BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

Cited by (302)

Items 201–300 of 302

1. Normalization of Single-Cell RNA-Seq Data
   Davide Risso · 2021 · Methods in molecular biology
2. Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis
   Marine Gauthier, Denis Agniel, Rodolphe Thiébaut, Boris P. Hejblum · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
3. Analysis of MicroRNA Regulation and Gene Expression Variability in Single Cell Data
   Wendao Liu, Noam Shomron · 2022 · Journal of Personalized Medicine
4. Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression
   Óscar García‐Blay, Pieter G. A. Verhagen, Benjamin Martin, Maike M. K. Hansen · 2023 · BioEssays
5. Feature selection using co-occurrence correlation improves cell clustering and embedding in single cell RNAseq data
   Evan S. Walsh, H. Troy Ghashghaei, Xinxia Peng · 2021 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
6. Pseudoreplication bias in single-cell studies; a practical solution
   Zimmerman, Kip D., Espeland, Mark A., Langefeld, Carl D. · 2020
7. Enabling scalable single-cell transcriptomic analysis through distributed computing with Apache spark
   Asif Adil, N Bhattacharya, Aadam, Naveed Jeelani Khan, Mohammed Asger · 2025 · Scientific Reports
8. SAREV : A review on statistical analytics of single‐cell RNA sequencing data
   Dorothy D. Ellis, Dongyuan Wu, Susmita Datta · 2021 · Wiley Interdisciplinary Reviews Computational Statistics
9. Distortion-free PCA on sample space for highly variable gene detection from single-cell RNA-seq data
   Momo Matsuda, Yasunori Futamura, Xiucai Ye, Tetsuya Sakurai · 2022 · Frontiers of Computer Science
10. Essential procedures of single-cell RNA sequencing in multiple myeloma and its translational value
    Jun Du, Xiao-Ran Gu, Xiaoxiao Yu, Yang-Jia Cao, Jian Hou · 2023 · Blood Science
11. Single Cell RNA Sequencing in Colorectal Cancer Immunology: Recent Updates, Application, and Emerging Challenges
    Sabrina George, Nor Adzimah Johdi · 2025 · Current Molecular Medicine
12. cytoKernel: robust kernel embeddings for assessing differential expression of single-cell data
    Tusharkanti Ghosh, Ryan Michael Baxter, Souvik Seal, Victor G Lui, Pratyaydipta Rudra, Thao Vu, Elena W.Y. Hsieh, Debashis Ghosh · 2025 · Bioinformatics
13. Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues
    Kaia Achim, Nils Eling, Hernando Martínez Vergara, Paola Yanina Bertucci, Thibaut Brunet, Paul G. Collier, Vladimı́r Beneš, John C. Marioni, Detlev Arendt · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
14. CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq
    Logan A. Walker, Michael G. Sovic, Chi‐Ling Chiang, Eileen Y. Hu, Jiyeon K. Denninger, Xi Chen, Elizabeth D. Kirby, John C. Byrd, Natarajan Muthusamy, Ralf A. Bundschuh et al. · 2018 · arXiv (Cornell University)
15. Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
    Zilu Zhou, Bihui Xu, Andy J. Minn, Nancy Ruonan Zhang · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
16. Reply to The contribution of cell cycle to heterogeneity in single-cell RNA-seq data
    Andrew McDavid, Greg Finak, Raphaël Gottardo · 2016 · Nature Biotechnology
17. Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data
    Fu, Yile, Youness, Mohamad, Virzì, Alessia, Song, Xinran, Tubeeckx, Michiel R L, De Keulenaer, Gilles W, Heidbuchel, Hein, Segers, Vincent F M, Sipido, Karin R, Thienpont, Bernard et al. · 2025 · Briefings in Bioinformatics
18. Sequencing-based methods for single-cell multi-omics studies
    Shanshan Qin, Songmei Liu, Xiaocheng Weng · 2023 · Science China Chemistry
19. BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data
    Alan O’Callaghan, Nils Eling, John C. Marioni, Catalina A. Vallejos · 2022 · F1000Research
20. scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data
    Chih–Yuan Hsu, Chih‐Han Chang, Qi Liu, Yu Shyr · 2024 · Bioinformatics
21. Differential Expression Analysis
    Khalid Raza · 2024 · SpringerBriefs in applied sciences and technology
22. A primer on single‐cell RNA ‐seq analysis using dendritic cells as a case study
    Giulia Protti, Roberto Spreafico · 2024 · FEBS Letters
23. DSAVE: Detection of misclassified cells in single-cell RNA-Seq data
    Johan Gustafsson, Jonathan L. Robinson, Juan Salvador Inda-Díaz, Elias Björnson, Rebecka J. Jörnsten, Jens Nielsen · 2020 · PLoS ONE
24. Design of soft x-ray fluorescence microscopy beyond 100-nm spatial resolution with ultrashort Kirkpatrick-Baez mirror
    Takenori Shimamura, Yoko Takeo, Fumika Moriya, Takashi Kimura, Mari Shimura, Yasunori Senba, Hikaru Kishimoto, Haruhiko Ohashi, Kenta Shimba, Yasuhiko Jimbo et al. · 2022
25. Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption
    Michelle M McDonald, Weng Hua Khoo, Pei Ying Ng, Ya Xiao, Jad Zamerli, Peter Thatcher, Wunna Kyaw, Karrnan Pathmanandavel, Abigail K. Grootveld, Imogen Moran et al. · 2021 · Yearbook of pediatric endocrinology
26. Controlling for confounding effects in single cell RNA sequencing studies using both control and target genes
    Mengjie Chen, Xiang Zhou · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
27. BEARscc determines robustness of single-cell clusters using simulated technical replicates
    David Tyler Severson, Richard Peter Owen, MJ White, Xin Lü, Benjamin Schuster‐Böckler · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
28. Statistical Methods for Single‐Cell RNA‐Sequencing
    Tallulah S. Andrews, Vladimir Yu Kiselev, Martin Hemberg · 2019 · Wiley eBooks
29. A mathematical framework for raw counts of single-cell RNA-seq data analysis
    Silvia Giulia Galfrè, Francesco Morandin · 2020 · arXiv (Cornell University)
30. Scalable computation for Bayesian hierarchical models
    Omiros Papaspiliopoulos, Timothée Stumpf-Fétizon, Giacomo Zanella · 2021 · arXiv (Cornell University)
31. A Review of Computational Learning and IoT Applications to High‐Throughput Array‐Based Sequencing and Medical Imaging Data in Drug Discovery and Other Health Care Systems
    Soham Choudhuri, Saurav Mallik, Bhaswar Ghosh, Tapas Si, Tapas Bhadra, Ujjwal Maulik, Aimin Li · 2022 · Wiley eBooks
32. Gene Expression Noise Dynamics Unveil Functional Heterogeneity of Ageing Hematopoietic Stem Cells
    Reyna Edith Rosales-Alvarez, Jasmin Rettkowski, Josip S. Herman, Gabrijela Dumbović, Nina Cabezas‐Wallscheid, Dominic Grün · 2022 · SSRN Electronic Journal
33. Total-mRNA-Aware Analysis for Droplet-Based Single Cell Sequencing
    Qiuyu Lian, Jianzhu Ma, Kui Hua, Ziqi Rong, Jinpu Cai, Xinzhu Jiang, Jieli Zhou, Jiaying Xu, Zhiyuang Zhang, Li Fan et al. · 2022 · Research Square
34. Incorporating extrinsic noise into mechanistic modelling of single-cell transcriptomics
    Kaan Öcal · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
35. Chaos and complexity: Hallmarks of cancer progression
    Abicumaran Uthamacumaran · 2025 · Oxford University Press eBooks
36. Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material
    Eliseos J. Mucaki, Wenhan Zhang, A Saha, Sabina Trebinjac, Sharon Nofech‐Mozes, E Rakovitch, Vanessa Dumeaux, Michael T. Hallett · 2025 · Journal of Translational Medicine
37. Genetic determinants of gene expression noise and its role in complex trait variation
    Yuexuan Long, Xiaolin Ni, Ting-Wei Chen, Xianzhe Huang, Qiyang Hong, Jixin Wang, Cong Wang, Zigeng Huang, Haiqing Xu, Mengyi Sun et al. · 2025 · Cell Reports
38. Histone H3K4/H3K9 Methylation Dynamics Gate Cell Fate Plasticity in Pediatric High-Grade Gliomas: A Systems-Level Attractor Reconstruction
    Abicumaran Uthamacumaran · 2025 · Journal of Computational Biophysics and Chemistry
39. Likelihood-free parameter inference for spatiotemporal stochastic biological models using neural posterior estimation
    Tom Kimpson, Jennifer Flegg, Matthew J. Simpson · 2026 · Journal of Theoretical Biology
40. Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering
    Yunhe Liu, Bisheng Shi, Aoshen Wu, Xueqing Peng, Zhenghong Yuan, Lei Liu, Lei Liu · 2021 · Life
41. Capturing hidden regulation based on noise change of gene expression level from single cell RNA-seq in yeast
    Thoma Itoh, Takashi Makino · 2021 · Scientific Reports
42. visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data
    Lijun Tang, Nan Zhou · 2017 · Interdisciplinary Sciences Computational Life Sciences
43. Automated cell cycle and cell size measurements for single-cell gene expression studies
    Anissa Guillemin, Angélique Richard, Sandrine Gonin-Giraud, Olivier Gandrillon · 2018 · BMC Research Notes
44. RNA-Seq Analysis: Methods, Applications and Challenges
    Autori vari, Geraci, F., Saha, I., Bianchini, M. · 2020 · Frontiers research topics
45. Single-Cell RNA Sequencing Technologies
    Manoj Kumar Gupta, Gayatri Gouda, Ravindra Donde, S. Sabarinathan, Piyali Goswami, Goutam Kumar Dash, N. Rajesh, Pallabi Pati, Sushil Kumar Rathode, Ramakrishna Vadde et al. · 2021 · Springer eBooks
46. Proteobacteria drive significant functional variability in the human gut microbiome
    Patrick H. Bradley, Katherine S. Pollard · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
47. Adaptation to ex vivo culture drives human haematopoietic stem cell loss of repopulation capacity in a cell cycle independent manner
    Carys S. Johnson, Kendig Sham, Serena Belluschi, Xiaonan Wang, Winnie W. Y. Lau, Kerstin B. Kaufmann, Gabriela Krivdova, Emily F. Calderbank, Nicole Mende, Jessica L. McLeod et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
48. Quantitative comparison of single-cell RNA sequencing versus single-molecule RNA imaging for quantifying transcriptional noise
    Neha Khetan, Binyamin Zuckerman, Giuliana Calia, Xinyue Chen, Ximena Garcia Arceo, Leor S. Weinberger · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
49. Normalization of Single-cell RNA-seq Data Using Partial Least Squares with Adaptive Fuzzy Weight
    Vikas Singh, Nikhil Kirtipal, Songwon Lim, Sunjae Lee · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
50. From Noise to Models to Numbers: Evaluating Negative Binomial Models and Parameter Estimations in Single-Cell RNA-seq
    Yiling Wang, Zhanpeng Shu, Zhixing Cao, Ramon Grima · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
51. Inferring Functional Neural Connectivity with Deep Residual Convolutional Networks
    Timothy Dunn, Peter K. Koo · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
52. Lineages and molecular heterogeneity in the developing nervous system
    Gioele La Manno · 2018 · Figshare
53. Robust Nonparametric Descriptors for Clustering Quantification in Single-Molecule Localization Microscopy
    Shenghang Jiang, Sai Divya Challapalli, Yong Wang · 2017 · Biophysical Journal
54. Multilevel linear models, Gibbs samplers and multigrid decompositions
    Giacomo Zanella, Gareth O. Roberts · 2017 · arXiv (Cornell University)
55. Data Analysis in Single-Cell RNA-Seq
    Xun Zhu, Lana Xia Garmire · 2019 · Elsevier eBooks
56. Gene Screening for Autism Based on Cell-type-specific Predictive Models
    Yang Wang, Yiping Lin, Guoli Ji, Jinting Guan · 2020 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
57. Transcriptional Profiling During Neural Conversion
    Yohannes Afeworki Tecleab, Hannah Wollenzien, Michael S. Kareta · 2021 · Methods in molecular biology
58. Statistical approaches of gene set analysis with quantitative trait loci for high-throughput genomic studies.
    Samarendra Das · 2020 · ThinkIR: The University of Louisville's Institutional Repository (University of Louisville)
59. Simulation-based Evaluation of the Reliability of Bayesian Hierarchical Models for sc-RNAseq Data
    Sijia Li, Martín López‐García, Luisa Cutillo · 2021 · International Conference on Ubiquitous Computing and Communications (IUCC)
60. Faculty Opinions recommendation of Gene expression variability across cells and species shapes innate immunity.
    Luis Bruno Barreiro · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
61. Faculty Opinions recommendation of The human cell atlas.
    Roderic Guigó · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
62. Faculty Opinions recommendation of SAVER: gene expression recovery for single-cell RNA sequencing.
    Chao Cheng · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
63. Optimization and redevelopment of single-cell data analysis workflow based on deep generative models
    Yunhe Liu, Qiqing Fu, Chenyu Dong, Xiaoqiong Xia, Gang Liu, Lei Liu · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
64. Computational and Statistical Methods for Single-Cell RNA Sequencing Data
    Zuoheng Wang, Xiting Yan · 2022 · Springer handbooks of computational statistics
65. Inter individual variability in neuronal expression of heat shock protein genes predicts stress survival in Caenorhabditis elegans
    Pia Todtenhaupt, Sharlene Murdoch, Catalina A. Vallejos, Olivia Casanueva, Laetitia Chauve · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
66. Additional file 2 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
67. A Differential Evolution-based Pseudotime Estimation Method for Single-cell Data
    Nazifa Tasnim Hia, Ishrat Jahan Emu, Muhammad Ibrahim, Sumon Ahmed · 2024 · International Journal of Advanced Computer Science and Applications
68. Multimodal screen reveals noise regulatory proteins
    Óscar García‐Blay, Xinyu Hu, Christin L. Wassermann, Tom van Bokhoven, Fréderique M.B. Struijs, Maike M. K. Hansen · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
69. Theory of Diffusive Dynamics of Bacteria Population from Probabilistic Interactions
    Huber Nieto–Chaupis · 2024 · International Conference on Electrical, Computer and Energy Technologies (ICECET)
70. scDCABC: A Deep Biclustering Method Integrating Denoising, Dimensionality Reduction, and Clustering for scRNA-seq Data
    Xiaoqi Tang, Chaowang Lan · 2024 · International Conference on Bioinformatics and Biomedical Science (ICBBS)
71. Protocol to identify proteins as regulators of gene expression noise
    Óscar García‐Blay, Maike M. K. Hansen · 2025 · STAR Protocols
72. A Probabilistic Mixture Model Framework for scRNA-seq Read Simulation
    Wenshan Li, Wenbo Fang, Ao Liu, Beibei Li, Junjiang He, Hongxia Wang · 2025 · WSEAS TRANSACTIONS ON BIOLOGY AND BIOMEDICINE
73. Scalable inference of transcriptional variability with BASiCS
    Alan O’Callaghan, Catalina A. Vallejos · 2025 · Journal of Theoretical Biology
74. A Mixture Model Based Read Simulating Method for Single Cell RNA Sequencing
    Wenshan Li, Wenbo Fang, Ao Liu, Beibei Li, Junjiang He, Hongxia Wang · 2025 · MOLECULAR SCIENCES AND APPLICATIONS
75. Additional file 3 of Cytomulate: accurate and efficient simulation of CyTOF data
    Yang, Yuqiu, Kaiwen Wang, Lu, Zeyu, Wang, Tao, Xinlei Wang · 2024 · Figshare
76. 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
77. Additional file 1 of Interleukin-6 actions in the hypothalamus protects against obesity and is involved in the regulation of neurogenesis
    Vanessa Cristina Dias Bóbbo, Engel, Daiane F., Jara, Carlos Poblete, Natália Ferreira Mendes, Roberta Haddad-Tóvolli, Thaís Paulino do Prado, Sidarta-Oliveira, Davi, Joseane Morari, Licio Augusto Velloso, Araujo, Eliana P. · 2021 · Figshare
78. 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
79. 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
80. Additional file 2 of iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
    Yunqing Liu, Zhao, Jiayi, Taylor Sterling Adams, Ningya Wang, Jonas C. Schupp, Wu, Weimiao, McDonough, John E., Geoffrey Lowell Chupp, Naftali Kaminski, Wang, Zuoheng et al. · 2023 · Figshare
81. Additional file 1 of Cytomulate: accurate and efficient simulation of CyTOF data
    Yang, Yuqiu, Kaiwen Wang, Lu, Zeyu, Wang, Tao, Xinlei Wang · 2023 · Figshare
82. Additional file 3 of The shaky foundations of simulating single-cell RNA sequencing data
    Helena Lucia Crowell, Sarah X. Morillo Leonardo, Soneson, Charlotte, Mark D. Robinson · 2023 · Figshare
83. Additional file 2 of The shaky foundations of simulating single-cell RNA sequencing data
    Helena Lucia Crowell, Sarah X. Morillo Leonardo, Soneson, Charlotte, Mark D. Robinson · 2023 · Figshare
84. 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
85. Additional file 3 of iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
    Yunqing Liu, Zhao, Jiayi, Taylor Sterling Adams, Ningya Wang, Jonas C. Schupp, Wu, Weimiao, McDonough, John E., Geoffrey Lowell Chupp, Naftali Kaminski, Wang, Zuoheng et al. · 2023 · Figshare
86. Additional file 1 of The shaky foundations of simulating single-cell RNA sequencing data
    Helena Lucia Crowell, Sarah X. Morillo Leonardo, Soneson, Charlotte, Mark D. Robinson · 2023 · Figshare
87. 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
88. Additional file 2 of Cytomulate: accurate and efficient simulation of CyTOF data
    Yang, Yuqiu, Kaiwen Wang, Lu, Zeyu, Wang, Tao, Xinlei Wang · 2024 · Figshare
89. 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
90. Additional file 1 of iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
    Yunqing Liu, Zhao, Jiayi, Taylor Sterling Adams, Ningya Wang, Jonas C. Schupp, Wu, Weimiao, McDonough, John E., Geoffrey Lowell Chupp, Naftali Kaminski, Wang, Zuoheng et al. · 2023 · Figshare
91. 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
92. Single-Cell Genomics
    Mehmet Ali Balcı, Selim Can Kuralay, Esma Gamze Aksel, Zahra Shahpar, Özgecan Kayalar, Vahap Eldem · 2025 · Springer handbooks
93. Kernel Non-negative Matrix Factorization Framework for Single Cell Clustering
    Hao Jiang, Wai‐Ki Ching · 2026 · Intelligent control and learning systems
94. Structure learning to unravel mechanisms of the immune system
    Helena Todorov · 2020 · theses.fr (ABES)
95. La différenciation érythrocytaire : caractérisation moléculaire de l'engagement cellulaire
    Souad Zreika · 2021 · theses.fr (ABES)
96. Dissecting human population variation in single-cell responses to SARS-CoV-2
    Yann Aquino · 2023 · theses.fr (ABES)
97. From gene correlations to cell clusters: COTAN improved scRNA-seq analysis
    Silvia Giulia Galfrè, Marco Fantozzi, Alina Sîrbu, Irene Testa, Matteo Tolloso, Andrea Alberti, Corrado Priami, Francesco Morandin · 2026 · NAR Genomics and Bioinformatics
98. EMD-HVG: a normalization-independent method for highly variable gene selection based on Earth mover’s distance
    Chunfang Peng, Guobin Li, Jiamiao Wu, Feng Tan, Xiaobo Guo · 2026 · BMC Bioinformatics
99. Overinflation and overconcentration: why Cauchy perturbation kernels are the right choice for ABC-SMC
    Marc Sturrock, Vahid Shahrezaei · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
100. Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics
     Jung Hee Koh, Chun Ye · 2026 · Immune Network