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2025	sigRGCN: A Robust Residual Graph Convolutional Network for scRNA-Seq Data Clustering IEEE Transactions on Computational Biology and Bioinformatics Zhenqiu Shu, Min Xia, Kaiwen Tan, Zhengtao Yu, Xiao-Jun Wu
2025	A semi-supervised non-negative matrix factorization model for scRNA-seq data analysis Applied Soft Computing Junjie Lan, Xiaoling Zhuo, Siman Ye, Jin Deng
2024	Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data Bioinformatics Valérie Marot-Lassauzaie, Sergi Beneyto-Calabuig, Benedikt Obermayer, Lars Velten, Dieter Beule, Laleh Haghverdi
2024	Analyzing single cell RNA sequencing with topological nonnegative matrix factorization Journal of Computational and Applied Mathematics Yuta Hozumi, Guo-Wei Wei
2024	Preprocessing of Single Cell RNA Sequencing Data Using Correlated Clustering and Projection Journal of Chemical Information and Modeling Yuta Hozumi, Kiyoto Aramis Tanemura, Guo-Wei Wei
2024	Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering Briefings in Bioinformatics Zhenqiu Shu, Min Xia, Kaiwen Tan, Yongbing Zhang, Zhengtao Yu
2024	Analyzing scRNA-seq data by CCP-assisted UMAP and tSNE PLOS ONE Yuta Hozumi, Guo-Wei Wei
2024	The rise of nonnegative matrix factorization: Algorithms and applications Information Systems Yi-Ting Guo, Qin-Qin Li, Chun-Sheng Liang
2024	Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data Computers in Biology and Medicine Hongsong Feng, Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
2024	Identification of Fatty Acid Metabolism-Related Subtypes in Gastric Cancer Aided by Machine Learning Cancer Management and Research Maolin Hou, Jinghua Chen, Le Yang, Lei Qin, Jie Liu, Haibo Zhao, Yujin Guo, Qing-Qing Yu, Qiujie Zhang
2023	A review on semi-supervised clustering Information Sciences Jianghui Cai, Jing Hao, Haifeng Yang, Xujun Zhao, Yuqing Yang
2023	A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data Frontiers in Genetics Xiaoqin Huang, Akhilesh K. Bajpai, Jian Sun, Fuyi Xu, Lu Lu, Siamak Yousefi
2023	A phenotype driven integrative framework uncovers molecular mechanisms of a rare hereditary thrombophilia PLOS ONE Noël Malod-Dognin, Gaia Ceddia, Maja Gvozdenov, Branko Tomić, Sofija Dunjić Manevski, Valentina Djordjević, Nataša Pržulj
2023	SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data Briefings in Bioinformatics Yushan Qiu, Chang Yan, Pu Zhao, Quan Zou
2022	Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases Frontiers in Cell and Developmental Biology Raquel Cuevas-Diaz Duran, Juan Carlos González-Orozco, Iván Velasco, Jia Qian Wu
2022	2022 International Conference on Algorithms, Data Mining, and Information Technology (ADMIT) Ailian Yu, Yuan Zhu
2022	Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering Journal of Chemical Information and Modeling Zhenqiu Shu, Qinghan Long, Luping Zhang, Zhengtao Yu, Xiao-Jun Wu
2021	CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data Bioinformatics Ziyang Wei, Shuqin Zhang
2021	Identification and Validation of Three PDAC Subtypes and Individualized GSVA Immune Pathway-Related Prognostic Risk Score Formula in Pancreatic Ductal Adenocarcinoma Patients Journal of Oncology Deyu Zhang, Meiqi Wang, Lisi Peng, Xiaoli Yang, Keliang Li, Hua Yin, Chuanchao Xia, Fang Cui, Haojie Huang, Zhendong Jin
2021	SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization PeerJ Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda
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