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Single-cell chromatin accessibility reveals principles of regulatory variation

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Cited by:

  1. Songming Tang & Xuejian Cui & Rongxiang Wang & Sijie Li & Siyu Li & Xin Huang & Shengquan Chen, 2024. "scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  2. Shengen Shawn Hu & Lin Liu & Qi Li & Wenjing Ma & Michael J. Guertin & Clifford A. Meyer & Ke Deng & Tingting Zhang & Chongzhi Zang, 2022. "Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  3. Youtao Lu & Jaehee Lee & Jifen Li & Srinivasa Rao Allu & Jinhui Wang & HyunBum Kim & Kevin L. Bullaughey & Stephen A. Fisher & C. Erik Nordgren & Jean G. Rosario & Stewart A. Anderson & Alexandra V. U, 2023. "CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  4. Aaron T L Lun & Hervé Pagès & Mike L Smith, 2018. "beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-15, May.
  5. Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  6. Haowen Zhang & Li Song & Xiaotao Wang & Haoyu Cheng & Chenfei Wang & Clifford A. Meyer & Tao Liu & Ming Tang & Srinivas Aluru & Feng Yue & X. Shirley Liu & Heng Li, 2021. "Fast alignment and preprocessing of chromatin profiles with Chromap," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
  7. Gaoyang Hao & Yi Fan & Zhuohan Yu & Yanchi Su & Haoran Zhu & Fuzhou Wang & Xingjian Chen & Yuning Yang & Guohua Wang & Ka-chun Wong & Xiangtao Li, 2025. "Topological identification and interpretation for single-cell epigenetic regulation elucidation in multi-tasks using scAGDE," Nature Communications, Nature, vol. 16(1), pages 1-26, December.
  8. B. Edginton-White & A. Maytum & S. G. Kellaway & D. K. Goode & P. Keane & I. Pagnuco & S. A. Assi & L. Ames & M. Clarke & P. N. Cockerill & B. Göttgens & J. B. Cazier & C. Bonifer, 2023. "A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  9. Parashar Dhapola & Johan Rodhe & Rasmus Olofzon & Thomas Bonald & Eva Erlandsson & Shamit Soneji & Göran Karlsson, 2022. "Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  10. Vianne R. Gao & Rui Yang & Arnav Das & Renhe Luo & Hanzhi Luo & Dylan R. McNally & Ioannis Karagiannidis & Martin A. Rivas & Zhong-Min Wang & Darko Barisic & Alireza Karbalayghareh & Wilfred Wong & Yi, 2024. "ChromaFold predicts the 3D contact map from single-cell chromatin accessibility," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  11. Suhas V. Vasaikar & Adam K. Savage & Qiuyu Gong & Elliott Swanson & Aarthi Talla & Cara Lord & Alexander T. Heubeck & Julian Reading & Lucas T. Graybuck & Paul Meijer & Troy R. Torgerson & Peter J. Sk, 2023. "A comprehensive platform for analyzing longitudinal multi-omics data," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  12. Yuyao Liu & Zhen Li & Xiaoyang Chen & Xuejian Cui & Zijing Gao & Rui Jiang, 2025. "INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation," Nature Communications, Nature, vol. 16(1), pages 1-23, December.
  13. Wenjing Ma & Jiaying Lu & Hao Wu, 2023. "Cellcano: supervised cell type identification for single cell ATAC-seq data," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
  14. Zhijian Li & Christoph Kuppe & Susanne Ziegler & Mingbo Cheng & Nazanin Kabgani & Sylvia Menzel & Martin Zenke & Rafael Kramann & Ivan G. Costa, 2021. "Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
  15. Anna Laddach & Song Hui Chng & Reena Lasrado & Fränze Progatzky & Michael Shapiro & Alek Erickson & Marisol Sampedro Castaneda & Artem V. Artemov & Ana Carina Bon-Frauches & Eleni-Maria Amaniti & Jens, 2023. "A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  16. Zhen Miao & Jianqiao Wang & Kernyu Park & Da Kuang & Junhyong Kim, 2025. "Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  17. Xiang Lin & Tian Tian & Zhi Wei & Hakon Hakonarson, 2022. "Clustering of single-cell multi-omics data with a multimodal deep learning method," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  18. Samir Rachid Zaim & Mark-Phillip Pebworth & Imran McGrath & Lauren Okada & Morgan Weiss & Julian Reading & Julie L. Czartoski & Troy R. Torgerson & M. Juliana McElrath & Thomas F. Bumol & Peter J. Ske, 2024. "MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  19. Yoshiharu Muto & Eryn E. Dixon & Yasuhiro Yoshimura & Haojia Wu & Kohei Omachi & Nicolas Ledru & Parker C. Wilson & Andrew J. King & N. Eric Olson & Marvin G. Gunawan & Jay J. Kuo & Jennifer H. Cox & , 2022. "Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  20. Alan Yue Yang Teo & Jordan W. Squair & Gregoire Courtine & Michael A. Skinnider, 2024. "Best practices for differential accessibility analysis in single-cell epigenomics," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  21. Ruohan Wang & Yumin Zheng & Zijian Zhang & Kailu Song & Erxi Wu & Xiaopeng Zhu & Tao P. Wu & Jun Ding, 2024. "MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  22. Alan Selewa & Kaixuan Luo & Michael Wasney & Linsin Smith & Xiaotong Sun & Chenwei Tang & Heather Eckart & Ivan P. Moskowitz & Anindita Basu & Xin He & Sebastian Pott, 2023. "Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  23. Fangfang Yan & Akiko Suzuki & Chihiro Iwaya & Guangsheng Pei & Xian Chen & Hiroki Yoshioka & Meifang Yu & Lukas M. Simon & Junichi Iwata & Zhongming Zhao, 2024. "Single-cell multiomics decodes regulatory programs for mouse secondary palate development," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  24. Yu Zhao & Ran Zhou & Bingqing Xie & Cambrian Y. Liu & Martin Kalski & Candace M. Cham & Zhiwei Jiang & Jason Koval & Christopher R. Weber & David T. Rubin & Mitch Sogin & Sean Crosson & Mengjie Chen &, 2025. "Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  25. Kristina Handler & Karsten Bach & Costanza Borrelli & Salvatore Piscuoglio & Xenia Ficht & Ilhan E. Acar & Andreas E. Moor, 2023. "Fragment-sequencing unveils local tissue microenvironments at single-cell resolution," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  26. Lei Xiong & Kang Tian & Yuzhe Li & Weixi Ning & Xin Gao & Qiangfeng Cliff Zhang, 2022. "Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
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