Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
Ma, Sai, Zhang, Bing, LaFave, Lindsay M., Earl, Andrew S., Chiang, Zachary, Hu, Yan, Ding, Jiarui, Brack, Alison, Kartha, Vinay K., Tay, Tristan, Law, Travis, Lareau, Caleb, Hsu, Ya-Chieh, Regev, Aviv, Buenrostro, Jason D.·2020·Cell
Cited by (1,003)
Items 401–500 of 1,003
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- SnapATAC2: a fast, scalable and versatile tool for analysis of single-cell omics dataKai Zhang, Nathan R. Zemke, Ethan J. Armand, Bing Ren · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
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- Single-cell epigenomics and proteomics methods integrated in multiomicsHaiyue Bi, Xiaocheng Weng · 2024 · Fundamental Research
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- A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disordersArthur S. Lee, Lauren J. Ayers, Michael Kosicki, Wai Man Chan, Lydia Fozo, Brandon M. Pratt, Thomas E. Collins, Boxun Zhao, Matthew F. Rose, Alba Sanchis‐Juan et al. · 2024 · Nature Communications
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- Mapping the tumor immune landscape: single-cell RNA sequencing in cancer immunotherapyYingying Huang, Mao Zhang, Qiang Gao · 2025 · Cancer Letters
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- Single-cell multiomics data integration and generation with scPairingJeffrey Niu, Carlos Vasquez-Rios, Jiarui Ding · 2025 · Cell Reports Methods
- SHARE-seq reveals chromatin potentialDorothy Clyde · 2020 · Nature Reviews Genetics
- Epigenome rewiring in human pluripotent stem cellsJielin Yan, Danwei Huangfu · 2021 · Trends in Cell Biology
- Machine Learning Approaches to Single-Cell Data Integration and TranslationCaroline Uhler, G. V. Shivashankar · 2022 · Proceedings of the IEEE
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- Single-Cell Molecular Barcoding to Decode Multimodal Information Defining Cell StatesIk Soo Kim · 2023 · Molecules and Cells
- CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing dataGabriele Lubatti, Marco Stock, Ane Iturbide, Mayra L. Ruiz Tejada Segura, Melina Riepl, Richard C. V. Tyser, Anna Danese, Maria Colomé‐Tatché, Fabian Joachim Theis, Shankar Srinivas et al. · 2023 · Development
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- Learning Consistency and Specificity of Cells From Single-Cell Multi-Omic DataHaiyue Wang, Zaiyi Liu, Xiaoke Ma · 2024 · IEEE Journal of Biomedical and Health Informatics
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- Computational approaches to understand transcription regulation in developmentMaarten van der Sande, Siebren Frölich, Simon J. van Heeringen · 2023 · Biochemical Society Transactions
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- TEA-seq: a trimodal assay for integrated single cell measurement of transcription, epitopes, and chromatin accessibilityElliott G. Swanson, Cara Lord, Julian Reading, Alexander T. Heubeck, Adam K. Savage, Richard R. Green, Xiaojun Li, Troy R. Torgerson, Thomas F. Bumol, Lucas T. Graybuck et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
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- Computational tools for analyzing single-cell data in pluripotent cell differentiation studiesJun Ding, Amir Alavi, Mo R. Ebrahimkhani, Ziv Bar‐Joseph · 2021 · Cell Reports Methods
- Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq PlatformUlrike Gerdemann, Ryan A. Fleming, James Kaminski, Connor McGuckin, Xianliang Rui, Jennifer F. Lane, Paula Keskula, Lorenzo S Cagnin, Alex K. Shalek, Victor Tkachev et al. · 2022 · Frontiers in Immunology
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