A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Cusanovich, Darren A., Hill, Andrew J., Aghamirzaie, Delasa, Daza, Riza M., Pliner, Hannah A., Berletch, Joel B., Filippova, Galina N., Huang, Xingfan +9 more·2018·Cell

Cited by (789)

Items 101–200 of 789

  1. Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures
    Vivek Rai, Daniel X. Quang, Michael R. Erdos, Darren A. Cusanovich, Riza M. Daza, Narisu Narisu, Luli S. Zou, John P. Didion, Yuanfang Guan, Jay Shendure et al. · 2019 · Molecular Metabolism
  2. Cardiac cell type–specific gene regulatory programs and disease risk association
    James D. Hocker, Olivier Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui‐Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang Eric Li et al. · 2021 · Science Advances
  3. scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks
    Han Yuan, David R. Kelley · 2022 · Nature Methods
  4. Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
    Fortelny, Nikolaus, Bock, Christoph · 2020 · Genome Biology
  5. Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction
    Li, Chen, Virgilio, Maria C., Collins, Kathleen L., Welch, Joshua D. · 2023 · Nature Biotechnology
  6. Single-cell omics in ageing: a young and growing field
    Xiaojuan He, Sebastian Memczak, Jing Tao Qu, Juan Carlos Izpisúa Belmonte, Guang‐Hui Liu · 2020 · Nature Metabolism
  7. Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen
    Zhijian Li, Christoph Kuppe, Susanne Maria Ziegler, Mingbo Cheng, Nazanin Kabgani, Sylvia Menzel, Martin Zenke, Rafael Kramann, Ivan G. Costa · 2021 · Nature Communications
  8. A mouse tissue atlas of small noncoding RNA
    Isakova, Alina, Fehlmann, Tobias, Keller, Andreas, Quake, Stephen R. · 2020 · Proceedings of the National Academy of Sciences
  9. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci
    Tiit Örd, Kadri Õunap, Lindsey K. Stolze, Rédouane Aherrahrou, Valtteri Nurminen, Anu Toropainen, Ilakya Selvarajan, Tapio Lönnberg, Einari Aavik, Seppo Ylä‐Herttuala et al. · 2021 · Circulation Research
  10. scGCN is a graph convolutional networks algorithm for knowledge transfer in single cell omics
    Qianqian Song, Jing Su, Wei Zhang · 2021 · Nature Communications
  11. Multi-omic profiling of the developing human cerebral cortex at the single-cell level
    Kaiyi Zhu, Jaroslav M. Bendl, Samir Rahman, James M. Vicari, Claire Coleman, Tereza Clarence, Ovaun Latouche, Nadejda M. Tsankova, Aiqun Li, Kristen Brennand et al. · 2023 · Science Advances
  12. Single-cell technologies: From research to application
    Lu Wen, Guoqiang Li, Tao Huang, Wei Geng, Hao Pei, Jialiang Yang, Miao Zhu, Pengfei Zhang, Rui Hou, Geng Tian et al. · 2022 · The Innovation
  13. The immune niche of the liver
    Michael L. Cheng, Diana Nakib, Catia T. Perciani, Sonya A. MacParland · 2021 · Clinical Science
  14. Spatiotemporal modeling of molecular holograms
    Xiaojie Qiu, Daniel Y. Zhu, Yifan Lu, Jiajun Yao, Zehua Jing, Kyung Hoi Min, Mengnan Cheng, Hailin Pan, Lulu Zuo, S. B. King et al. · 2024 · Cell
  15. Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development
    Lijiang Fei, Haide Chen, Lifeng Ma, E Weigao, Renying Wang, Xing Fang, Ziming Zhou, Huiyu Sun, Jingjing Wang, Mengmeng Jiang et al. · 2022 · Nature Genetics
  16. Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma
    Long, Zhilin, Sun, Chengfang, Tang, Min, Wang, Yin, Ma, Jiayan, Yu, Jichuan, Wei, Jingchao, Ma, Jianzhu, Wang, Bohan, Xie, Qi et al. · 2022 · Cell Discovery
  17. Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease
    Mohamed Ameen, Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D. Wilson, Avyay Varadarajan et al. · 2022 · Cell
  18. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
    González-Blas, Carmen Bravo, De Winter, Seppe, Hulselmans, Gert, Hecker, Nikolai, Matetovici, Irina, Christiaens, Valerie, Poovathingal, Suresh, Wouters, Jasper, Aibar, Sara, Aerts, Stein · 2022
  19. Genomic methods in profiling DNA accessibility and factor localization
    David C. Klein, Sarah J. Hainer · 2019 · Chromosome Research
  20. Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders
    Hu, Benxia, Won, Hyejung, Mah, Won, Park, Royce B., Kassim, Bibi, Spiess, Keeley, Kozlenkov, Alexey, Crowley, Cheynna A., Pochareddy, Sirisha, The PsychENCODE Consortium et al. · 2021 · Nature Communications
  21. Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag
    Michael P. Meers, Geneva Llagas, Derek H. Janssens, Christine A. Codomo, Steven Henikoff · 2022 · Nature Biotechnology
  22. Deep learning of immune cell differentiation
    Alexandra Maslova, Ricardo N. Ramírez, Ke Ma, Hugo Schmutz, Chendi Wang, Curtis Fox, Bernard Ng, Christophe O. Benoist, Sara Mostafavi, Immunological Genome Project · 2020 · Proceedings of the National Academy of Sciences
  23. A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data
    Gaoyang Li, Shaliu Fu, Shuguang Wang, Chenyu Zhu, Bin Duan, Chen Tang, Xiaohan Chen, Guohui Chuai, Ping Q. Wang, Qi Liu · 2022 · Genome biology
  24. Integrated analysis of multimodal single-cell data with structural similarity
    Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Hua Nie, Jing Zhang, Xiaohui S. Xie · 2022 · Nucleic Acids Research
  25. Simultaneous deep generative modelling and clustering of single-cell genomic data
    Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong · 2021 · Nature Machine Intelligence
  26. The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus
    Thomas Cremer, Marion Cremer, Barbara Hübner, Asli Silahtaroglu, Michael J. Hendzel, Christian Lanctôt, Hilmar Strickfaden, Christoph G. Cremer · 2020 · BioEssays
  27. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application
    Minghui Wang, Won‐Min Song, Ming Chen, Qian Wang, Xianxiao Zhou, Peng Xu, Azra Krek, Yonejung Yoon, Lap Ho, Miranda E. Orr et al. · 2022 · Molecular Neurodegeneration
  28. Endothelial cell plasticity at the single-cell level
    Alessandra Pasut, Lisa M. Becker, Anne Cuypers, Peter Carmeliet · 2021 · Angiogenesis
  29. Multimodal deep learning approaches for single-cell multi-omics data integration
    Tasbiraha Athaya, Rony Chowdhury Ripan, Xiaoman Li, Haiyan Hu · 2023 · Briefings in Bioinformatics
  30. A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains
    Sziraki, Andras, Lu, Ziyu, Lee, Jasper, Banyai, Gabor, Anderson, Sonya, Abdulraouf, Abdulraouf, Metzner, Eli, Liao, Andrew, Banfelder, Jason, Epstein, Alexander et al. · 2023 · Nature Genetics
  31. CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution
    Wenjun Kong, Brent A. Biddy, Kenji Kamimoto, Junedh Amrute, Emily G. Butka, Samantha A. Morris · 2020 · Nature Protocols
  32. Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps
    Camden S. Jansen, Ricardo N. Ramírez, Nicole C. El-Ali, David Gómez-Cabrero, Jesper N. Tegner, Matthias Merkenschlager, Ana Conesa, Ali Mortazavi · 2019 · PLoS Computational Biology
  33. Spatial and temporal organization of the genome: current state and future aims of the 4D Nucleome Project
    J. Dekker, F. Alber, S. Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, A. Belmont, Lacramioara Bintu, A. Boettiger, Riccardo Calandrelli, C. Disteche et al. · 2023 · Molecules and Cells
  34. Selective vulnerability in α-synucleinopathies
    Javier Alegre‐Abarrategui, Katherine R. Brimblecombe, Rosalind F. Roberts, Elisavet Velentza‐Almpani, Bension Shlomo Tilley, Nora Bengoa‐Vergniory, Christos Proukakis · 2019 · Acta Neuropathologica
  35. Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding
    Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijing Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang · 2022 · Nature Machine Intelligence
  36. The role of environmental exposures and the epigenome in health and disease
    Bambarendage P. U. Perera, Christopher D. Faulk, Laurie Kathleen Svoboda, Jaclyn M. Goodrich, Dana C. Dolinoy · 2019 · Environmental and Molecular Mutagenesis
  37. Spatially mapped single-cell chromatin accessibility
    Casey A. Thornton, Ryan M. Mulqueen, Kristof A. Torkenczy, Andrew Nishida, Eve G. Lowenstein, Andrew J. Fields, Frank J. Steemers, Wenri H. Zhang, Heather L. McConnell, Randy L Woltjer et al. · 2021 · Nature Communications
  38. Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
    Jiajia Liu, Zhiwei Fan, Weiling Zhao, Xiaobo Zhou · 2021 · Frontiers in Genetics
  39. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
    Ioannis Sarropoulos, Mari Sepp, Robert Frömel, Kevin Leiss, Nils Trost, Evgeny V. Leushkin, Konstantin Okonechnikov, Piyush K. Joshi, Peter Giere, Lena M. Kutscher et al. · 2021 · Science
  40. scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
    Ziqi Zhang, Chengkai Yang, Xiuwei Zhang · 2022 · Genome biology
  41. Evolutionary cell type mapping with single-cell genomics
    Amos Tanay, Arnau Sebé-Pedrós · 2021 · Trends in Genetics
  42. CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
    Kamimoto, Kenji, Hoffmann, Christy M., Morris, Samantha A. · 2020
  43. MeCP2 represses enhancers through chromosome topology-associated DNA methylation
    Adam W. Clemens, Dennis Y. Wu, J. Moore, Diana L. Christian, Guoyan Zhao, Harrison W. Gabel · 2019 · Molecules and Cells
  44. Multiscale PHATE identifies multimodal signatures of COVID-19
    Kuchroo, Manik, Huang, Jessie, Wong, Patrick, Grenier, Jean-Christophe, Shung, Dennis, Tong, Alexander, Lucas, Carolina, Klein, Jon, Burkhardt, Daniel B., Gigante, Scott et al. · 2022 · Nature Biotechnology
  45. Single nucleus multi-omics regulatory landscape of the murine pituitary
    Frederique Murielle Ruf-Zamojski, Zidong Zhang, Michel Zamojski, Gregory R. Smith, Natalia Mendelev, Hanqing Liu, German Nudelman, Mika Moriwaki, Hanna Pinças, Rosa Castanon et al. · 2021 · Nature Communications
  46. Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single‐cell RNA sequencing analyses
    Jorge A. Tzec-Interián, Daianna González‐Padilla, Elsa Góngora‐Castillo · 2025 · Quantitative Biology
  47. The accessible chromatin landscape of the murine hippocampus at single-cell resolution
    John R. Sinnamon, Kristof A. Torkenczy, Michael W. Linhoff, Sarah A. Vitak, Ryan M. Mulqueen, Hannah A. Pliner, Cole Trapnell, Frank J. Steemers, Gail Mandel, Andrew Adey · 2019 · Genome Research
  48. Perspectives on defining cell types in the brain
    Mukamel, Eran A, Ngai, John · 2019 · Current Opinion in Neurobiology
  49. X-chromosome regulation and sex differences in brain anatomy
    Armin Raznahan, Christine M. Distèche · 2020 · Neuroscience & Biobehavioral Reviews
  50. A guide to systems-level immunomics
    Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas, Anna C. Aschenbrenner, Marc Beyer, Joachim Ludwig Schultze · 2022 · Nature Immunology
  51. DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data
    Wan-Wen Zeng, Xi Chen, Z. Duren, Yong Wang, Rui Jiang, Wing H Wong · 2019 · Nature Communications
  52. Spirits in the Material World: Enhancer RNAs in Transcriptional Regulation
    Tim Y. Hou, W. Lee Kraus · 2020 · Trends in Biochemical Sciences
  53. The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders
    Tychele N. Turner, Evan E. Eichler · 2018 · Trends in Neurosciences
  54. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility
    Xu, Wei, Wen, Yi, Liang, Yingying, Xu, Qiushi, Wang, Xuefei, Jin, Wenfei, Chen, Xi · 2021 · Nature Protocols
  55. Automatic cell type identification methods for single-cell RNA sequencing
    Xie, Bingbing, Jiang, Qin, Mora, Antonio, Li, Xuri · 2021 · Computational and Structural Biotechnology Journal
  56. Applications of deep learning in understanding gene regulation
    Zhongxiao Li, Elva Gao, Juexiao Zhou, Wenkai Han, Xiaopeng Xu, Xin Gao · 2023 · Cell Reports Methods
  57. Bi-order multimodal integration of single-cell data
    Jinzhuang Dou, Shaoheng Liang, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li et al. · 2022 · Genome biology
  58. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A
    Chen Weng, Anniya Gu, Shanshan Zhang, Leina Lu, Luxin Ke, Peidong Gao, Xiaoxiao Liu, Yuntong Wang, Peinan Hu, Dylan Plummer et al. · 2023 · Nature Communications
  59. Classifying cells with Scasat, a single-cell ATAC-seq analysis tool
    Syed Murtuza Baker, Connor Rogerson, Andrew Hayes, Andrew D Sharrocks, Magnus Rattray · 2018 · Nucleic Acids Research
  60. RETRACTED ARTICLE: KDM4 orchestrates epigenomic remodeling of senescent cells and potentiates the senescence-associated secretory phenotype
    2021 · Retracted
  61. CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis
    Fulong Yu, Vijay G. Sankaran, Guo‐Cheng Yuan · 2021 · Bioinformatics
  62. Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer
    Karan Kumar Budhraja, Bradon R. McDonald, Michelle D. Stephens, Tania Contente‐Cuomo, Havell Markus, Maria Farooq, Patricia Filippsen Favaro, Sydney C Connor, Sara Ann Byron, Jan B. Egan et al. · 2023 · Science Translational Medicine
  63. Advances and applications in single-cell and spatial genomics
    Jingjing Wang, Fang Ye, Haoxi Chai, Yujia Jiang, Teng Wang, Xia Ran, Qimin Xia, Ziye Xu, Yuting Fu, Guodong Zhang et al. · 2024 · Science China Life Sciences
  64. Blocking CHOP-dependent TXNIP shuttling to mitochondria attenuates albuminuria and mitigates kidney injury in nephrotic syndrome
    Sun-Ji Park, Yeawon Kim, Chuang Li, Junwoo Suh, Jothilingam Sivapackiam, Tássia Mangetti Gonçalves, George Jarad, Guoyan Zhao, Fumihiko Urano, Vijay Sharma et al. · 2022 · Proceedings of the National Academy of Sciences
  65. Electrochemiluminescence-Microscopy for microRNA Imaging in Single Cancer Cell Combined with Chemotherapy-Photothermal Therapy
    Huairong Zhang, Wanxia Gao, Yong Liu, Yingnan Sun, Yanxialei Jiang, Shusheng Zhang · 2019 · Analytical Chemistry
  66. SMILE: mutual information learning for integration of single-cell omics data
    Yang Xu, Priyojit Das, Rachel Patton McCord · 2021 · Bioinformatics
  67. Using single-cell technologies to map the human immune system — implications for nephrology
    Benjamin J. Stewart, John R. Ferdinand, Menna Ruth Clatworthy · 2019 · Nature Reviews Nephrology
  68. The epigenetically-encoded memory of the innate immune system
    Sarah Sun, Luis Bruno Barreiro · 2020 · Current Opinion in Immunology
  69. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
    Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan · 2020 · Genome biology
  70. A multimodal cell census and atlas of the mammalian primary motor cortex
    BRAIN Initiative Cell Census Network (BICCN), Ricky S. Adkins, Andrew I. Aldridge, Shona W. Allen, Seth A. Ament, Xu An, Ethan J. Armand, Giorgio A. Ascoli, Trygve E. Bakken, Anita E. Bandrowski et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types
    Li, Jiaqi, Wang, Jingjing, Zhang, Peijing, Wang, Renying, Mei, Yuqing, Sun, Zhongyi, Fei, Lijiang, Jiang, Mengmeng, Ma, Lifeng, E, Weigao et al. · 2022 · Nature Genetics
  72. Systematic benchmarking of single-cell ATAC-sequencing protocols
    Florian V. De Rop, Gert J. Hulselmans, Christopher Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González‐Blas, Doménica Marchese, Ginevra Caratù, Suresh Kumar Poovathingal et al. · 2023 · Nature Biotechnology
  73. Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory
    Megan S. F. Soon, Hyun Jae Lee, Jessica A. Engel, Jasmin Straube, Bryce S. Thomas, Clara P. S. Pernold, Lachlan S. Clarke, Pawat Laohamonthonkul, Rohit Haldar, Cameron G. Williams et al. · 2020 · Nature Immunology
  74. Single-cell joint profiling of multiple epigenetic proteins and gene transcription
    Haiqing Xiong, Qianhao Wang, Chen C. Li, Aibin He · 2024 · Science Advances
  75. Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity
    Jiyang Yu, Junmin Peng, Hongbo Chi · 2019 · Current Opinion in Systems Biology
  76. Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network
    Isabella V Soluri, Lauren M Zumerling, Omar A. Payán Parra, Eleanor G. Clark, Shelby A. Blythe · 2020 · eLife
  77. A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma
    Nikos Kourtis, Qingqing Wang, Bei Wang, Erin M. Oswald, Christina Adler, Samvitha Cherravuru, Evangelia Malahias, Lance Zhang, Jacquelynn Golubov, Qiaozhi Wei et al. · 2022 · Nature Cancer
  78. Leveraging Single-Cell Multi-Omics to Decode Tumor Microenvironment Diversity and Therapeutic Resistance
    Hussein Sabit, Borros Michael Arneth, Timothy Michael Pawlik, Shaimaa E. Abdel-Ghany, Aysha Ghazy, Rawan M. Abdelazeem, Amany I. Alqosaibi, Ibtesam S. Al-Dhuayan, Jawaher Almulhim, Noof Abdulrahman Alrabiah et al. · 2025 · Pharmaceuticals
  79. Perspectives on Bulk-Tissue RNA Sequencing and Single-Cell RNA Sequencing for Cardiac Transcriptomics
    Jana-Charlotte Hegenbarth, Giuliana Lezzoche, León J. De Windt, Monika Stoll · 2022 · Frontiers in Molecular Medicine
  80. NF-κB dynamics in the language of immune cells
    Mohammad Aqdas, Myong‐Hee Sung · 2022 · Trends in Immunology
  81. Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks
    Paco Majic, Joshua L. Payne · 2019 · Molecular Biology and Evolution
  82. Understanding the kidney one cell at a time
    Jihwan Park, Chang Liu, Junhyong Kim, Katalin Suszták · 2019 · Kidney International
  83. Enhancer RNAs: mechanisms in transcriptional regulation and functions in diseases
    Qianhui Li, Xin Liu, Jingtao Wen, Xi Chen, Bumin Xie, Yang Zhao · 2023 · Cell Communication and Signaling
  84. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types
    Kim, Samuel S., Truong, Buu, Jagadeesh, Karthik, Dey, Kushal K., Shen, Amber Z., Raychaudhuri, Soumya, Kellis, Manolis, Price, Alkes L. · 2024 · Nature Communications
  85. A decade of molecular cell atlases
    Stephen R. Quake · 2022 · Trends in Genetics
  86. RA3 is a reference-guided approach for epigenetic characterization of single cells
    Shengquan Chen, Guanao Yan, Wenyu Zhang, Jinzhao Li, Rui Jiang, Zhixiang Lin · 2021 · Nature Communications
  87. Transcriptomic encoding of sensorimotor transformation in the midbrain
    Zhiyong Xie, Mengdi Wang, Zeyuan Liu, Congping Shang, Changjiang Zhang, Le Sun, Huating Gu, Gengxin Ran, Qing Pei, Qiang Ma et al. · 2021 · eLife
  88. Single-cell chromatin accessibility landscape in kidney identifies additional cell-of-origin in heterogenous papillary renal cell carcinoma
    Qi Wang, Yang Zhang, Bolei Zhang, Yao Shi Fu, Xiaozhi Zhao, Jing Zhang, Ke Zuo, Yuexian Xing, Song Jiang, Zhaohui Steve Qin et al. · 2022 · Nature Communications
  89. Cellcano: supervised cell type identification for single cell ATAC-seq data
    Wenjing Ma, Jiaying Lu, Hao Wu · 2023 · Nature Communications
  90. Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision
    Kathleen Abadie, Elisa C. Clark, Rajesh M. Valanparambil, Obinna Ukogu, Wei Yang, Riza M. Daza, Kenneth K.H. Ng, Jumana Fathima, Allan L. Wang, Judong Lee et al. · 2024 · Immunity
  91. Network Approaches for Dissecting the Immune System
    Hao Shi, Koon‐Kiu Yan, Liang Ding, Chenxi Qian, Hongbo Chi, Jiyang Yu · 2020 · iScience
  92. Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips
    Dan Feng, Zhe Liang, Yifan Wang, Jiaying Yao, Zan Yuan, Guihua Hu, Ruihong Qu, Shang Bo Xie, Dongwei Li, Liwen Yang et al. · 2022 · BMC Biology
  93. Tracking cell-type-specific temporal dynamics in human and mouse brains
    Zi-Yu Lu, Melissa Zhang, Jasper Lee, András Sziráki, Sonya Anderson, Zehao Zhang, Zi-Han Xu, Weirong Jiang, Shaoyu Ge, Peter T. Nelson et al. · 2023 · Cell
  94. Unveiling heterogeneity in MSCs: exploring marker-based strategies for defining MSC subpopulations
    Si Chen, Bowei Liang, Jianyong Xu · 2024 · Journal of Translational Medicine
  95. The Role of Insulation in Patterning Gene Expression
    Isa Özdemir, Maria Cristina Gambetta · 2019 · Genes
  96. Single-cell ATAC-Seq reveals cell type-specific transcriptional regulation and unique chromatin accessibility in human spermatogenesis
    Xiaolong Wu, Mujun Lu, Damin Yun, Sheng Gao, Shitao Chen, Longfei Hu, Yunhao Wu, Xiaorong Wang, Enkui Duan, C. Yan Cheng et al. · 2021 · Human Molecular Genetics
  97. Single-cell Hi-C data analysis: safety in numbers
    Aleksandra A. Galitsyna, Mikhail Sergeevich Gelfand · 2021 · Briefings in Bioinformatics
  98. FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression
    Ricardo N. Ramírez, Kaitavjeet Chowdhary, Juliette Léon, Diane J. Mathis, Christophe O. Benoist · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  99. Profiling Chromatin Accessibility at Single-Cell Resolution
    Sarthak Sinha, Ansuman T. Satpathy, Weiqiang Zhou, Hongkai Ji, Jo Anne Stratton, Arzina Jaffer, Nizar Jacques Bahlis, A. Sorana Morrissy, Jeff A. Biernaskie · 2021 · Genomics Proteomics & Bioinformatics
  100. Heterogeneity and Molecular Markers for CNS Glial Cells Revealed by Single-Cell Transcriptomics
    Junjie Sun, Yixing Song, Zhiheng Chen, Jiaying Qiu, Shunxing Zhu, Liucheng Wu, Lingyan Xing · 2021 · Cellular and Molecular Neurobiology