MD
Minghua Deng
Gene Expression ProfilingAlgorithmsbioinformaticsSingle-Cell Analysiscs.CVSoftwareDeep LearningSingle-Cell Gene Expression Analysiscs.IRcs.LG
On Valency
published · living versionsW_267uj4ev·v1 · currentpublished
Preprints & journals
59 papers in the corpus · 2002–2025Compositional data modeling of high-dimensional single cell RNA-seq (CoDA-hd): its advantages over commonly used normalization approaches.41121316 · Huang, Jinghan, Yam, Sheung Chi Phillip, Leung, K S et al.2025 · 1 citationJournal of translational medicine. 2025;23(1):1143
Improving Tree Probability Estimation with Stochastic Optimization and Variance Reduction.39314503 · Xie, Tianyu, Yuan, Musu, Deng, Minghua et al.2024 · 2 citationsArXiv. 2024
scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement.38935069 · Guo, Qirui, Yuan, Musu, Zhang, Lei et al.2024 · 3 citationsBriefings in bioinformatics. 2024;25(4)
scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data.38678389 · Zhai, Yuyao, Chen, Liang, Deng, Minghua2024 · 14 citationsBriefings in bioinformatics. 2024;25(3)
SPANN: annotating single-cell resolution spatial transcriptome data with scRNA-seq data.38279647 · Yuan, Musu, Wan, Hui, Wang, Zihao et al.2024 · 9 citationsBriefings in bioinformatics. 2024;25(2)
scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data.38366803 · Zhai, Yuyao, Chen, Liang, Deng, Minghua2024 · 3 citationsBriefings in bioinformatics. 2024;25(2)
Continually adapting pre-trained language model to universal annotation of single-cell RNA-seq data.38388681 · Wan, Hui, Yuan, Musu, Fu, Yiwei et al.2024 · 10 citationsBriefings in bioinformatics. 2024;25(2)
Learning a generalized graph transformer for protein function prediction in dissimilar sequences.39657158 · Fu, Yiwei, Gu, Zhonghui, Luo, Xiao et al.2024 · 13 citationsGigaScience. 2024;13
ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods.37827697 · Luo, Jiaxin, Deng, Minghua, Zhang, Xuegong et al.2023 · 74 citationsGenome research. 2023;33(10):1788-1805
Hierarchical graph transformer with contrastive learning for protein function prediction.37369035 · Gu, Zhonghui, Luo, Xiao, Chen, Jiaxiao et al.2023 · 86 citationsBioinformatics (Oxford, England). 2023;39(7)
TGNN: A Joint Semi-supervised Framework for Graph-level Classification2304.11688v1 · Wei Ju, Xiao Luo, Meng Qu et al.2023 · 43 citationsarXiv
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery.36869836 · Zhai, Yuyao, Chen, Liang, Deng, Minghua2023 · 17 citationsBriefings in bioinformatics. 2023;24(2)
Coevolution-based prediction of key allosteric residues for protein function regulation.36799896 · Xie, Juan, Zhang, Weilin, Zhu, Xiaolei et al.2023 · 40 citationseLife. 2023;12
Clustering single-cell multi-omics data with MoClust.36383167 · Yuan, Musu, Chen, Liang, Deng, Minghua2023 · 22 citationsBioinformatics (Oxford, England). 2023;39(1)
scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception.36608843 · Wan, Hui, Chen, Liang, Deng, Minghua2023 · 10 citationsGenomics, proteomics & bioinformatics. 2022;20(5):939-958
Clustering CITE-seq data with a canonical correlation-based deep learning method.36072672 · Yuan, Musu, Chen, Liang, Deng, Minghua2022 · 9 citationsFrontiers in genetics. 2022;13:977968
CLEAR: Cluster-Enhanced Contrast for Self-Supervised Graph Representation Learning.35675236 · Luo, Xiao, Ju, Wei, Qu, Meng et al.2024 · 65 citationsIEEE transactions on neural networks and learning systems. 2022;PP
Statistical Methods for Microbiome Compositional Data Network Inference: A Survey.35404093 · Chen, Liang, Wan, Hui, He, Qiuyan et al.2022 · 12 citationsJournal of computational biology : a journal of computational molecular cell biology. 2022;29(7):704-723
GHNN: Graph Harmonic Neural Networks for semi-supervised graph-level classification.35398673 · Ju, Wei, Luo, Xiao, Ma, Zeyu et al.2022 · 47 citationsNeural networks : the official journal of the International Neural Network Society. 2022;151:70-79
scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data.34999761 · Wan, Hui, Chen, Liang, Deng, Minghua2023 · 74 citationsBioinformatics (Oxford, England). 2022;38(6):1575-1583
scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets.34623390 · Yuan, Musu, Chen, Liang, Deng, Minghua2023 · 39 citationsBioinformatics (Oxford, England). 2022;38(3):738-745
ARGO: Modeling Heterogeneity in E-commerce Recommendation2109.05789v2 · Daqing Wu, Xiao Luo, Zeyu Ma et al.2021 · 9 citationsarXiv
Statistical computation methods for microbiome compositional data network inference2109.01993v1 · Liang Chen, Qiuyan He, Hui Wan et al.2021 · 0 citationsarXiv
Neighborhood Consensus Contrastive Learning for Backward-Compatible Representation2108.03372v4 · Shengsen Wu, Liang Chen, Yihang Lou et al.2021 · 10 citationsarXiv
DNA-GCN: Graph convolutional networks for predicting DNA-protein binding2106.01836v1 · Yuhang Guo, Xiao Luo, Liang Chen et al.2021 · 7 citationsIn ICIC 2021
Criterion-based Heterogeneous Collaborative Filtering for Multi-behavior Implicit Recommendation2105.11876v4 · Xiao Luo, Daqing Wu, Yiyang Gu et al.2021 · 11 citationsarXiv
Deep Unsupervised Hashing by Distilled Smooth Guidance2105.06125v1 · Xiao Luo, Zeyu Ma, Daqing Wu et al.2021 · 3 citationsICME 2021
Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation.33098418 · Chen, Liang, He, Qiuyan, Zhai, Yuyao et al.2021 · 55 citationsBioinformatics (Oxford, England). 2021;37(6):775-784
Graph Contrastive Clustering2104.01429v1 · Huasong Zhong, Jianlong Wu, Chong Chen et al.2021 · 157 citationsarXiv
Direct interaction network inference for compositional data via codaloss.33106076 · Chen, Liang, He, Shun, Zhai, Yuyao et al.2021 · 1 citationJournal of bioinformatics and computational biology. 2020;18(6):2050037
CIMON: Towards High-quality Hash Codes2010.07804v4 · Xiao Luo, Daqing Wu, Zeyu Ma et al.2020 · 36 citationsarXiv
Integrating Deep Supervised, Self-Supervised and Unsupervised Learning for Single-Cell RNA-seq Clustering and Annotation.32674393 · Chen, Liang, Zhai, Yuyao, He, Qiuyan et al.2021 · 48 citationsGenes. 2020;11(7)
Deep soft K-means clustering with self-training for single-cell RNA sequence data.33575592 · Chen, Liang, Wang, Weinan, Zhai, Yuyao et al.2021 · 143 citationsNAR genomics and bioinformatics. 2020;2(2):lqaa039
Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-Seq Data.32403260 · Chi, Weilai, Deng, Minghua2021 · 13 citationsGenes. 2020;11(5)
scRMD: imputation for single cell RNA-seq data via robust matrix decomposition.32119079 · Chen, Chong, Wu, Changjing, Wu, Linjie et al.2020 · 63 citationsBioinformatics (Oxford, England). 2020;36(10):3156-3161
Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm.32362908 · Chen, Liang, Wang, Weinan, Zhai, Yuyao et al.2024 · 35 citationsFrontiers in genetics. 2020;11:295
A Survey on Deep Hashing Methods2003.03369v5 · Xiao Luo, Haixin Wang, Daqing Wu et al.2020 · 239 citationsarXiv
Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding.31598637 · Luo, Xiao, Tu, Xinming, Ding, Yang et al.2020 · 39 citationsBioinformatics (Oxford, England). 2020;36(5):1405-1412
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.31783729 · Zhang, Haicang, Zhang, Qi, Ju, Fusong et al.2020 · 1 citationBMC bioinformatics. 2019;20(1):616
Deepprune: Learning Efficient and Interpretable Convolutional Networks Through Weight Pruning for Predicting DNA-Protein Binding.31824562 · Luo, Xiao, Chi, Weilai, Deng, Minghua2024 · 20 citationsFrontiers in genetics. 2019;10:1145
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.31664895 · Zhang, Haicang, Zhang, Qi, Ju, Fusong et al.2019 · 15 citationsBMC bioinformatics. 2019;20(1):537
Compositional data network analysis via lasso penalized D-trace loss.31220226 · Yuan, Huili, He, Shun, Deng, Minghua2020 · 21 citationsBioinformatics (Oxford, England). 2019;35(18):3404-3411
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning.29745828 · Gao, Yujuan, Wang, Sheng, Deng, Minghua et al.2019 · 52 citationsBMC bioinformatics. 2018;19(Suppl 4):100
Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation.29235710 · Xie, Wei, Luo, Haiwei, Murugapiran, Senthil K et al.2019 · 73 citationsEnvironmental microbiology. 2018;20(2):734-754
Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning1712.07244v1 · Yujuan Gao, Sheng Wang, Minghua Deng et al.2017 · 5 citationsarXiv
SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms.29036467 · Xia, Yuchao, Liu, Yun, Deng, Minghua et al.2018 · 8 citationsBioinformatics (Oxford, England). 2017;33(21):3348-3354
Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix.26920058 · Zhang, Haicang, Gao, Yujuan, Deng, Minghua et al.2016 · 20 citationsBiochemical and biophysical research communications. 2016;472(1):217-22
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.26130573 · Ren, Jie, Song, Kai, Deng, Minghua et al.2017 · 28 citationsBioinformatics (Oxford, England). 2016;32(7):993-1000
CCLasso: correlation inference for compositional data through Lasso.26048598 · Fang, Huaying, Huang, Chengcheng, Zhao, Hongyu et al.2016 · 191 citationsBioinformatics (Oxford, England). 2015;31(19):3172-80
Integrative Approaches for microRNA Target Prediction: Combining Sequence Information and the Paired mRNA and miRNA Expression Profiles.23467572 · Naifang, Su, Minping, Qian, Minghua, Deng2021 · 16 citationsCurrent bioinformatics. 2013;8(1):37-45
Career total: 106 works. 59 are in this corpus.Showing the 50 most recent.
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