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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Items 101–136 of 136

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  3. Shared Differential Expression-Based Distance Reflects Global Cell Type Relationships in Single-Cell RNA Sequencing Data
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  4. Consensus Nature Inspired Clustering of Single-Cell RNA-Sequencing Data
    Amany H. Abou El-Naga, Sabah Sayed, Akram Salah, Heba Mohsen · 2022 · IEEE Access
  5. Peer Review #2 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.1)"
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  6. Peer Review #1 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.2)"
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  7. Peer Review #1 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.1)"
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  8. Peer Review #3 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.1)"
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  9. Peer Review #3 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.2)"
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  10. Peer Review #2 of "A clustering method for small scRNA-seq data based on subspace and weighted distance (v0.2)"
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  11. Differences between Bioinformatics and Computational Biology
    Dr P Hariharan, S.V.A.R Sastry · 2022 · Transaction on Biomedical Engineering Applications and Healthcare
  12. Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis
    Kazuki Kitamura, Takayoshi Yamamoto, Haruki Ochi, Makoto Suzuki, Nanoka Suzuki, Takeshi Igawa, Tadashi Yoshida, Mitsuru Futakuchi, Hajime Ogino, Tatsuo Michiue · 2023 · Scientific Reports
  13. Cross-Dataset Identification of Human Disease-Specific Cell Subtypes Enabled by the Gene Print-based Algorithm--gPRINT
    Ruojin Yan, Chunmei Fan, Shen Gu, Tingzhang Wang, Zi Yin, Xiao Chen · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Stereotyped cell lineage trees support robust development
    Xiaoyu Zhang, Zizhang Li, Jingyu Chen, Wenjing Yang, Peng Wu, Feng Chen, Xingxing He, Xiaoshu Chen, Jian‐Rong Yang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  15. Machine Learning-based Approaches to Integrate Heterogeneous Data for Biological Knowledge Transfer
    Youngjun Park · 2024
  16. TopoMetry systematically learns and evaluates the latent geometry of single-cell data
    Davi Sidarta-Oliveira, Ana Isabel Domingos, Licio Augusto Velloso · 2024 · eLife
  17. Evaluating the relevance of health-related topics using three similarity measures
    Yifan Zhu, Jin Zhang · 2025 · Information Development
  18. Gene print-based cell subtypes annotation of human disease across heterogeneous datasets with gPRINT
    Ruojin Yan, Chunmei Fan, Shen Gu, Tingzhang Wang, Zi Yin, Xiao Chen · 2025 · Protein & Cell
  19. Stereotyped Subclones Revealed by High‐Density Single‐Cell Lineage Tracing Support Robust Development
    Xiaoyu Zhang, Zizhang Li, Jingyu Chen, Wenjing Yang, Xiaoshun He, Peng Wu, Feng Chen, Ziwei Zhou, Chenze Ren, Yuyan Shan et al. · 2025 · Advanced Science
  20. High-resolution comparative single-cell transcriptomics of doublesex -expressing neurons reveals evolutionary conservation and diversity of sexual circuits in Drosophila
    Justin T. Walsh, Ian P. Junker, Yu‐Chieh Chen, Yen‐Chung Chen, Helena Gifford, Yun Ding · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  21. Consensus spectral clustering with weighted similarity functions for single-cell RNA sequencing data
    Xiaodan Zhu, Zhide Fang · 2025 · Communications in Statistics - Simulation and Computation
  22. Clustering Single-Cell RNA Sequencing Data Using LEIDEN Algorithm
    Mothe Rajesh, Soora Narasimha Reddy, Rakesh Mamidi, Sayyed Hasanoddin, Pallavi Gudimilla, Ambigalla Sharada · 2025 · International Conference on Emerging Techniques in Computational Intelligence (ICETCI)
  23. Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories
    Solène Song, Paul Villoutreix · 2025 · PLoS Computational Biology
  24. Additional file 1 of treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data
    Chan, Adam, Jiang, Wei, Emily Blyth, Jean Yee Hwa Yang, Ellis Patrick · 2021 · Figshare
  25. Additional file 1 of Euclidean distance-optimized data transformation for cluster analysis in biomedical data (EDOtrans)
    Alfred Ultsch, Jörn Lötsch · 2022 · Figshare
  26. Additional file 2 of treekoR: identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data
    Chan, Adam, Jiang, Wei, Emily Blyth, Jean Yee Hwa Yang, Ellis Patrick · 2021 · Figshare
  27. Additional file 1 of The effect of data transformation on low-dimensional integration of single-cell RNA-seq
    Youngjun Park, Anne-Christin Hauschild · 2024 · Figshare
  28. Additional file 1 of Improving replicability in single-cell RNA-Seq cell type discovery with Dune
    Hector 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
  29. Information Geometry Reconciles Discrete and Continuous Variation in Single-Cell and Spatial Transcriptomic Analysis
    Jinpu 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)
  30. Mécanismes développementaux orchestrant la différenciation des cellules souches pluripotentes induites en cellules souches hématopoïétiques
    Olivier Piau · 2023 · theses.fr (ABES)
  31. Uncovering cellular composition changes: Cutting-edge differential abundance methods for single-cell RNA sequencing
    Yingxue 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)
  32. The Spatial Landscape of Extracellular Matrix Gene Expression in Healthy and Type 2 Diabetic Human Pancreas
    Luisa K. Meneses, Honesty Kim, Gregory L. Szot, Julie B. Sneddon, Zev J. Gartner · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  33. RAG: a regularized adaptive graph-based method for rare-cell identification from single-cell expression data
    X X Wang, Yanyan Chen, Dian Huang, Zhen Ju, Qi Wei, Shu Li, Shengzhong Feng · 2026 · Briefings in Bioinformatics
  34. scDFVA: Single-Cell Deep Clustering by Fusing Variational Graph Attention Autoencoder and ZINB-Based Autoencoder
    Ge Zhang, Maohua Qin, Xuye Kou, Huimin Luo, Jianlin Wang, Junwei Luo · 2026 · Journal of Computational Biology
  35. A novel batch effect correction framework for robust integration of high-variance data via a global-information virtual reference batch
    Yuqian Liu, Lan Du, Jingxuan Jiang, Xin Tong, Junfei Xu, Jiayin Wang, Xin Lai · 2026 · Frontiers in Microbiology
  36. scDEAN: a lightweight adaptive fusion model for clustering scRNA-seq data
    Subhashis Chatterjee, Rohit Bose · 2026 · Applied Intelligence