ACM Trans. Comput. Biol. Bioinform.

Briefings Bioinform.

Publications

Zhigao Cai, Xing-Ming Zhao
Enhancing Generalized Fetal Brain MRI Segmentation using A Cascade Network with Depth-wise Separable Convolution and Attention Mechanism. CoRR (2024)
Xingzhong Zhao, Yucheng T. Yang, Xing-Ming Zhao
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues. BIBM (2023)
Xingzhong Zhao, Anyi Yang, Zi-Chao Zhang, Yucheng T. Yang, Xing-Ming Zhao
Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics. Briefings Bioinform. 24 (2) (2023)
Long-Hao Jia, Yingjian Wu, Yanqi Dong, Jingchao Chen, Wei-Hua Chen, Xing-Ming Zhao
A survey on computational strategies for genome-resolved gut metagenomics. Briefings Bioinform. 24 (3) (2023)
Zi-Chao Zhang, Xingzhong Zhao, Guiying Dong, Xing-Ming Zhao
Improving Alzheimer's Disease Diagnosis With Multi-Modal PET Embedding Features by a 3D Multi-Task MLP-Mixer Neural Network. IEEE J. Biomed. Health Informatics 27 (8) (2023)
Shaojun Pan, Xing-Ming Zhao, Luís Pedro Coelho
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. Bioinform. 39 (Supplement-1) (2023)
Nayang Shan, Yao Lu, Hao Guo, Dongyu Li, Jitong Jiang, Linlin Yan, Jiudong Gao, Yong Ren, Xing-Ming Zhao, Lin Hou
CITEdb: a manually curated database of cell-cell interactions in human. Bioinform. 38 (22) (2022)
Tianjiao Li, Xing-Ming Zhao, Limin Li
Co-VAE: Drug-Target Binding Affinity Prediction by Co-Regularized Variational Autoencoders. IEEE Trans. Pattern Anal. Mach. Intell. 44 (12) (2022)
Guiying Dong, Zi-Chao Zhang, Jianfeng Feng, Xing-Ming Zhao
MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network. Briefings Bioinform. 23 (4) (2022)
Die Dai, Jiaying Zhu, Chuqing Sun, Min Li, Jinxin Liu, Sicheng Wu, Ning Kang, Lijie He, Xing-Ming Zhao, Wei-Hua Chen
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison. Nucleic Acids Res. 50 (D1) (2022)
Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing-Ming Zhao, Wei-Hua Chen
mBodyMap: a curated database for microbes across human body and their associations with health and diseases. Nucleic Acids Res. 50 (D1) (2022)
Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Weisheng Liu, Shannon Erhardt, Fang-Xiang Wu, Xing-Ming Zhao, Yuanfang Guan, Jun Wang, Daifeng Wang, Bin Hu, Jianxin Wang
An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease. Briefings Bioinform. 23 (1) (2022)
Yanze Li, Wenming Cao, Na L. Gao, Xing-Ming Zhao, Wei-Hua Chen
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice. Genom. Proteom. Bioinform. 20 (2) (2022)
Hangyuan Yang, Minghui Wang, Xia Liu, Xing-Ming Zhao, Ao Li
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information. Bioinform. 37 (24) (2021)
Kai Shi, Wei Lin, Xing-Ming Zhao
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
Senying Lai, Long-Hao Jia, Balakrishnan Subramanian, Shaojun Pan, Jinglong Zhang, Yanqi Dong, Wei-Hua Chen, Xing-Ming Zhao
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. Nucleic Acids Res. 49 (Database-Issue) (2021)
Jinglong Zhang, Xu Zhang, Ying Wang, Feng Zeng, Xing-Ming Zhao
MAT2: manifold alignment of single-cell transcriptomes with cell triplets. Bioinform. 37 (19) (2021)
Liting Song, Shaojun Pan, Zichao Zhang, Long-Hao Jia, Wei-Hua Chen, Xing-Ming Zhao
STAB: a spatio-temporal cell atlas of the human brain. Nucleic Acids Res. 49 (Database-Issue) (2021)
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
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Res. 49 (Database-Issue) (2021)
Anyi Yang, Jingqi Chen, Xing-Ming Zhao
nMAGMA: a network-enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia. Briefings Bioinform. 22 (4) (2021)
Liangliang Liu, Shaowu Chen, Xiaofeng Zhu, Xing-Ming Zhao, Fang-Xiang Wu, Jianxin Wang
Deep convolutional neural network for accurate segmentation and quantification of white matter hyperintensities. Neurocomputing 384 (2020)
Hang Yang, Minghui Wang, Zhenhua Yu, Xing-Ming Zhao, Ao Li
GANcon: Protein Contact Map Prediction With Deep Generative Adversarial Network. IEEE Access 8 (2020)
Ke Jin, Le Ou-Yang, Xing-Ming Zhao, Hong Yan, Xiao-Fei Zhang
scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation. Bioinform. 36 (10) (2020)
Zi-Chao Zhang, Xiao-Fei Zhang, Min Wu, Le Ou-Yang, Xing-Ming Zhao, Xiaoli Li
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks. Bioinform. 36 (11) (2020)
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, Ning Kang, Lijie He, Xing-Ming Zhao, Wei-Hua Chen
GMrepo: a database of curated and consistently annotated human gut metagenomes. Nucleic Acids Res. 48 (Database-Issue) (2020)
Samantha Sayers, Li Li, Edison Ong, Shunzhou Deng, Guanghua Fu, Yu Lin, Brian Yang, Shelley Zhang, Zhenzong Fa, Bin Zhao, Zuoshuang Xiang, Yongqing Li, Xing-Ming Zhao, Michal Olszewski, Luonan Chen, Yongqun He
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res. 47 (Database-Issue) (2019)
Wen-Bin Xie, Hong Yan, Xing-Ming Zhao
EmDL: Extracting miRNA-Drug Interactions from Literature. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Fenglin Luo, Minghui Wang, Yu Liu, Xing-Ming Zhao, Ao Li
DeepPhos: prediction of protein phosphorylation sites with deep learning. Bioinform. 35 (16) (2019)
Yin-Ying Wang, Chunfeng Cui, Liqun Qi, Hong Yan, Xing-Ming Zhao
DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xing-Ming Zhao, Xiaohua Hu, Hong Yan
EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning. Bioinform. 35 (22) (2019)
Le Ou-Yang, Xiao-Fei Zhang, Xing-Ming Zhao, Debby Dan Wang, Fu Lee Wang, Baiying Lei, Hong Yan
Joint Learning of Multiple Differential Networks With Latent Variables. IEEE Trans. Cybern. 49 (9) (2019)
Suyun Huang, Xing-Ming Zhao
Prediction of Drug Response with a Topology Based Dual-Layer Network Model. ISBRA (2018)
Na L. Gao, Chengwei Zhang, Zhanbing Zhang, Songnian Hu, Martin J. Lercher, Xing-Ming Zhao, Peer Bork, Zhi Liu, Wei-Hua Chen
MVP: a microbe-phage interaction database. Nucleic Acids Res. 46 (Database-Issue) (2018)
Guanghui Zhu, Rui Jiang, Xing-Ming Zhao
PPIM: A protein-protein interaction database for Maize. CASE (2017)
Wei-Hua Chen, Guanting Lu, Xiao Chen, Xing-Ming Zhao, Peer Bork
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Res. 45 (Database-Issue) (2017)
Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao
PhosD: inferring kinase-substrate interactions based on protein domains. Bioinform. 33 (8) (2017)
Tianyi Sun, Zhuo Liu, Xing-Ming Zhao, Rui Jiang
Exploring functional variant using a deep learning framework. CASE (2017)
Guanghui Zhu, Hui Yang, Xiao Chen, Jun Wu, Yong Zhang, Xing-Ming Zhao
CSTEA: a webserver for the Cell State Transition Expression Atlas. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Feng He, Guanghui Zhu, Yin-Ying Wang, Xing-Ming Zhao, De-Shuang Huang
PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (3) (2017)
Ao Li, Xing-Ming Zhao, Shuigeng Zhou
Data mining in systems biology. Neurocomputing 206 (2016)
Gui-Min Qin, Yi-Bo Hou, Xing-Ming Zhao
A systematic exploration of the associations between amino acid variants and post-translational modifications. Neurocomputing 206 (2016)
Yang Han, Xing-Ming Zhao
A hybrid sequential feature selection approach for the diagnosis of Alzheimer's Disease. IJCNN (2016)
Wei-Li Guo, Lin Zhu, Suping Deng, Xing-Ming Zhao, Deshuang Huang
Understanding tissue-specificity with human tissue-specific regulatory networks. Sci. China Inf. Sci. 59 (7) (2016)
Peipei Xiao, Xing-Ming Zhao
The exploration of functional divergence between human and macaque brains based on gene networks. BIBM (2016)
Guanghui Zhu, Xing-Ming Zhao, Jun Wu
A survey on biomarker identification based on molecular networks. Quant. Biol. 4 (4) (2016)
Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao
Identifying Disease Associated miRNAs Based on Protein Domains. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (6) (2016)
Xing-Ming Zhao
Data Mining in Systems Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (6) (2016)
Xing-Ming Zhao
Editorial - Data mining in bioinformatics. J. Bioinform. Comput. Biol. 13 (6) (2015)
Hong-Qiang Wang, Chun-Hou Zheng, Xing-Ming Zhao
NMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data. Bioinform. 31 (4) (2015)
Xing-Ming Zhao, Keqin Liu, Guanghui Zhu, Feng He, Béatrice Duval, Jean-Michel Richer, De-Shuang Huang, Changjun Jiang, Jin-Kao Hao, Luonan Chen
Identifying cancer-related microRNAs based on gene expression data. Bioinform. 31 (8) (2015)
Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication". PLoS Comput. Biol. 10 (7) (2014)
Xing-Ming Zhao, Alioune Ngom, Jin-Kao Hao
Pattern recognition in bioinformatics. Neurocomputing 145 (2014)
Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinform. 30 (1) (2014)
Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinform. 29 (1) (2013)
Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork
Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs. PLoS Comput. Biol. 9 (5) (2013)
Yan-Fen Dai, Yin-Ying Wang, Xing-Ming Zhao
Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources. PRIB (2013)
Xiaoping Liu, Xiaodong Zhang, Weihua Tang, Luonan Chen, Xing-Ming Zhao
. Database J. Biol. Databases Curation 2013 (2013)
Xiaoping Liu, Zhi-Ping Liu, Xing-Ming Zhao, Luonan Chen
Identifying disease genes and module biomarkers by differential interactions. J. Am. Medical Informatics Assoc. 19 (2) (2012)
Keqin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao
Identifying dysregulated pathways in cancers from pathway interaction networks. BMC Bioinform. 13 (2012)
Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao
The drug cocktail network. BMC Syst. Biol. 6 (S-1) (2012)
Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu, Luonan Chen
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinform. 28 (1) (2012)
Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao
Exploring drug combinations in genetic interaction network. BMC Bioinform. 13 (S-7) (2012)
Haiying Wang, Huiru Zheng, Francisco Azuaje, Xing-Ming Zhao
Drug-target network in myocardial infarction: A structural analysis. BIBM (2012)
Fu-Yan Hu, Xing-Ming Zhao, Nelson L. S. Tang, Yan Zhang, Luonan Chen
Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations. ISB (2012)
Xing-Ming Zhao, Murat Iskar, Georg Zeller, Michael Kuhn, Vera van Noort, Peer Bork
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data. PLoS Comput. Biol. 7 (12) (2011)
Zikai Wu, Xing-Ming Zhao, Luonan Chen
A systems biology approach to identify effective cocktail drugs. BMC Syst. Biol. 4 (S-2) (2010)
Xing-Ming Zhao, Yiu-ming Cheung, De-Shuang Huang
Analysis of Gene Expression Data Using Rpem Algorithm in Normal Mixture Model with Dynamic Adjustment of Learning Rate. Int. J. Pattern Recognit. Artif. Intell. 24 (4) (2010)
Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen
FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures. BMC Syst. Biol. 4 (S-2) (2010)
Junfeng Xia, Xing-Ming Zhao, Jiangning Song, De-Shuang Huang
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinform. 11 (2010)
Xing-Ming Zhao, Luonan Chen
A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures. BMEI (2009)
Ruiqi Wang, Xing-Ming Zhao, Zengrong Liu
Modeling and Dynamical Analysis of Molecular Networks. Complex (2) (2009)
Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara
Automatic Modeling of Signaling Pathways by Network Flow Model. J. Bioinform. Comput. Biol. 7 (2) (2009)
Peng Chen, De-Shuang Huang, Xing-Ming Zhao, Xueling Li
Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function. Int. J. Bioinform. Res. Appl. 4 (2) (2008)
Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara
Gene function prediction using labeled and unlabeled data. BMC Bioinform. 9 (2008)
Xing-Ming Zhao, Luonan Chen
Domain-Domain Interaction Identification with a Feature Selection Approach. PRIB (2008)
Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara
Protein function prediction with the shortest path in functional linkage graph and boosting. Int. J. Bioinform. Res. Appl. 4 (4) (2008)
Chun-Hou Zheng, De-Shuang Huang, Xiangzhen Kong, Xing-Ming Zhao
Gene Expression Data Classification Using Consensus Independent Component Analysis. Genom. Proteom. Bioinform. 6 (2) (2008)
Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara
Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks. APBC (2008)
Xing-Ming Zhao, De-Shuang Huang, Shiwu Zhang, Yiu-ming Cheung
Classifying G-Protein Coupled Receptors with Hydropathy Blocks and Support Vector Machines. ICIC (3) (2006)
De-Shuang Huang, Xing-Ming Zhao, Guang-Bin Huang, Yiu-ming Cheung
Classifying protein sequences using hydropathy blocks. Pattern Recognit. 39 (12) (2006)
Xing-Ming Zhao, Ji-Xiang Du, Hong-Qiang Wang, Yunping Zhu, Yixue Li
A new technique for selecting features from protein sequences. Int. J. Pattern Recognit. Artif. Intell. 20 (2) (2006)
Xing-Ming Zhao, Yiu-ming Cheung, De-Shuang Huang
A novel approach to extracting features from motif content and protein composition for protein sequence classification. Neural Networks 18 (8) (2005)
Hong-Qiang Wang, De-Shuang Huang, Xing-Ming Zhao, Xin Huang
A Novel Clustering Analysis Based on PCA and SOMs for Gene Expression Patterns. ISNN (2) (2004)
Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, Hong-Qiang Wang, Xin Huang
A Novel Hybrid GA/SVM System for Protein Sequences Classification. IDEAL (2004)