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

Kolodziejczyk, Aleksandra A., Kim, Jong Kyoung, Tsang, Jason C.H., Ilicic, Tomislav, Henriksson, Johan, Natarajan, Kedar N., Tuck, Alex C., Gao, Xuefei +4 more·2015·Cell Stem Cell

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  1. An Adaptive Sparse Subspace Clustering for Cell Type Identification
    Ruiqing Zheng, Zhenlan Liang, Xiang Chen, Yu Tian, Chen Cao, Min Li · 2020 · Frontiers in Genetics
  2. Visualizing Single-Cell RNA-seq Data with Semisupervised Principal Component Analysis
    Zhenqiu Liu · 2020 · International Journal of Molecular Sciences
  3. Single-cell RNA-seq data clustering: A survey with performance comparison study
    Ruiyi Li, Jihong Guan, Shuigeng Zhou · 2020 · Journal of Bioinformatics and Computational Biology
  4. Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies
    Ik Soo Kim, Jingyi Wu, Gilbert J. Rahme, Sofia Battaglia, Atray C. Dixit, Elizabeth Gaskell, Huidong Chen, Luca Pinello, B Bernstein · 2020 · Cell Reports
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  6. Epigenetic Regulation of Transition Among Different Pluripotent States: Concise Review
    Ting Geng, Dong-Hui Zhang, Wei Jiang · 2019 · Stem Cells
  7. scGCC: Graph Contrastive Clustering With Neighborhood Augmentations for scRNA-Seq Data Analysis
    Sheng-Wen Tian, Jiancheng Ni, Yutian Wang, Chun-Hou Zheng, Cunmei Ji · 2023 · IEEE Journal of Biomedical and Health Informatics
  8. Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
    Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson‐Rechavi · 2020 · BMC Biology
  9. Transcription factor antagonism regulates heterogeneity in embryonic stem cell states
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  10. Absolute scaling of single-cell transcriptomes identifies pervasive hypertranscription in adult stem and progenitor cells
    Yun‐Kyo Kim, Brandon Cho, David P. Cook, Daniel Trcka, Jeffrey L. Wrana, Miguel Ramalho‐Santos · 2023 · Cell Reports
  11. MUSE Stem Cells Can Be Isolated from Stromal Compartment of Mouse Bone Marrow, Adipose Tissue, and Ear Connective Tissue: A Comparative Study of Their In Vitro Properties
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  12. High-throughput identification and quantification of single bacterial cells in the microbiota
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  13. Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data
    Jonathan A. Griffiths, Antonio Scialdone, John C. Marioni · 2017 · BMC Genomics
  14. β-catenin-mediated Wnt signal transduction proceeds through an endocytosis-independent mechanism
    Ellen Youngsoo Rim, Leigh Katherine Kinney, Roel Nusse · 2020 · Molecular Biology of the Cell
  15. Transcriptome sequencing and molecular markers discovery in the gonads of Portunus sanguinolentus
    Yin Zhang, Guidong Miao, Qingyang Wu, Fan Lin, Cuihong You, Shuqi Wang, Jude Juventus Aweya, Hongyu Ma · 2018 · Scientific Data
  16. Reconstructing cell histories in space with image-readable base editor recording
    Duncan M. Chadly, Kirsten L. Frieda, Chen Gui, Leslie Klock, Martin Tran, Margaret Y Sui, Yodai Takei, Remco Bouckaert, Carlos Lois, Long Cai et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  17. CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type
    Junil Kim, Diana E. Stanescu, Kyoung‐Jae Won · 2018 · Nucleic Acids Research
  18. Pathway-Based Single-Cell RNA-Seq Classification, Clustering, and Construction of Gene-Gene Interactions Networks Using Random Forests
    Hailun Wang, Pak Chung Sham, Tiejun Tong, Herbert Pang · 2019 · IEEE Journal of Biomedical and Health Informatics
  19. DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data
    Guanhua Zou, Yilong Lin, Tianyang Han, Le Ou-Yang · 2022 · Briefings in Bioinformatics
  20. Nanog Expression in Embryonic Stem Cells – An Ideal Model System to Dissect Enhancer Function
    Steven M. Blinka, Sridhar Rao · 2017 · BioEssays
  21. FEATS: feature selection-based clustering of single-cell RNA-seq data
    Edwin Vans, Ashwini Patil, Alok K. Sharma · 2020 · Briefings in Bioinformatics
  22. Organization of the Pluripotent Genome
    Patrick Siang Lin Lim, Eran Meshorer · 2020 · Cold Spring Harbor Perspectives in Biology
  23. SC3s: efficient scaling of single cell consensus clustering to millions of cells
    Fu Xiang Quah, Martin Hemberg · 2022 · BMC Bioinformatics
  24. Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing
    Ruoyu Zhang, Gurinder S. Atwal, Wei Keat Lim · 2021 · Patterns
  25. Pluripotency of embryo-derived stem cells from rodents, lagomorphs, and primates: Slippery slope, terrace and cliff
    Pierre Savatier, Pierre Osteil, Patrick Tam · 2017 · Stem Cell Research
  26. Transcription-coupled changes in genomic region proximities during transcriptional bursting
    Hiroaki Ohishi, Soya Shinkai, Hitoshi Owada, Takeru Fujii, Kazufumi Hosoda, Shuichi Onami, Takashi Yamamoto, Yasuyuki Ohkawa, Hiroshi Ochiai · 2024 · Science Advances
  27. ScGSLC: An unsupervised graph similarity learning framework for single-cell RNA-seq data clustering
    Junyi Li, Wei Jiang, Henry Han, Jing Liu, Bo Liu, Yadong Wang · 2020 · Computational Biology and Chemistry
  28. Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency
    Geethika Arekatla, Christoph Trenzinger, Andreas Reimann, Dirk Loeffler, Tobías Kull, Timm Schroeder · 2023 · Developmental Cell
  29. Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells
    Arsham Ghahramani, Giacomo Donati, Nicholas M. Luscombe, Fiona M. Watt · 2018 · Genome biology
  30. 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. · 2020 · Journal of Translational Medicine
  31. An extended model for culture-dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells
    Simon Godwin, Daniel Ward, Elisa Pedone, Martin Homer, Alexander George Fletcher, Lucia Marucci · 2017 · npj Systems Biology and Applications
  32. Distinct transcription kinetics of pluripotent cell states
    Rui Shao, Banushree Kumar, Katja Lidschreiber, M. Lidschreiber, P. Cramer, S. Elsässer · 2022 · Molecular Systems Biology
  33. Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency
    Fatemeh Mirzadeh Azad, Eduard A. Struys, Victoria Wingert, Luciana Hannibal, Ken Mills, Joop H. Jansen, Daniel B. Longley, Hendrik G. Stunnenberg, Yaser Atlasi · 2023 · Science Advances
  34. Gene regulatory network inference from single-cell data using multivariate information measures
    Thalia E. Chan, Michael P. H. Stumpf, Ann C. Babtie · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  35. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells
    Durand, Sébastien, Bruelle, Marion, Bourdelais, Fleur, Bennychen, Bigitha, Blin-Gonthier, Juliana, Isaac, Caroline, Huyghe, Aurélia, Martel, Sylvie, Seyve, Antoine, Vanbelle, Christophe et al. · 2023 · Nature Communications
  36. Early autonomous patterning of the anteroposterior axis in gastruloids
    Kerim Anlaş, Nicola Gritti, Fumio Nakaki, Laura Salamó Palau, Sham Tlili, David Oriola, Krisztina Arató, Jia Le Lim, James A. Sharpe, Vikas Trivedi · 2024 · Development
  37. SUSCC: Secondary Construction of Feature Space based on UMAP for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data
    Haiyun Wang, Jianping Zhao, Chun-Hou Zheng · 2021 · Interdisciplinary Sciences Computational Life Sciences
  38. MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection
    Zhenyi Wang, Yanjie Zhong, Zhaofeng Ye, Lang Zeng, Yang Chen, Minglei Shi, Zhiyuan Yuan, Qiming Zhou, Minping Qian, Michael Q. Zhang · 2021 · Nucleic Acids Research
  39. 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 · 2023 · Genome biology
  40. DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency
    Julien Richard Albert, Teresa Urli, Ana Monteagudo, Anna Le Breton, Amina Sultanova, Angélique David, Margherita Scarpa, Mathieu Schulz, Max Greenberg · 2024 · Nature Structural & Molecular Biology
  41. Autonomy in the Development of Stem Cell-Derived Embryoids: Sprouting Blastocyst-Like Cysts, and Ethical Implications
    Hans‐Werner Denker · 2021 · Cells
  42. Incorporating cell hierarchy to decipher the functional diversity of single cells
    Lingxi Chen, Shuai Cheng Li · 2022 · Nucleic Acids Research
  43. Multivariable regulation of gene expression plasticity in metazoans
    Long Xiao, Zhiguang Zhao, Fei He, Zhuo Du · 2019 · Open Biology
  44. Upregulation of mitotic bookmarking factors during enhanced proliferation of human stromal cells in human platelet lysate
    Sandra Laner‐Plamberger, Michaela Oeller, Cornelia Mrazek, Arnulf Josef Hartl, Alina Sonderegger, Eva Rohde, Dirk Strunk, Katharina Schallmoser · 2019 · Journal of Translational Medicine
  45. Deconstructing transcriptional variations and their effects on immunomodulatory function among human mesenchymal stromal cells
    Changbin Sun, Kehua Zhang, Jianhui Yue, Shufang Meng, Xi Zhang · 2021 · Stem Cell Research & Therapy
  46. Somatic Reprogramming—Above and Beyond Pluripotency
    Yaa‐Jyuhn James Meir, Guigang Li · 2021 · Cells
  47. A Similar Speciation Process Relying on Cellular Stochasticity in Microbial and Cancer Cell Populations
    Jean‐Pascal Capp, Frédéric Thomas A · 2020 · iScience
  48. Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis
    Yuanchao Zhang, Man Soo Kim, Erin Renée Reichenberger, Benjamin J. Stear, Deanne M. Taylor · 2020 · PLoS Computational Biology
  49. Dissecting stem cell differentiation using single cell expression profiling
    Victoria Moignard, Berthold Göttgens · 2016 · Current Opinion in Cell Biology
  50. Mind the Map: Technology Shapes the Myeloid Cell Space
    Patrick S. Günther, Joachim Ludwig Schultze · 2019 · Frontiers in Immunology
  51. 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 · Genome biology
  52. A Feature Selection Method Based on Feature-Label Correlation Information and Self-Adaptive MOPSO
    Fei Han, Fanyu Li, Qing-Hua Ling, Henry Han, Tianyi Lu, Zijian Jiao, Haonan Zhang · 2024 · Neural Processing Letters
  53. Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation
    Kedar Nath Natarajan, Sarah Amalia Teichmann, Aleksandra A. Kolodziejczyk · 2017 · Current Opinion in Genetics & Development
  54. Vicus: Exploiting local structures to improve network-based analysis of biological data
    Bo Wang, Lin Huang, Yuke Zhu, Anshul Bharat Kundaje, Serafim Batzoglou, Anna Goldenberg · 2017 · PLoS Computational Biology
  55. Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing
    Robert Durruthy-Durruthy, Manisha Ray · 2018 · Methods in molecular biology
  56. zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications
    Koen Van den Berge, Charlotte Soneson, Michael I. Love, Mark D. Robinson, Lieven Clement · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  57. De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments
    Jun Woo, Boris J. N. Winterhoff, Timothy K. Starr, Constantin Aliferis, Jinhua Wang · 2019 · Life Science Alliance
  58. β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus
    Meng Zhang, Yiwei Lai, Vladislav Krupalnik, Pengcheng Guo, Xiangpeng Guo, Jian‐Guo Zhou, Yan Xu, Zhijun Yu, Longqi Liu, Ao Jiang et al. · 2020 · Science Advances
  59. TransSynW: A single-cell RNA-sequencing based web application to guide cell conversion experiments
    Mariana Messias Ribeiro, Satoshi Okawa, Antonio del Sol · 2020 · Stem Cells Translational Medicine
  60. Improving Single-Cell RNA-seq Clustering by Integrating Pathways
    Chenxing Zhang, Lin Gao, Bingbo Wang, Yong Gao · 2021 · Briefings in Bioinformatics
  61. Clustering by Direct Optimization of the Medoid Silhouette
    Lars Lenssen, Erich Schubert · 2022 · Lecture notes in computer science
  62. Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability
    Aedan G. K. Roberts, Daniel Robin Catchpoole, Paul J Kennedy · 2022 · NAR Genomics and Bioinformatics
  63. SLRRSC: Single-Cell Type Recognition Method Based on Similarity and Graph Regularization Constraints
    Nana Zhang, Jin‐Xing Liu, Chun-Hou Zheng, Juan Wang · 2022 · IEEE Journal of Biomedical and Health Informatics
  64. BMP4 preserves the developmental potential of mESCs through Ube2s- and Chmp4b-mediated chromosomal stability safeguarding
    Mingzhu Wang, Kun Zhao, Meng Liu, Mengting Wang, Zhibin Qiao, Shanru Yi, Yonghua Jiang, Xiaochen Kou, Yanhong Zhao, Jiqing Yin et al. · 2022 · Protein & Cell
  65. Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug challenge
    Eva Sanchez-Quant, Maria Lucia Richter, Maria Colomé‐Tatché, Celia Pilar Martinez‐Jimenez · 2023 · Genome biology
  66. Transcriptional and epigenetic control in mouse pluripotency: lessons from in vivo and in vitro studies
    Ehsan Habibi, Hendrik G. Stunnenberg · 2017 · Current Opinion in Genetics & Development
  67. Blastocyst-Inspired Hydrogels to Maintain Undifferentiation of Mouse Embryonic Stem Cells
    Yingjie Hang, Xiaoliang Ma, Chunxiao Liu, Siyuan Li, Sixuan Zhang, Ruyan Feng, Qianwen Shang, Qi Liu, Zhaozhao Ding, Xiaoyi Zhang et al. · 2021 · ACS Nano
  68. Characteristics and homogeneity of N6-methylation in human genomes
    Clare Pacini, Charles Richard Bradshaw, Nigel Garrett, Magdalena J. Koziol · 2019 · Scientific Reports
  69. A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells
    Mary V. Arrastia, Joanna W. Jachowicz, Noah Ollikainen, Matthew S. Curtis, Charlotte Lai, Sofia A. Quinodoz, David A. Selck, Mitchell Guttman, Rustem F. Ismagilov · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  70. Single-cell RNA sequencing of murine hearts for studying the development of the cardiac conduction system
    Huiying Ren, Xiaolin Zhou, Jun Yang, Kun Kou, Tangting Chen, Zhaoli Pu, Kejun Ye, Xuehui Fan, Dan Zhang, Xinjiang Kang et al. · 2023 · Scientific Data
  71. Epiblast-like stem cells established by Wnt/β-catenin signaling manifest distinct features of formative pluripotency and germline competence
    Qing Luo, Han‐Pin Pui, Jiayu Chen, Leqian Yu, Paulo R. Jannig, Yu Pei, Linxuan Zhao, Xingqi Chen, Sophie Petropoulos A, Jorge Lira Ruas et al. · 2023 · Cell Reports
  72. scMAGS: Marker gene selection from scRNA-seq data for spatial transcriptomics studies
    Yusuf Baran, Berat Doğan · 2023 · Computers in Biology and Medicine
  73. Imprinted X chromosome inactivation at the gamete-to-embryo transition
    Chunyao Wei, Barry Kesner, Hao Yin, Jeannie T. Lee · 2024 · Molecular Cell
  74. Plasticity and lineage commitment of individual TH1 cells are determined by stable T-bet expression quantities
    Ahmed Nabil Hegazy, Caroline Peine, Dominik Niesen, Isabel Panse, Yevhen Vainshtein, Christoph Kommer, Qin Zhang, Tobias M. Brunner, Michael Peine, Anja Fröhlich et al. · 2024 · Science Advances
  75. Single-cell analysis via manifold fitting: A framework for RNA clustering and beyond
    Zhigang Yao, Bingjie Li, Yukun Lu, Shing–Tung Yau · 2024 · Proceedings of the National Academy of Sciences
  76. scCNC: a method based on capsule network for clustering scRNA-seq data
    Haiyun Wang, Jianping Zhao, Chun-Hou Zheng, Yansen Su · 2022 · Bioinformatics
  77. Genomic and molecular control of cell type and cell type conversions
    Xiuling Fu, Fangfang He, Yuhao Li, Allahverdi Shahveranov, Andrew P. Hutchins · 2017 · Cell Regeneration
  78. A Gene Rank Based Approach for Single Cell Similarity Assessment and Clustering
    Yunpei Xu, Hong‐Dong Li, Yi Feng Pan, Feng Luo, Fang‐Xiang Wu, Jianxin Wang · 2019 · IEEE Transactions on Computational Biology and Bioinformatics
  79. LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells
    Alessandro Fiorenzano, Emilia Pascale, Eduardo Jorge Patriarca, Gabriella Minchiotti, Annalisa Fico · 2019 · Epigenomes
  80. Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model
    Zhenqiu Liu · 2021 · Genes
  81. Applications of Community Detection Algorithms to Large Biological Datasets
    Itamar Kanter, Gur Yaari, Tomer Kalisky C · 2020 · Methods in molecular biology
  82. CBLRR: a cauchy-based bounded constraint low-rank representation method to cluster single-cell RNA-seq data
    Qian Ding, Wenyi Yang, Meng Luo, Chang Xu, Zhaochun Xu, Fenglan Pang, Yideng Cai, Anastasia A. Anashkina, Xi Su, Na Chen et al. · 2022 · Briefings in Bioinformatics
  83. Plakoglobin is a mechanoresponsive regulator of naive pluripotency
    Ilaria Di Meglio, Joachim De Jonghe, Anna L. Ellermann, Ayaka Yanagida, Michael Herger, Erin M. Slatery, Antonia Weberling, Clara Munger, Katrin Fischer, Carla Mulas et al. · 2023 · Nature Communications
  84. Thymine DNA glycosylase regulates cell-cycle-driven p53 transcriptional control in pluripotent cells
    Sergi Aranda, Anna Alcaine-Colet, Cecilia Ballaré, Enrique Blanco, Ivano Mocavini, Aleksandra Sparavier, Pedro Vizán, Eva Borràs, Eduard Sabidó, Luciano Di Croce · 2023 · Molecular Cell
  85. scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis
    Mehrshad Sadria, Anita T. Layton · 2025 · Genome biology
  86. Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data
    Siamak Zamani Dadaneh, Paul de Figueiredo, Sing‐Hoi Sze, Mingyuan Zhou, Xiaoning Qian · 2020 · BMC Genomics
  87. Stat3 phosphorylation is required for embryonic stem cells ground state maintenance in 2i culture media
    Dan Wang, Hui Sang, Kaiyue Zhang, Yan Nie, Shuang Zhao, Yan Zhang, Ningning He, Yuebing Wang, Yang Xu, Xiaoyan Xie et al. · 2017 · Oncotarget
  88. SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies
    Srikanth Ravichandran, András Hartmann, Antonio del Sol · 2019 · Bioinformatics
  89. Single-Cell RNA Sequencing Data Interpretation by Evolutionary Multiobjective Clustering
    Xiangtao Li, Ka‐Chun Wong · 2019 · IEEE Transactions on Computational Biology and Bioinformatics
  90. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
    Chiaowen Joyce Hsiao, Po‐Yuan Tung, John Blischak, Jonathan E. Burnett, Kenneth Barr, Kushal K. Dey, Matthew Stephens, Yoav Gilad · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  91. Advancing Stem Cell Research through Multimodal Single-Cell Analysis
    Iwo Kuciński, Berthold Göttgens · 2020 · Cold Spring Harbor Perspectives in Biology
  92. Single-cell RNA-seq data analysis based on directed graph neural network
    Xiang Feng, Hongqi Zhang, Hao Lin, Haixia Long · 2023 · Methods
  93. Dimension reduction, cell clustering, and cell–cell communication inference for single-cell transcriptomics with DcjComm
    Qian Ding, Wenyi Yang, Guangfu Xue, Hongxin Liu, Yideng Cai, Jinhao Que, Xiyun Jin, Meng Luo, Fenglan Pang, Yuexin Yang et al. · 2024 · Genome biology
  94. Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation
    Marloes Blotenburg, Lianne C Suurenbroek, Danique J. C. Bax, Joelle de Visser, Vivek Bhardwaj, Luca Braccioli, Elzo de Wit, Antonius L. van Boxtel, Hendrik Marks, Peter J. Zeller · 2025 · PLoS ONE
  95. Identifying cell types from single-cell data based on similarities and dissimilarities between cells
    Yuanyuan Li, Ping Luo, Yi Lu, Fang‐Xiang Wu · 2021 · BMC Bioinformatics
  96. scASGC: An adaptive simplified graph convolution model for clustering single-cell RNA-seq data
    Shudong Wang, Yunxin Zhang, Yulin Zhang, Wenhao Wu, Lan Ye, Yunyin Li, Jionglong Su, Shanchen Pang · 2023 · Computers in Biology and Medicine
  97. Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data
    Philipp Angerer, David S. Fischer, Fabian Joachim Theis, Antonio Scialdone, Carsten Marr · 2020 · Bioinformatics
  98. A murine aging cell atlas reveals cell identity and tissue-specific trajectories of aging
    2019
  99. Detecting Zero-Inflated Genes in Single-Cell Transcriptomics Data
    Oscar Clivio, Romain Lopez, Jeffrey Regier, Adam Gayoso, Michael I. Jordan, Nir Yosef · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  100. Charting Developmental Dissolution of Pluripotency.
    Joerg Betschinger · 2017 · Journal of Molecular Biology