Power analysis of single-cell RNA-sequencing experiments

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1. Additional file 4 of Transcriptomic changes in single yeast cells under various stress conditions
   Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis, Zhengchang Su · 2023 · Figshare
2. Additional file 3 of Transcriptomic changes in single yeast cells under various stress conditions
   Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis, Zhengchang Su · 2023 · Figshare
3. Additional file 5 of Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
   Tracy Yamawaki, Daniel Lu, Daniel Christian Ellwanger, Dev M. Bhatt, Paolo S. Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver R. Homann, Songli Wang et al. · 2021 · Figshare
4. Additional file 3 of Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
   Tracy Yamawaki, Daniel Lu, Daniel Christian Ellwanger, Dev M. Bhatt, Paolo S. Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver R. Homann, Songli Wang et al. · 2021 · Figshare
5. Additional file 4 of Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
   Tracy Yamawaki, Daniel Lu, Daniel Christian Ellwanger, Dev M. Bhatt, Paolo S. Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver R. Homann, Songli Wang et al. · 2021 · Figshare
6. Additional file 6 of Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
   Tracy Yamawaki, Daniel Lu, Daniel Christian Ellwanger, Dev M. Bhatt, Paolo S. Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver R. Homann, Songli Wang et al. · 2021 · Figshare
7. Additional file 2 of Transcriptomic changes in single yeast cells under various stress conditions
   Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis, Zhengchang Su · 2023 · Figshare
8. Unlocking the mysteries of Alzheimer’s disease: Role of single-cell sequencing in uncovering microbial infections
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9. Insights in RNA: 2022
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12. RGAST: A Relational Graph Attention Network for Multi-Scale Cell-Cell Communication Inference from Spatial Transcriptomics
    Yuqiao Gong, Zhangsheng Yu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
13. Ligand-dependent enhancer activation indirectly modulates non-target promoters in a chromatin domain
    Darshika Bohra, Zubairul Islam, Sundarraj Nidharshan, Aprotim Mazumder, Dimple Notani · 2026 · eLife
14. Single Cell Isolation from Human Diabetic Fibrovascular Membranes for Single-Cell RNA Sequencing
    Katia Corano Scheri, Thomas R. Tedeschi, Amani A. Fawzi · 2024 · BIO-PROTOCOL
15. Reviewer #1 (Public review): Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
    2024 · eLife
16. Ligand-dependent enhancer activation indirectly modulates non-target promoters in a chromatin domain
    Darshika Bohra, Zubairul Islam, Sundarraj Nidharshan, Aprotim Mazumder, Dimple Notani · 2024 · eLife
17. Application and Progress of Single-Cell Rna Sequencing Technology in Lung Transplantation Research
    YiZhuo Chen, Xin Wang, Ziqing Xu, Zhouqi Zhang, Dongrui Feng, Ming Dong · 2024 · SSRN Electronic Journal
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20. UMIche: A platform for robust UMI-centric simulation and analysis in bulk and single-cell sequencing
    Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
21. How to view the female reproductive tract through single-cell looking glasses
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22. Recovering undersampled single-cell transcriptomes with HyperCell
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23. UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing
    Jianfeng Sun, Shuang Li, Stefan Canzar, Adam P. Cribbs · 2025 · Research Square
24. Single-cell RNA sequencing as a precision medicine approach for complex metabolic disorders
    Sourav Sharma, Rohini Ravindran Nair, Surya Ramachandran · 2025 · Elsevier eBooks
25. A single-cell RNA sequencing data imputation method based on non-negative matrix factorization and multi-kernel similarity network fusion
    Pei Liu, Cheng Chen, Hao Liu, Jin Gu, Xinya Chen, Ying Su, Zhiyuan Cheng, Xiaoyi Lv, Chen Chen · 2025 · Engineering Applications of Artificial Intelligence
26. A drop-based workflow for fast and robust joint profiling of transcriptome and chromatin accessibility in the same cell
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27. 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
28. Additional file 3 of scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
    Sun, Tianyi, Song, Dongyuan, Li, Wei Vivian, Jingyi Jessica Li · 2021 · Figshare
29. Additional file 1 of Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues
    Jia, Erteng, Huajuan Shi, Wang, Ying, Zhou, Ying, Liu, Zhiyu, Min Pan, Bai, Yunfei, Zhao, Xiangwei, Ge, Qinyu · 2021 · Figshare
30. Additional file 3 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis
    Lyu, Jun, Chongyi Chen · 2023 · Figshare
31. Additional file 1 of LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis
    Lyu, Jun, Chongyi Chen · 2023 · Figshare
32. Additional file 1 of TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
    Melzer, Michael Karl, Silvia Schirge, Johann Gout, Frank Arnold, Dharini Srinivasan, Ingo Burtscher, Chantal Allgöwer, Mulaw, Medhanie, Zengerling, Friedemann, Çagatay Güneş et al. · 2024 · Figshare
33. Additional file 3 of scMTD: a statistical multidimensional imputation method for single-cell RNA-seq data leveraging transcriptome dynamic information
    Qi, Jing, Qiongyu Sheng, Zhou, Yang, Jiao Hua, Shutong Xiao, Shuilin Jin · 2022 · Figshare
34. Additional file 1 of baredSC: Bayesian approach to retrieve expression distribution of single-cell data
    Lucille Lopez‐Delisle, J.-B. Delisle · 2022 · Figshare
35. Additional file 2 of TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
    Melzer, Michael Karl, Silvia Schirge, Johann Gout, Frank Arnold, Dharini Srinivasan, Ingo Burtscher, Chantal Allgöwer, Mulaw, Medhanie, Zengerling, Friedemann, Çagatay Güneş et al. · 2024 · Figshare
36. Additional file 1 of The effect of methanol fixation on single-cell RNA sequencing data
    Xinlei Wang, Lei Yu, Angela Ruohao Wu · 2021 · Figshare
37. Additional file 2 of scMTD: a statistical multidimensional imputation method for single-cell RNA-seq data leveraging transcriptome dynamic information
    Qi, Jing, Qiongyu Sheng, Zhou, Yang, Jiao Hua, Shutong Xiao, Shuilin Jin · 2022 · Figshare
38. Additional file 2 of Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues
    Jia, Erteng, Huajuan Shi, Wang, Ying, Zhou, Ying, Liu, Zhiyu, Min Pan, Bai, Yunfei, Zhao, Xiangwei, Ge, Qinyu · 2021 · Figshare
39. Additional file 1 of Benchmarking full-length transcript single cell mRNA sequencing protocols
    Victoria Probst, Arman Simonyan, Felix Pacheco, Yuliu Guo, Finn Cilius Nielsen, Frederik Otzen Bagger · 2024 · Figshare
40. Additional file 4 of TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
    Melzer, Michael Karl, Silvia Schirge, Johann Gout, Frank Arnold, Dharini Srinivasan, Ingo Burtscher, Chantal Allgöwer, Mulaw, Medhanie, Zengerling, Friedemann, Çagatay Güneş et al. · 2024 · Figshare
41. Additional file 1 of Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
    Lause, Jan, Berens, Philipp, Dmitry Kobak · 2021 · Figshare
42. Additional file 1 of scMTD: a statistical multidimensional imputation method for single-cell RNA-seq data leveraging transcriptome dynamic information
    Qi, Jing, Qiongyu Sheng, Zhou, Yang, Jiao Hua, Shutong Xiao, Shuilin Jin · 2022 · Figshare
43. Additional file 1 of Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
    Yamawaki, Tracy M., Daniel Lu, Daniel Christian Ellwanger, Dev M. Bhatt, Paolo S. Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver R. Homann, Wang, Songli et al. · 2021 · 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 3 of TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
    Melzer, Michael Karl, Silvia Schirge, Johann Gout, Frank Arnold, Dharini Srinivasan, Ingo Burtscher, Chantal Allgöwer, Mulaw, Medhanie, Zengerling, Friedemann, Çagatay Güneş et al. · 2024 · Figshare
46. Additional file 2 of scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
    Sun, Tianyi, Song, Dongyuan, Li, Wei Vivian, Jingyi Jessica Li · 2021 · Figshare
47. Additional file 1 of scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
    Sun, Tianyi, Song, Dongyuan, Li, Wei Vivian, Jingyi Jessica Li · 2021 · Figshare
48. Additional file 1 of Transcriptomic changes in single yeast cells under various stress conditions
    Yangqi Su, Xu, Chen, Jonathan Shea, Darla DeStephanis, Su, Zhengchang · 2023 · Figshare
49. Additional file 2 of Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing
    Benjamin P. Kellman, Hratch Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid Gazestani, Arjana Begzati, Li, Shangzhong, Srinivasa R. Nalabolu, Sarah Shaw Murray, Linda Lopez et al. · 2021 · Figshare
50. Additional file 2 of Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
    Lause, Jan, Berens, Philipp, Dmitry Kobak · 2021 · Figshare
51. Additional file 1 of An information-theoretic approach to single cell sequencing analysis
    Casey, Michael J., Fliege, Jörg, Rubén J. Sánchez-García, MacArthur, Ben D. · 2023 · Figshare
52. Deep Neural Network with Kernel Nonnegative Matrix Factorization for Single Cell Clustering
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53. Multi-scale transcriptomic integration reveals cell-type immune networks and lncRNA remodeling in Alzheimer’s disease
    Jonathan Alexis Cortes Silva, Michael Gertig, Tonatiuh Pena Centeno, Susanne Burkhardt, Anna‐Lena Schütz, Farahnaz Sananbenesi, André Fischer · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
54. Deep Single-Cell Transcriptomic Profiling of Bovine Milk Somatic Cells Revealed Expression of Stem Cell Related Transcription Factors
    Mateja Dolinar, Peter Dovč, Minja Zorc · 2026 · Genes
55. FUNCellA: A Tool for Single-Sample Enrichment Analysis and Relative Pathway Activity Estimation in Single-Cell RNA Sequencing Data
    Joanna Żyła, Anna Mrukwa, Aleksandra G. Bilska, Kamila Szumała, Joanna Polańska, Michał Marczyk · 2026 · Computational and Structural Biotechnology Journal
56. Inferring circadian phases and quantifying biological desynchrony across single-cell transcriptomes
    Andrea Salati, Yves Paychère, Vincent Hahaut, Cédric Gobet, Félix Naef · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
57. Le plasmide Ti d’Agrobacterium fabrum C58 : analyse fonctionnelle d’ARN régulateurs
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60. Analyses intégratives de la différenciation des lymphocytes B normaux et néoplasiques à l'échelle de la cellule unique
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63. Comprehensive guide for optimizing octopus immune cell preparation to enhance single cell RNA sequencing success
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64. PICDGI: A framework for predicting cancer driver genes through dynamic gene-gene interaction modeling of single-cell data
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65. Reviewer #1 (Public review): Ligand-dependent Enhancer Activation Indirectly Modulates Non-target Promoters in a Chromatin Domain
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66. eLife Assessment: Ligand-dependent Enhancer Activation Indirectly Modulates Non-target Promoters in a Chromatin Domain
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67. Ligand-dependent Enhancer Activation Indirectly Modulates Non-target Promoters in a Chromatin Domain
    Darshika Bohra, Zubairul Islam, Sundarraj Nidharshan, Aprotim Mazumder, Dimple Notani · 2026 · eLife
68. Author response: Ligand-dependent Enhancer Activation Indirectly Modulates Non-target Promoters in a Chromatin Domain
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69. Single-cell RNA sequencing in ovarian cancer: decoding the tumor microenvironment for personalized therapy
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