Impact of similarity metrics on single-cell RNA-seq data clustering
Kim, Taiyun, Chen, Irene Rui, Lin, Yingxin, Wang, Andy Yi-Yang, Yang, Jean Yee Hwa, Yang, Pengyi·2019·Briefings in Bioinformatics
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- Peer Review #2 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.1)"2023 · PeerJ
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- Differences between Bioinformatics and Computational BiologyDr P Hariharan, S.V.A.R Sastry · 2022 · Transaction on Biomedical Engineering Applications and Healthcare
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- Machine Learning-based Approaches to Integrate Heterogeneous Data for Biological Knowledge TransferYoungjun Park · 2024
- TopoMetry systematically learns and evaluates the latent geometry of single-cell dataDavi Sidarta-Oliveira, Ana Isabel Domingos, Licio Augusto Velloso · 2024 · eLife
- Evaluating the relevance of health-related topics using three similarity measuresYifan Zhu, Jin Zhang · 2025 · Information Development
- Gene print-based cell subtypes annotation of human disease across heterogeneous datasets with gPRINTRuojin Yan, Chunmei Fan, Shen Gu, Tingzhang Wang, Zi Yin, Xiao Chen · 2025 · Protein & Cell
- Stereotyped Subclones Revealed by High‐Density Single‐Cell Lineage Tracing Support Robust DevelopmentXiaoyu Zhang, Zizhang Li, Jingyu Chen, Wenjing Yang, Xiaoshun He, Peng Wu, Feng Chen, Ziwei Zhou, Chenze Ren, Yuyan Shan et al. · 2025 · Advanced Science
- High-resolution comparative single-cell transcriptomics of doublesex -expressing neurons reveals evolutionary conservation and diversity of sexual circuits in DrosophilaJustin T. Walsh, Ian P. Junker, Yu‐Chieh Chen, Yen‐Chung Chen, Helena Gifford, Yun Ding · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Consensus spectral clustering with weighted similarity functions for single-cell RNA sequencing dataXiaodan Zhu, Zhide Fang · 2025 · Communications in Statistics - Simulation and Computation
- Clustering Single-Cell RNA Sequencing Data Using LEIDEN AlgorithmMothe Rajesh, Soora Narasimha Reddy, Rakesh Mamidi, Sayyed Hasanoddin, Pallavi Gudimilla, Ambigalla Sharada · 2025 · International Conference on Emerging Techniques in Computational Intelligence (ICETCI)
- Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectoriesSolène Song, Paul Villoutreix · 2025 · PLoS Computational Biology
- Additional file 1 of treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry dataChan, Adam, Jiang, Wei, Emily Blyth, Jean Yee Hwa Yang, Ellis Patrick · 2021 · Figshare
- Additional file 1 of Euclidean distance-optimized data transformation for cluster analysis in biomedical data (EDOtrans)Alfred Ultsch, Jörn Lötsch · 2022 · Figshare
- Additional file 2 of treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry dataChan, Adam, Jiang, Wei, Emily Blyth, Jean Yee Hwa Yang, Ellis Patrick · 2021 · Figshare
- Additional file 1 of The effect of data transformation on low-dimensional integration of single-cell RNA-seqYoungjun Park, Anne-Christin Hauschild · 2024 · Figshare
- Additional file 1 of Improving replicability in single-cell RNA-Seq cell type discovery with DuneHector Roux de Bézieux, Street, Kelly, Stephan Fischer, Van den Berge, Koen, Rebecca K. Chance, Davide Risso, Jesse A Gillis, John Ngai, Elizabeth A. Purdom, Sandrine Dudoit · 2024 · Figshare
- Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic AnalysisJinpu Cai, Yuxuan Wang, Yunhao Qiao, Cheng Wang, Ziqi Rong, 禄庭 周, Haoyang Liu, Meng Jiang, Hong-Bin Shen, Jingyi Jessica Li et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Mécanismes développementaux orchestrant la différenciation des cellules souches pluripotentes induites en cellules souches hématopoïétiquesOlivier Piau · 2023 · theses.fr (ABES)
- Uncovering cellular composition changes: Cutting-edge differential abundance methods for single-cell RNA sequencingYingxue Xiao, J. Sun, You-Jin Hao, Ling-Ling Xie, Hongrui Duo, Yue Zou, Yinghong Li, Dan Qin, Qingxia Yang, Bo Li · 2026 · Trends in Analytical Chemistry (TrAC)
- The Spatial Landscape of Extracellular Matrix Gene Expression in Healthy and Type 2 Diabetic Human PancreasLuisa K. Meneses, Honesty Kim, Gregory L. Szot, Julie B. Sneddon, Zev J. Gartner · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- RAG: a regularized adaptive graph-based method for rare-cell identification from single-cell expression dataX X Wang, Yanyan Chen, Dian Huang, Zhen Ju, Qi Wei, Shu Li, Shengzhong Feng · 2026 · Briefings in Bioinformatics
- scDFVA: Single-Cell Deep Clustering by Fusing Variational Graph Attention Autoencoder and ZINB-Based AutoencoderGe Zhang, Maohua Qin, Xuye Kou, Huimin Luo, Jianlin Wang, Junwei Luo · 2026 · Journal of Computational Biology
- A novel batch effect correction framework for robust integration of high-variance data via a global-information virtual reference batchYuqian Liu, Lan Du, Jingxuan Jiang, Xin Tong, Junfei Xu, Jiayin Wang, Xin Lai · 2026 · Frontiers in Microbiology
- scDEAN: a lightweight adaptive fusion model for clustering scRNA-seq dataSubhashis Chatterjee, Rohit Bose · 2026 · Applied Intelligence