Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

Cited by (576)

Items 501–576 of 576

1. A Network Propagation Based Approach for Measuring Cell-Cell Similarity
   Jie Li, Bingbo Wang, Jiaqi Li · 2023 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2. Additional file 5 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
   Matan Sorek, Walaa Oweis, Malka Nissim‐Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi et al. · 2021 · Figshare
3. Additional file 2 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
   Matan Sorek, Walaa Oweis, Malka Nissim‐Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi et al. · 2021 · Figshare
4. Additional file 4 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
   Matan Sorek, Walaa Oweis, Malka Nissim‐Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi et al. · 2021 · Figshare
5. Additional file 3 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
   Matan Sorek, Walaa Oweis, Malka Nissim‐Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi et al. · 2021 · Figshare
6. Additional file 2 of ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
   Yang Li, Mingcong Wu, Shuangge Ma, Mengyun Wu · 2023 · Figshare
7. A Fusion Learning Model Based on Deep Learning for Single-Cell RNA Sequencing Data Clustering
   Tian-Jing Qiao, Feng Li, Shasha Yuan, Ling-Yun Dai, Juan Wang · 2024 · Journal of Computational Biology
8. MLRR-ATV: A Robust Manifold Nonnegative Low-Rank Representation With Adaptive Total-Variation Regularization for scRNA-seq Data Clustering
   Gao-Fei Wang, Juan Wang, Shasha Yuan, Chun-Hou Zheng, Jin‐Xing Liu · 2024 · IEEE Transactions on Computational Biology and Bioinformatics
9. Hypergraph-based Clustering for Single-Cell RNA Sequencing Data
   Can Hu, Yuxia Sheng · 2024 · Chinese Control Conference (CCC)
10. scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data
    Yutian Wang, Ke Gao, Zhaomei Li, Chuanxin Liu, Cunmei Ji, Lijuan Qiao, Chun-Hou Zheng · 2025 · Current Bioinformatics
11. CycleMix: Gaussian mixture modeling of the cell cycle
    Jack E. Peplinski, Tallulah S. Andrews · 2026 · Bioinformatics Advances
12. Compressed Representation of Extreme Learning Machine with Self-Diffusion Graph Denoising Applied for Dissecting Molecular Heterogeneity
    Xin Duan, Xinnan Ding, Yuelin Lu · 2025 · Journal of Computational Biology
13. Gene selection for single cell RNA-seq data via fuzzy rough iterative computation model
    Zhaowen Li, Jie Zhang, Yuxian Wang, Fang Liu, Ching‐Feng Wen · 2025 · Artificial Intelligence Review
14. Identifying Damage-Related Features in scRNA-seq Data
    Giovanni Marteletto, Bruno G. Galuzzi, Chiara Damiani · 2025 · Lecture notes in computer science
15. Subspace clustering with self-representation sparsification and regression via connected components
    Zhiguo Long, Rui Guan, Yi Qin Gao, Hua Meng, Rong Luo · 2025 · Applied Soft Computing
16. Low-Rank Multiple Kernel Model Based on Local Structures Learning and Adaptive Similarity Preserving for scRNA-seq Data Clustering
    Juan Wang, Tian-Jing Qiao, Zhenduo Zhang, Chun-Hou Zheng, Shasha Yuan · 2025 · Lecture notes in computer science
17. A novel gene expression stability metric to unveil homeostasis and regulation
    Mengjie Chen · 2025 · Genome biology
18. Joint Low Rank Representation with Symmetric Orthogonal Decomposition for Clustering of scRNA-seq Data
    Wei Zhang, Yue Yu, Yuanyuan Li, Xiaoying Zheng, Juan Shen · 2025 · Interdisciplinary Sciences Computational Life Sciences
19. Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes
    Wei Wei, Xing Wu, Chandler A. Sutherland, Yu-Ting Lin, China F. Lunde, Moisés Expósito‐Alonso, Ksenia V. Krasileva · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
20. CycleVI: isolating cell cycle variation with an interpretable deep generative model
    Pia Mozdzanowski, Marcel Tarbier, Gustavo S. Jeuken · 2026 · Bioinformatics
21. Redefining Housekeeping Genes in the Context of Vertebrate Development
    Alicia Lou, Juan F. Poyatos, Mónica Chagoyen · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
22. Additional file 1 of Obstacles to detecting isoforms using full-length scRNA-seq data
    Jennifer Westoby, Pavel Artemov, Hemberg, Martin, Ferguson-Smith, Anne · 2020 · Figshare
23. Additional file 1 of Deconstructing transcriptional variations and their effects on immunomodulatory function among human mesenchymal stromal cells
    Sun, Changbin, Zhang, Kehua, Yue, Jianhui, Shufang Meng, Zhang, Xi · 2021 · Figshare
24. Additional file 4 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
25. Additional file 5 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
26. Additional file 8 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
27. Additional file 2 of A new and effective two-step clustering approach for single cell RNA sequencing data
    Ruiyi Li, Jihong Guan, Zhiye Wang, ShuiGeng ZHOU · 2023 · Figshare
28. Additional file 2 of Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages
    Ji, Xiangjun, Junwei Cai, Liang, Lixin, Tieliu SHI, J. Liu · 2024 · Figshare
29. Additional file 10 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
30. Additional file 1 of VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells
    Reyna Edith Rosales-Alvarez, Jasmin Rettkowski, Josip S. Herman, Gabrijela Dumbović, Nina Cabezas‐Wallscheid, Dominic Grün · 2023 · Figshare
31. Additional file 1 of Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging
    Huiwen Zheng, Jan Vijg, Atefeh Taherian Fard, Jessica C. Mar · 2024 · Figshare
32. Additional file 2 of ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics
    Hao, Yajing, Shuyang Zhang, Changwei Shao, Li, Junhui, Zhao, Guofeng, Dong‐Er Zhang, Fu, Xiang-Dong · 2022 · Figshare
33. Additional file 1 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
34. Additional file 1 of ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
    Li, Yang, Mingcong Wu, Ma, Shuangge, Wu, Mengyun · 2023 · Figshare
35. Additional file 9 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
36. Additional file 1 of Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
    Liu, Jialin, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson‐Rechavi · 2020 · Figshare
37. Additional file 6 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
    Matan Sorek, Walaa Oweis, Nissim-Rafinia, Malka, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi et al. · 2021 · Figshare
38. Additional file 2 of Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging
    Huiwen Zheng, Jan Vijg, Atefeh Taherian Fard, Jessica C. Mar · 2024 · Figshare
39. Additional file 1 of Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages
    Ji, Xiangjun, Cai, Junwei, Liang, Lixin, Tieliu SHI, J. Liu · 2024 · Figshare
40. Additional file 2 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Nie, Qing, Arthur D. Lander · 2024 · Figshare
41. Additional file 3 of A new and effective two-step clustering approach for single cell RNA sequencing data
    Ruiyi Li, Jihong Guan, Zhiye Wang, ShuiGeng ZHOU · 2023 · Figshare
42. Additional file 1 of A new and effective two-step clustering approach for single cell RNA sequencing data
    Ruiyi Li, Jihong Guan, Zhiye Wang, ShuiGeng ZHOU · 2023 · Figshare
43. Additional file 2 of Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
    Liu, Jialin, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson‐Rechavi · 2020 · Figshare
44. Additional file 2 of Obstacles to detecting isoforms using full-length scRNA-seq data
    Jennifer Westoby, Pavel Artemov, Hemberg, Martin, Ferguson-Smith, Anne · 2020 · Figshare
45. Additional file 1 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity
    Matan Sorek, Walaa Oweis, Nissim-Rafinia, Malka, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean Simmons, Neville E. Sanjana, Xi Shi et al. · 2021 · Figshare
46. Additional file 3 of ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
    Li, Yang, Mingcong Wu, Ma, Shuangge, Wu, Mengyun · 2023 · Figshare
47. Additional file 7 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
48. Additional file 11 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
49. Additional file 4 of ZINBMM: a general mixture model for simultaneous clustering and gene selection using single-cell transcriptomic data
    Li, Yang, Mingcong Wu, Ma, Shuangge, Wu, Mengyun · 2023 · Figshare
50. Additional file 3 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
51. Additional file 2 of VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells
    Reyna Edith Rosales-Alvarez, Jasmin Rettkowski, Josip S. Herman, Gabrijela Dumbović, Nina Cabezas‐Wallscheid, Dominic Grün · 2023 · Figshare
52. Additional file 1 of ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics
    Hao, Yajing, Shuyang Zhang, Changwei Shao, Li, Junhui, Zhao, Guofeng, Dong‐Er Zhang, Fu, Xiang-Dong · 2022 · Figshare
53. Additional file 6 of Leveraging gene correlations in single cell transcriptomic data
    Kai Silkwood, Emmanuel Dollinger, Joshua Gervin, Scott X. Atwood, Qing Nie, Arthur D. Lander · 2024 · Figshare
54. Kernel Non-negative Matrix Factorization Framework for Single Cell Clustering
    Hao Jiang, Wai‐Ki Ching · 2026 · Intelligent control and learning systems
55. Heterogeneous Gene Network Estimation for Single-Cell Transcriptomic Data via a Joint Regularized Deep Neural Network
    Jingyuan Yang, Tao Li, Tianyi Wang, Shuangge Ma, Mengyun Wu · 2026 · Journal of the American Statistical Association
56. Self-Training Clustering Algorithm with AdaptiveConfidence for Single-Cell Sequencing Data
    Tong Wu, Dan Li · 2025 · International Conference on Systems and Informatics (ICSAI)
57. An Adaptive Single-Cell Sequencing Data Cluster Method Under Weight Fusion Constraint
    Zhenchang Wang, ShaSha Yuan, Feng Li, Juan Wang · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
58. sxFusion: A Novel Single-Cell Clustering Tool Based on Feature Fusion and Co-Optimization of Low-Rank Representation
    Linping Wang, Jiarong Wu, Jinqiao Wang, Jiayi Zhang, Hongxing Xu, Keyi Xiong, Xiangqi Bai, Kaida Ning, Li Charlie Xia · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
59. sc3M: Multi-Level Graph Contrastive Learning with Min-Max Principle for Clustering scRNA-Seq Data
    Zongpei Ma, Cunmei Ji, Chuanxin Liu, Haoze Li, Yutian Wang, Chunhou Zheng · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
60. GAEKLRR: A novel clustering method of the low-rank representation based on graph auto-encoder and relaxed k-means for single-cell type identification
    Linping Wang, Junliang Shang, Lingyun Dai, Juan Wang · 2025 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
61. Gateway analysis reveals transient molecular programs at cell-fate transitions
    Hu Cang, Sha Sun · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
62. A Novel Low-Dimensional Sparse and Low-Rank Representation Method for Single-Cell RNA Sequencing Data Clustering
    Zhenduo Zhang, Junliang Shang, Lingyun Dai, Juan Wang · 2026 · IEEE Transactions on Computational Biology and Bioinformatics
63. Netrin signaling function in human and non-human primates’ pluripotency regulation
    Etienne Masfaraud · 2021 · theses.fr (ABES)
64. Neuronal activity drives microglial calcium signaling through purinergic signaling system
    Giorgio Cignitti · 2021 · theses.fr (ABES)
65. Dynamics of H3.1 and H3.3 histone variants at mouse chromocenters during cell cycle and differentiation
    Stefano Arfè · 2022 · theses.fr (ABES)
66. Functional Separation of mRNA Domains Coordinates Pluripotent Cell Behavior
    Ze Yang, Shaoyi Ji, Kristina Ivanov, Priyanka Kadav, Mengmeng Song, Leonardi Gozali, Sophie Parsa, Barry R. Behr, Mary Hynes · 2026 · eLife
67. Functional Separation of mRNA Domains Coordinates Pluripotent Cell Behavior
    Ze Yang, Shaoyi Ji, Kristina Ivanov, Priyanka Kadav, Mengmeng Song, Leonardi Gozali, Sophie Parsa, Barry R. Behr, Mary Hynes · 2026 · eLife
68. Development and comparison of evaluation metrics for batch correction reveals performance differences
    Aleksi Laiho, M P E Laitinen, Liisa Holm, Petri Törönen · 2026 · Bioinformatics Advances
69. scFANCL: Dual contrastive learning with false-negative correction at cell level for single-cell RNA-seq clustering
    Gunho Choi, Minsik Oh · 2026 · BMC Genomics
70. Single‐cell marker gene clustering: A unified deep learning framework for marker gene‐based clustering of single‐cell RNA‐sequencing data
    Shahriar Rahman Niloy, Toushif Muktashid Hasan, Md. Saiduzzaman Apu, Fahim Hafiz, Salekul Islam, Riasat Azim · 2026 · Quantitative Biology
71. Ligand‐dependent transcriptional heterogeneity in cell cycle gene expression delays G1 /S entry
    Ririn Rahmala Febri, Ayaka Ichikawa Nagasato, Keita Iida, Shuhei Kimura, Akira Imamoto, Mariko Okada · 2026 · FEBS Letters
72. Clonal memory in human embryonic stem cells biases fate potential during endoderm differentiation
    Madeleine Linneberg-Agerholm, Álvaro Bustos Gutiérrez, Stine Lind Hansen, 裕 清水, Nicolaj Strøyer Christophersen, Samantha A. Morris, Atefeh Lafzi · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
73. Developmental and tissue expression breadth define distinct but overlapping classes of housekeeping genes
    Alicia Lou, Juan F. Poyatos, Mónica Chagoyen · 2026 · PLoS Computational Biology
74. MiCAS: Mixture-based Cell Annotation with Open-Set Recognition for scRNA-seq Data
    Elif İzci, Berat Doğan · 2026 · Research Square
75. Explainable t-SNE for Single-Cell RNA-seq Data Analysis: A Cell-Driven Information Fusion Framework
    Henry Han, Tianyu Zhang, Luyu Niu, Jiacun Wang, Fei Han, Chun Li, Junyi Li, Huaixin CAO · 2026 · SSRN Electronic Journal
76. PDSFLRR: Low-rank representation with projection distance and sparsity constraints for clustering single-cell RNA sequencing data
    Juan Wang, Zhenduo Zhang · 2026 · Computational Biology and Chemistry