Xing-Ming Zhao

89 papers B 5C 1Journal 69Unranked 13
YearRankTypeTitle / Venue / Authors
2025 B conf
Generalized Fetal Brain Segmentation and Identification from Multi-View MRI.
SMC
Zhigao Cai, Qiongjie Zhou, Xiaotian Li, Xing-Ming Zhao
2025 J jnl
Regulatory Genomic Circuitry of Brain Age by Integrative Functional Genomic Analyses.
Genom. Proteom. Bioinform.
Xingzhong Zhao, Anyi Yang, Jing Ding, Yucheng T. Yang, Xing-Ming Zhao
2024 J jnl
Enhancing Generalized Fetal Brain MRI Segmentation using A Cascade Network with Depth-wise Separable Convolution and Attention Mechanism.
CoRR
Zhigao Cai, Xing-Ming Zhao
2024 J jnl
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework.
Briefings Bioinform.
Kai Shi, Qiaohui Liu, Qingrong Ji, Qisheng He, Xing-Ming Zhao
2023 J jnl
A survey on computational strategies for genome-resolved gut metagenomics.
Briefings Bioinform.
Long-Hao Jia, Yingjian Wu, Yanqi Dong, Jingchao Chen, Wei-Hua Chen, Xing-Ming Zhao
2023 J jnl
Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics.
Briefings Bioinform.
Xingzhong Zhao, Anyi Yang, Zi-Chao Zhang, Yucheng T. Yang, Xing-Ming Zhao
2023 J jnl
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
Zi-Chao Zhang, Xingzhong Zhao, Guiying Dong, Xing-Ming Zhao
2023 — conf
Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues.
BIBM
Xingzhong Zhao, Yucheng T. Yang, Xing-Ming Zhao
2023 J jnl
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing.
Bioinform.
Shaojun Pan, Xing-Ming Zhao, Luís Pedro Coelho
2022 J jnl
An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.
Briefings Bioinform.
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
2022 J jnl
CITEdb: a manually curated database of cell-cell interactions in human.
Bioinform.
Nayang Shan, Yao Lu, Hao Guo, Dongyu Li, Jitong Jiang, Linlin Yan, Jiudong Gao, Yong Ren, Xing-Ming Zhao, Lin Hou
2022 J jnl
Co-VAE: Drug-Target Binding Affinity Prediction by Co-Regularized Variational Autoencoders.
IEEE Trans. Pattern Anal. Mach. Intell.
Tianjiao Li, Xing-Ming Zhao, Limin Li
2022 J jnl
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice.
Genom. Proteom. Bioinform.
Yanze Li, Wenming Cao, Na L. Gao, Xing-Ming Zhao, Wei-Hua Chen
2022 J jnl
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.
Nucleic Acids Res.
Die Dai, Jiaying Zhu, Chuqing Sun, Min Li, Jinxin Liu, Sicheng Wu, Ning Kang, Lijie He, Xing-Ming Zhao, Wei-Hua Chen
2022 J jnl
MorbidGCN: prediction of multimorbidity with a graph convolutional network based on integration of population phenotypes and disease network.
Briefings Bioinform.
Guiying Dong, Zi-Chao Zhang, Jianfeng Feng, Xing-Ming Zhao
2022 J jnl
mBodyMap: a curated database for microbes across human body and their associations with health and diseases.
Nucleic Acids Res.
Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing-Ming Zhao, Wei-Hua Chen
2021 J jnl
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics.
IEEE ACM Trans. Comput. Biol. Bioinform.
Kai Shi, Wei Lin, Xing-Ming Zhao
2021 J jnl
Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes.
Briefings Bioinform.
Xingzhong Zhao, Jingqi Chen, Peipei Xiao, Jianfeng Feng, Qing Nie, Xing-Ming Zhao
2021 J jnl
MAT2: manifold alignment of single-cell transcriptomes with cell triplets.
Bioinform.
Jinglong Zhang, Xu Zhang, Ying Wang, Feng Zeng, Xing-Ming Zhao
2021 J jnl
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Nucleic Acids Res.
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
2021 J jnl
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information.
Bioinform.
Hangyuan Yang, Minghui Wang, Xia Liu, Xing-Ming Zhao, Ao Li
2021 J jnl
STAB: a spatio-temporal cell atlas of the human brain.
Nucleic Acids Res.
Liting Song, Shaojun Pan, Zichao Zhang, Long-Hao Jia, Wei-Hua Chen, Xing-Ming Zhao
2021 J jnl
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements.
Nucleic Acids Res.
Senying Lai, Long-Hao Jia, Balakrishnan Subramanian, Shaojun Pan, Jinglong Zhang, Yanqi Dong, Wei-Hua Chen, Xing-Ming Zhao
2021 J jnl
nMAGMA: a network-enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia.
Briefings Bioinform.
Anyi Yang, Jingqi Chen, Xing-Ming Zhao
2020 J jnl
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks.
Bioinform.
Zi-Chao Zhang, Xiao-Fei Zhang, Min Wu, Le Ou-Yang, Xing-Ming Zhao, Xiaoli Li
2020 J jnl
Deep convolutional neural network for accurate segmentation and quantification of white matter hyperintensities.
Neurocomputing
Liangliang Liu, Shaowu Chen, Xiaofeng Zhu, Xing-Ming Zhao, Fang-Xiang Wu, Jianxin Wang
2020 J jnl
GANcon: Protein Contact Map Prediction With Deep Generative Adversarial Network.
IEEE Access
Hang Yang, Minghui Wang, Zhenhua Yu, Xing-Ming Zhao, Ao Li
2020 J jnl
GMrepo: a database of curated and consistently annotated human gut metagenomes.
Nucleic Acids Res.
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
2020 J jnl
scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation.
Bioinform.
Ke Jin, Le Ou-Yang, Xing-Ming Zhao, Hong Yan, Xiao-Fei Zhang
2019 J jnl
DeepPhos: prediction of protein phosphorylation sites with deep learning.
Bioinform.
Fenglin Luo, Minghui Wang, Yu Liu, Xing-Ming Zhao, Ao Li
2019 J jnl
DrPOCS: Drug Repositioning Based on Projection Onto Convex Sets.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yin-Ying Wang, Chunfeng Cui, Liqun Qi, Hong Yan, Xing-Ming Zhao
2019 J jnl
EmDL: Extracting miRNA-Drug Interactions from Literature.
IEEE ACM Trans. Comput. Biol. Bioinform.
Wen-Bin Xie, Hong Yan, Xing-Ming Zhao
2019 J jnl
EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning.
Bioinform.
Xiao-Fei Zhang, Le Ou-Yang, Shuo Yang, Xing-Ming Zhao, Xiaohua Hu, Hong Yan
2019 J jnl
Joint Learning of Multiple Differential Networks With Latent Variables.
IEEE Trans. Cybern.
Le Ou-Yang, Xiao-Fei Zhang, Xing-Ming Zhao, Debby Dan Wang, Fu Lee Wang, Baiying Lei, Hong Yan
2019 J jnl
Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
Nucleic Acids Res.
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
2018 J jnl
MVP: a microbe-phage interaction database.
Nucleic Acids Res.
Na L. Gao, Chengwei Zhang, Zhanbing Zhang, Songnian Hu, Martin J. Lercher, Xing-Ming Zhao, Peer Bork, Zhi Liu, Wei-Hua Chen
2018 — conf
Prediction of Drug Response with a Topology Based Dual-Layer Network Model.
ISBRA
Suyun Huang, Xing-Ming Zhao
2017 J jnl
CSTEA: a webserver for the Cell State Transition Expression Atlas.
Nucleic Acids Res.
Guanghui Zhu, Hui Yang, Xiao Chen, Jun Wu, Yong Zhang, Xing-Ming Zhao
2017 — conf
Exploring functional variant using a deep learning framework.
CASE
Tianyi Sun, Zhuo Liu, Xing-Ming Zhao, Rui Jiang
2017 J jnl
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.
Wei-Hua Chen, Guanting Lu, Xiao Chen, Xing-Ming Zhao, Peer Bork
2017 J jnl
PCID: A Novel Approach for Predicting Disease Comorbidity by Integrating Multi-Scale Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Feng He, Guanghui Zhu, Yin-Ying Wang, Xing-Ming Zhao, De-Shuang Huang
2017 — conf
PPIM: A protein-protein interaction database for Maize.
CASE
Guanghui Zhu, Rui Jiang, Xing-Ming Zhao
2017 J jnl
PhosD: inferring kinase-substrate interactions based on protein domains.
Bioinform.
Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao
2016 B conf
A hybrid sequential feature selection approach for the diagnosis of Alzheimer's Disease.
IJCNN
Yang Han, Xing-Ming Zhao
2016 J jnl
A survey on biomarker identification based on molecular networks.
Quant. Biol.
Guanghui Zhu, Xing-Ming Zhao, Jun Wu
2016 J jnl
A systematic exploration of the associations between amino acid variants and post-translational modifications.
Neurocomputing
Gui-Min Qin, Yi-Bo Hou, Xing-Ming Zhao
2016 J jnl
Data Mining in Systems Biology.
IEEE ACM Trans. Comput. Biol. Bioinform.
Xing-Ming Zhao
2016 J jnl
Data mining in systems biology.
Neurocomputing
Ao Li, Xing-Ming Zhao, Shuigeng Zhou
2016 J jnl
Identifying Disease Associated miRNAs Based on Protein Domains.
IEEE ACM Trans. Comput. Biol. Bioinform.
Gui-Min Qin, Rui-Yi Li, Xing-Ming Zhao
2016 — conf
The exploration of functional divergence between human and macaque brains based on gene networks.
BIBM
Peipei Xiao, Xing-Ming Zhao
2016 J jnl
Understanding tissue-specificity with human tissue-specific regulatory networks.
Sci. China Inf. Sci.
Wei-Li Guo, Lin Zhu, Suping Deng, Xing-Ming Zhao, Deshuang Huang
2015 J jnl
Editorial - Data mining in bioinformatics.
J. Bioinform. Comput. Biol.
Xing-Ming Zhao
2015 J jnl
Identifying cancer-related microRNAs based on gene expression data.
Bioinform.
Xing-Ming Zhao, Keqin Liu, Guanghui Zhu, Feng He, Béatrice Duval, Jean-Michel Richer, De-Shuang Huang, Changjun Jiang, Jin-Kao Hao, Luonan Chen
2014 J jnl
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Bioinform.
Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song
2014 J jnl
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication".
PLoS Comput. Biol.
Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork
2014 J jnl
Pattern recognition in bioinformatics.
Neurocomputing
Xing-Ming Zhao, Alioune Ngom, Jin-Kao Hao
2013 J jnl
Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs.
PLoS Comput. Biol.
Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork
2013 J jnl
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference.
Bioinform.
Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao, Jin-Kao Hao, Luonan Chen
2013 — ed.
Pattern Recognition in Bioinformatics - 8th IAPR International Conference, PRIB 2013, Nice, France, June 17-20, 2013. Proceedings
PRIB
Alioune Ngom, Enrico Formenti, Jin-Kao Hao, Xing-Ming Zhao, Twan van Laarhoven
2013 — conf
Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources.
PRIB
Yan-Fen Dai, Yin-Ying Wang, Xing-Ming Zhao
2012 — conf
Comparative analysis of protein-coding genes and long non-coding RNAs of prostate cancer between Caucasian and Chinese populations.
ISB
Fu-Yan Hu, Xing-Ming Zhao, Nelson L. S. Tang, Yan Zhang, Luonan Chen
2012 — conf
Drug-target network in myocardial infarction: A structural analysis.
BIBM
Haiying Wang, Huiru Zheng, Francisco Azuaje, Xing-Ming Zhao
2012 J jnl
Exploring drug combinations in genetic interaction network.
BMC Bioinform.
Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao
2012 J jnl
Identifying disease genes and module biomarkers by differential interactions.
J. Am. Medical Informatics Assoc.
Xiaoping Liu, Zhi-Ping Liu, Xing-Ming Zhao, Luonan Chen
2012 J jnl
Identifying dysregulated pathways in cancers from pathway interaction networks.
BMC Bioinform.
Keqin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao
2012 J jnl
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information.
Bioinform.
Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu, Luonan Chen
2012 J jnl
The drug cocktail network.
BMC Syst. Biol.
Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao
2011 J jnl
Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data.
PLoS Comput. Biol.
Xing-Ming Zhao, Murat Iskar, Georg Zeller, Michael Kuhn, Vera van Noort, Peer Bork
2010 J jnl
A systems biology approach to identify effective cocktail drugs.
BMC Syst. Biol.
Zikai Wu, Xing-Ming Zhao, Luonan Chen
2010 J jnl
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.
BMC Bioinform.
Junfeng Xia, Xing-Ming Zhao, Jiangning Song, De-Shuang Huang
2010 J jnl
Analysis of Gene Expression Data Using Rpem Algorithm in Normal Mixture Model with Dynamic Adjustment of Learning Rate.
Int. J. Pattern Recognit. Artif. Intell.
Xing-Ming Zhao, Yiu-ming Cheung, De-Shuang Huang
2010 J jnl
FGsub: Fusarium graminearum protein subcellular localizations predicted from primary structures.
BMC Syst. Biol.
Chenglei Sun, Xing-Ming Zhao, Weihua Tang, Luonan Chen
2009 — conf
A New Balanced Ensemble Classifier for Predicting Fungi Protein Subcellular Localization Based on Protein Primary Structures.
BMEI
Xing-Ming Zhao, Luonan Chen
2009 J jnl
Automatic Modeling of Signaling Pathways by Network Flow Model.
J. Bioinform. Comput. Biol.
Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara
2009 — conf
Modeling and Dynamical Analysis of Molecular Networks.
Complex (2)
Ruiqi Wang, Xing-Ming Zhao, Zengrong Liu
2008 B conf
Automatic Modeling of Signal Pathways from Protein-Protein Interaction Networks.
APBC
Xing-Ming Zhao, Rui-Sheng Wang, Luonan Chen, Kazuyuki Aihara
2008 — conf
Domain-Domain Interaction Identification with a Feature Selection Approach.
PRIB
Xing-Ming Zhao, Luonan Chen
2008 J jnl
Gene Expression Data Classification Using Consensus Independent Component Analysis.
Genom. Proteom. Bioinform.
Chun-Hou Zheng, De-Shuang Huang, Xiangzhen Kong, Xing-Ming Zhao
2008 J jnl
Gene function prediction using labeled and unlabeled data.
BMC Bioinform.
Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara
2008 J jnl
Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function.
Int. J. Bioinform. Res. Appl.
Peng Chen, De-Shuang Huang, Xing-Ming Zhao, Xueling Li
2008 J jnl
Protein function prediction with the shortest path in functional linkage graph and boosting.
Int. J. Bioinform. Res. Appl.
Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara
2006 J jnl
A new technique for selecting features from protein sequences.
Int. J. Pattern Recognit. Artif. Intell.
Xing-Ming Zhao, Ji-Xiang Du, Hong-Qiang Wang, Yunping Zhu, Yixue Li
2006 — conf
Classifying G-Protein Coupled Receptors with Hydropathy Blocks and Support Vector Machines.
ICIC (3)
Xing-Ming Zhao, De-Shuang Huang, Shiwu Zhang, Yiu-ming Cheung
2006 J jnl
Classifying protein sequences using hydropathy blocks.
Pattern Recognit.
De-Shuang Huang, Xing-Ming Zhao, Guang-Bin Huang, Yiu-ming Cheung
2005 J jnl
A novel approach to extracting features from motif content and protein composition for protein sequence classification.
Neural Networks
Xing-Ming Zhao, Yiu-ming Cheung, De-Shuang Huang
2004 — conf
A Novel Clustering Analysis Based on PCA and SOMs for Gene Expression Patterns.
ISNN (2)
Hong-Qiang Wang, De-Shuang Huang, Xing-Ming Zhao, Xin Huang
2004 C conf
A Novel Hybrid GA/SVM System for Protein Sequences Classification.
IDEAL
Xing-Ming Zhao, De-Shuang Huang, Yiu-ming Cheung, Hong-Qiang Wang, Xin Huang
2004 B conf
A feature_core and SVM-based algorithm for identification of bioprocess-specific genome features.
IJCNN
Hong-Qiang Wang, Deshuang Huang, Guang-Zheng Zhang, Xing-Ming Zhao
2004 B conf
Representation of DNA sequences with multiple resolutions and BP neural network based classification.
IJCNN
Xin Huang, De-Shuang Huang, Hong-Qiang Wang, Xing-Ming Zhao