Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

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  10. SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data
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  11. scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks
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  13. Current and future perspectives of single-cell multi-omics technologies in cardiovascular research
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  14. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance
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  16. Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status
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  17. Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex
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  18. EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling
    Chiara M. Schröder, Lea Zissel, Sophie‐Luise Mersiowsky, Mehmet Tekman, Simone Probst, Katrin M. Schüle, Sebastian Preißl, Oliver Schilling, H. T. Marc Timmers, Sebastian J. Arnold · 2024 · Developmental Cell
  19. Precision cardiovascular medicine: shifting the innovation paradigm
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  20. Recent advances in single-cell epigenomics
    Akihito Harada, Hiroshi Kimurâ, Yasuyuki Ohkawa · 2021 · Current Opinion in Structural Biology
  21. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues
    Joseph Swift, Kathleen Greenham, Joseph R. Ecker, Gloria M. Coruzzi, C. Robertson McClung · 2021 · The Plant Journal
  22. Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution
    Jose Ramon Barcenas-Walls, Federico Ansaloni, Bastien Hervé, Emilia Strandback, Tomas Nyman, Gonçalo Castelo‐Branco, Marek Bartošovič · 2023 · Nature Protocols
  23. Early neural specification of stem cells is mediated by a set of SOX2-dependent neural-associated enhancers
    Pavel A. Tsaytler, Gaby Blaess, Manuela Scholze‐Wittler, Frédéric Koch, Bernhard G. Herrmann · 2024 · Stem Cell Reports
  24. Revealing gene function with statistical inference at single-cell resolution
    Cole Trapnell · 2024 · Nature Reviews Genetics
  25. Deciphering breast cancer dynamics: insights from single-cell and spatial profiling in the multi-omics era
    Xin Xiong, Xin Wang, Cuicui Liu, Zhi-Ming Shao, Ke‐Da Yu · 2024 · Biomarker Research
  26. singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality
    David F. Stein, Huidong Chen, Michael E. Vinyard, Qian Qin, Rebecca D. Combs, Qian Zhang, Luca Pinello · 2021 · Frontiers in Genetics
  27. Single-Cell Epigenomics Reveals Mechanisms of Cancer Progression
    Lindsay M. LaFave, Rachel E. Savage, Jason D. Buenrostro · 2022 · Annual Review of Cancer Biology
  28. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects
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  29. The Analysis of the Human Megakaryocyte and Platelet Coding Transcriptome in Healthy and Diseased Subjects
    Koenraad De Wispelaere, Kathleen Freson · 2022 · International Journal of Molecular Sciences
  30. Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities
    Harmeet Kaur, Priyanka Jha, Sergio Ochatt, Vijay Kumar · 2023 · Critical Reviews in Biotechnology
  31. Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration
    Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li · 2023 · Bioinformatics
  32. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells
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  33. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
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  34. scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data
    Wei Li, Bin Xiang, Fan Yang, Yu Rong, Yanbin Yin, Jianhua Yao, Han Zhang · 2023 · Briefings in Bioinformatics
  35. Revealing spatial multimodal heterogeneity in tissues with SpaTrio
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  36. Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq
    Keyong Sun, Xin Liu, Runda Xu, Chang Liu, Anming Meng, Xun Lan · 2024 · Nature Cell Biology
  37. Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling
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  38. scPair: Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases
    Hongru Hu, Gerald Quon · 2024 · Nature Communications
  39. Dual alignment feature embedding network for multi-omics data clustering
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  40. Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro
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  42. Reconstructing developmental landscapes and trajectories from single-cell data
    Geoffrey R. Schiebinger · 2021 · Current Opinion in Systems Biology
  43. Fundamental and practical approaches for single-cell ATAC-seq analysis
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  44. Integration of scATAC-Seq with scRNA-Seq Data
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  46. A Single‐Nucleus Resolution Atlas of Transcriptome and Chromatin Accessibility for Peanut (Arachis Hypogaea L.) Leaves
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  47. Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
    Yang Li, Anjun Ma, Yizhong Wang, Qi Guo, Cankun Wang, Shuo Chen, Hongjun Fu, Bingqiang Liu, Qin Ma · 2024 · Briefings in Bioinformatics
  48. Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
    Rachel Yan, Alba Corman, Lyla Katgara, Wang Xiao, Xinhe Xue, Zoran Z. Gajic, Richard Sam, Michael Farid, Samuel M. Friedman, Jungwook Choo et al. · 2024 · Nature Biotechnology
  49. Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma
    Isabella S. Del Priore, Sai Ma, Jonathan Strecker, Tyler Jacks, Lindsay M. LaFave, Jason D. Buenrostro · 2021 · STAR Protocols
  50. One genome, many cell states: epigenetic control of innate immunity
    Isabella Rose Fraschilla, Hajera Amatullah, Kate L. Jeffrey · 2022 · Current Opinion in Immunology
  51. Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders
    Yuge Wang, Hongyu Zhao · 2022 · PLoS Computational Biology
  52. Scalable, multimodal profiling of chromatin accessibility and protein levels in single cells
    Eleni P. Mimitou, Caleb A. Lareau, Kelvin Y. Chen, André Luiz Zorzetto-Fernandes, Yusuke Takeshima, Wendy Luo, Tse-Shun Huang, Bertrand Z. Yeung, Pratiksha I. Thakore, James B. Wing et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Degradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assay
    Tristan Tay, Gayathri Bommakanti, Elizabeth S. Jaensch, Aparna Gorthi, Iswarya Karapa Reddy, Yan Hu, Ruochi Zhang, Aatman S. Doshi, Sin Lih Tan, Verena Brucklacher-Waldert et al. · 2024 · Cell Reports Medicine
  54. Single Cell Technologies: Beyond Microfluidics
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  55. Single-Cell Chromatin and Gene-Regulatory Dynamics of Mouse Nephron Progenitors
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  57. Efficient Generation of Paired Single‐Cell Multiomics Profiles by Deep Learning
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  60. Plant biotechnology research with single-cell transcriptome: recent advancements and prospects
    Muhammad Ali, Tianxia Yang, Hai Yan He, Yu Zhang · 2024 · Plant Cell Reports
  61. ImAge quantitates aging and rejuvenation
    Martin Alvarez-Kuglen, Kenta Ninomiya, Haodong Qin, Delany Rodriguez, Lorenzo Fiengo, Chen Farhy, Wei-Mien Hsu, Brian D. Kirk, Aaron P. Havas, Collin Kaufman et al. · 2024 · Nature Aging
  62. Best practices for differential accessibility analysis in single-cell epigenomics
    Alan Yue Yang Teo, Jordan W. Squair, Grégoire Courtine, Michael A. Skinnider · 2024 · Nature Communications
  63. Lineage tracing of stem cell–derived dopamine grafts in a Parkinson’s model reveals shared origin of all graft-derived cells
    Petter Storm, Yu Zhang, Fredrik Nilsson, Alessandro Fiorenzano, Niklas Krausse, Malin Åkerblom, Marcus Davidsson, Joan Yuan, Agnete Kirkeby, Tomas Björklund et al. · 2024 · Science Advances
  64. Single-cell technologies: current and near future
    Chenfei Wang, Qi Liu, Xiaohui Fan, Tieliu Shi · 2024 · Science China Life Sciences
  65. Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells
    Romuald Parmentier, Laëtitia Racine, Alice Moussy, Sophie Chantalat, Sudharshan Ravi, Nan Papili Gao, Daniel Stockholm, Guillaume Corre, Geneviève Fourel, Jean‐François Deleuze et al. · 2022 · PLoS Biology
  66. StabMap: Mosaic single cell data integration using non-overlapping features
    Ghazanfar, Shila, Guibentif, Carolina, Marioni, John C. · 2022
  67. Multiomic single-cell profiling identifies critical regulators of postnatal brain
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  68. Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC
    Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, Yinghui Zheng, Longzhi Tan, Dong Xing, X. Sunney Xie · 2022 · Proceedings of the National Academy of Sciences
  69. Osteogenic Differentiation Potential of Mesenchymal Stem Cells Using Single Cell Multiomic Analysis
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  70. Super-enhancer omics in stem cell
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  71. Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling
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  72. scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model
    Andy Tran, Pengyi Yang, Jean Yee Hwa Yang, John T. Ormerod · 2022 · NAR Genomics and Bioinformatics
  73. Multiomics and deep learning dissect regulatory syntax in human development
    Betty B. Liu, Selin Jessa, Samuel H. Kim, Yan Ting Ng, Soon Il Higashino, Georgi K. Marinov, Derek C. Chen, Benjamin E. Parks, Li Li, Tri C. Nguyen et al. · 2026 · Nature
  74. Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment
    Reema Baskar, Amy F. Chen, Patricia M.B. Favaro, Warren D. Reynolds, Fabian Müller, Luciene Borges, Sizun Jiang, Hyun Shin Park, Eric T. Kool, William James Greenleaf et al. · 2022 · Cell Reports Methods
  75. Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis
    Danni Hong, Hongli Lin, Lifang Liu, Muya Shu, Jianwu Dai, Falong Lu, Mengsha Tong, Jialiang Huang · 2022 · Briefings in Bioinformatics
  76. Nuclear receptor Nr5a2 promotes diverse connective tissue fates in the jaw
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  77. Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton
    Yu Bao, Yangyang Wei, Yuling Liu, Jingjing Gao, Shuang Cheng, Guanqing Liu, Qi You, Peng Liu, Quánwěi Lú, Pengtao Li et al. · 2023 · BMC Biology
  78. Neural cell diversity in the light of single-cell transcriptomics
    Sandra M. Fernández Moya, Akshay Jaya Ganesh, Mireya Plass · 2023 · Transcription
  79. DANCE: a deep learning library and benchmark platform for single-cell analysis
    Jiayuan Ding, Renming Liu, Hongzhi Wen, Wenzhuo Tang, Zhaoheng Li, Julian Venegas, Runze Su, Dylan Molho, Wei Jin, Yixin Wang et al. · 2024 · Genome biology
  80. A unified model-based framework for doublet or multiplet detection in single-cell multiomics data
    Haoran Hu, Xinjun Wang, Site Feng, Zhongli Xu, Jing Liu, Elisa Heidrich-O’Hare, Yanshuo Chen, Molin Yue, Lang Zeng, Ziqi Rong et al. · 2024 · Nature Communications
  81. Concepts and new developments in droplet-based single cell multi-omics
    Arthur Chow, Caleb A. Lareau · 2024 · Trends in biotechnology
  82. scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data
    Yunhee Jeong, Jonathan Ronen, Wolfgang Kopp, Pavlo Lutsik, Altuna Akalin · 2024 · BMC Bioinformatics
  83. scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics
    Wenwen Cheng, Changhui Yin, Shiya Yu, Xi Xian Chen, Ni Hong, Wenfei Jin · 2024 · Nucleic Acids Research
  84. A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions
    Xi Xi, Jiaqi Li, Jinmeng Jia, Qiuchen Meng, Chen Li, Xiaowo Wang, Lei Wei, Xuegong Zhang · 2025 · Nature Communications
  85. A molecular toolkit for superorganisms
    Bogdan Sieriebriennikov, Danny Reinberg, Claude Desplan · 2021 · Trends in Genetics
  86. Single-cell multi-omic velocity infers dynamic and decoupled gene regulation
    Chen Li, Maria Virgilio, Kathleen L. Collins, Joshua D. Welch · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  87. Increased matrix stiffness promotes fibrogenesis of hepatic stellate cells through AP-1-induced chromatin priming
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  88. scSPAF: Cell Similarity Purified Adaptive Fusion Network for Single-Cell Multi-Omics Clustering
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  90. Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data
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    Jeffrey D. Steimle, Chul Kim, Megan Rowton, Rangarajan D. Nadadur, Zhezhen Wang, Matthew Stocker, Andrew Daniel Hoffmann, Erika Hanson, Junghun Kweon, Tanvi Sinha et al. · 2023 · Cell Reports
  95. scapGNN: A graph neural network–based framework for active pathway and gene module inference from single-cell multi-omics data
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  99. Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks
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  100. Multimodal Data Visualization and Denoising with Integrated Diffusion
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