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

Cited by (1,003)

Items 101–200 of 1,003

  1. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy
    Haikuo Li, Dian Li, Nicolas Ledru, Qiao Xuanyuan, Hao Wu, Amish Asthana, Lori Nicole Byers, Stefan G. Tullius, Giuseppe Orlando, Sushrut S. Waikar et al. · 2024 · Cell Metabolism
  2. Stabilized mosaic single-cell data integration using unshared features
    Shila Ghazanfar, Carolina Guibentif, John C. Marioni · 2023 · Nature Biotechnology
  3. Multimodal deep learning approaches for single-cell multi-omics data integration
    Tasbiraha Athaya, Rony Chowdhury Ripan, Xiaoman Li, Haiyan Hu · 2023 · Briefings in Bioinformatics
  4. 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
  5. Single-nucleus multi-omic profiling of human placental syncytiotrophoblasts identifies cellular trajectories during pregnancy
    Meijiao Wang, Yawei Liu, Run Sun, Fen-Ting Liu, Jiaqian Li, Yan Long, Jixiang Zhang, Xinwei Xie, Dongxu Li, Yiming Wang et al. · 2024 · Nature Genetics
  6. Massively parallel phenotyping of coding variants in cancer with Perturb-seq
    Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir et al. · 2022 · Nature Biotechnology
  7. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines
    Qionghua Zhu, Xin Zhao, Yuanhang Zhang, Yanping Li, Shang Liu, Jingxuan Han, Zhiyuan Sun, Chunqing Wang, Daqi Deng, Yisen Tang et al. · 2023 · Nature Communications
  8. Single-nucleus multi-omics of human stem cell-derived islets identifies deficiencies in lineage specification
    Punn Augsornworawat, Nathaniel J. Hogrebe, Matthew Ishahak, Mason D. Schmidt, Erica Marquez, Marlie M. Maestas, Daniel Veronese-Paniagua, Sarah E. Gale, Julia R. Miller, Leonardo Velazco-Cruz et al. · 2023 · Nature Cell Biology
  9. Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity
    Yuhua Hu, Feng Shen, Xi Yang, Tingting Han, Zhuowen Long, Jiale Wen, Junxing Huang, Jiangfeng Shen, Qing Guo · 2023 · Clinical Epigenetics
  10. Deciphering the impact of genomic variation on function
    Writing group (ordered by contribution), J Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon, Hannah K. Carter, Nidhi Sahni, Timothy E. Reddy, Xihong Lin et al. · 2024 · Nature
  11. Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data
    Chunman Zuo, Hao Dai, Luonan Chen · 2021 · Bioinformatics
  12. Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes
    Jindal, Kunal, Adil, Mohd Tayyab, Yamaguchi, Naoto, Yang, Xue, Wang, Helen C., Kamimoto, Kenji, Rivera-Gonzalez, Guillermo C., Morris, Samantha A. · 2024 · Nature Biotechnology
  13. 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
  14. UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization
    April R. Kriebel, Joshua D. Welch · 2022 · Nature Communications
  15. SIMBA: single-cell embedding along with features
    Huidong Chen, Jayoung Ryu, Michael E. Vinyard, Adam K. Lerer, Luca Pinello · 2023 · Nature Methods
  16. scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration
    Xiuhui Yang, Koren Kathleen Mann, Hao Wu, Jun Ding · 2024 · Genome biology
  17. MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells
    Lynch, Allen W., Theodoris, Christina V., Long, Henry W., Brown, Myles, Liu, X. Shirley, Meyer, Clifford A. · 2022 · Nature Methods
  18. Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS
    He, Zhen, Hu, Shuofeng, Chen, Yaowen, An, Sijing, Zhou, Jiahao, Liu, Runyan, Shi, Junfeng, Wang, Jing, Dong, Guohua, Shi, Jinhui et al. · 2024 · Nature Biotechnology
  19. Feature selection revisited in the single-cell era
    Pengyi Yang, Hao Ming Huang, Chunlei Liu · 2021 · Genome biology
  20. Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases
    Ober-Reynolds, Benjamin, Wang, Chen, Ko, Justin M., Rios, Eon J., Aasi, Sumaira Z., Davis, Mark M., Oro, Anthony E., Greenleaf, William J. · 2023 · Nature Genetics
  21. Into the multiverse: advances in single-cell multiomic profiling
    Ogbeide, Silvia, Giannese, Francesca, Mincarelli, Laura, Macaulay, Iain C. · 2022 · Trends in Genetics
  22. scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously
    Ziqi Zhang, Chengkai Yang, Xiuwei Zhang · 2022 · Genome biology
  23. Current challenges in understanding the role of enhancers in disease
    Judith B. Zaugg, Pelin Sahlén, Robin Andersson, Meritxell Alberich-Jordà, Wouter L. de Laat, Bart Deplancke, Jorge P. Ferrer, Susanne Mandrup, Gioacchino Natoli, Dariusz Plewczyński et al. · 2022 · Nature Structural & Molecular Biology
  24. Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective
    Shuang Ge, Shuqing Sun, Huan Xu, Qiang Shawn Cheng, Zhixiang Ren · 2025 · Briefings in Bioinformatics
  25. Single-cell omics: experimental workflow, data analyses and applications
    Fengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing et al. · 2024 · Science China Life Sciences
  26. The future of rapid and automated single-cell data analysis using reference mapping
    Mohammad Lotfollahi, Yuhan Hao, Fabian Joachim Theis, Rahul Satija · 2024 · Cell
  27. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler
    Florian Noack, Silvia Vangelisti, Gerald Raffl, Madalena Carido, Jeisimhan Diwakar, Faye Chong, Boyan Bonev · 2022 · Nature Neuroscience
  28. Single-cell multiome sequencing clarifies enteric glial diversity and identifies an intraganglionic population poised for neurogenesis
    Richard A. Guyer, Rhian G Stavely, Keiramarie Robertson, Sukhada M. Bhave, Jessica L. Mueller, Nicole Picard, Ryo Hotta, Julia A. Kaltschmidt, Allan M. Goldstein · 2023 · Cell Reports
  29. Benchmarking algorithms for single-cell multi-omics prediction and integration
    Yinlei Hu, Siyuan Wan, Yuanhanyu Luo, Yuanzhe Li, Tong Wu, Wentao Deng, Chen Jiang, Shan Jiang, Yueping Zhang, Nianping Liu et al. · 2024 · Nature Methods
  30. Dissecting metastasis using preclinical models and methods
    Jess D. Hebert, Joel W. Neal, Monte M. Winslow · 2023 · Nature reviews. Cancer
  31. DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data
    Lihua Zhang, Jing Zhang, Qing Hua Nie · 2022 · Science Advances
  32. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening
    Ralph Patrick, Marina Naval-Sánchez, Nikita Deshpande, Yifei Huang, Jingyu Zhang, Xiaoli Chen, Ying Yang, Kanupriya Tiwari, Mohammadhossein Esmaeili, Minh Tran et al. · 2024 · Cell Metabolism
  33. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells
    Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T. Doty, Adam D. Munday, Daniel Gao, Li Xin, Janis L. Abkowitz, Zhijun Duan, Jian Ma · 2024 · Nature Genetics
  34. Optimal transport for single-cell and spatial omics
    Bunne, Charlotte, Schiebinger, Geoffrey, Krause, Andreas, Regev, Aviv, Cuturi, Marco · 2024 · Nature Reviews Methods Primers
  35. Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues
    Pengfei Guo, Liran Mao, Yu‐Fan Chen, Chin Nien Lee, Angelysia Cardilla, Mingyao Li, Marek Bartošovič, Yanxiang Deng · 2025 · Nature Methods
  36. A single-cell multi-omics atlas of rice
    Xiangyu Wang, Huanwei Huang, Sanjie Jiang, Jingmin Kang, Dongwei Li, Kailai Wang, Shang Bo Xie, Tong Cheng, Chaofan Liu, Guihua Hu et al. · 2025 · Nature
  37. Droplet-based single-cell joint profiling of histone modifications and transcriptomes
    Xie, Yang, Zhu, Chenxu, Wang, Zhaoning, Tastemel, Melodi, Chang, Lei, Li, Yang Eric, Ren, Bing · 2023 · Nature Structural & Molecular Biology
  38. Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing
    Nicolas Ledru, Parker C. Wilson, Yoshiharu Muto, Yasuhiro Yoshimura, Hao Wu, Dian Li, Amish Asthana, Stefan G. Tullius, Sushrut S. Waikar, Giuseppe Orlando et al. · 2024 · Nature Communications
  39. Decoding gene regulation in the mouse embryo using single-cell multi-omics
    Ricard Argelaguet, Tim Lohoff, Jingyu Li, Asif Nakhuda, Deborah Drage, Felix Krueger, Lars Velten, Stephen J. Clark, Wolf Reik · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Single-cell analysis reveals context-dependent, cell-level selection of mtDNA
    Anna V. Kotrys, Timothy Durham, Xiaoyan A. Guo, Venkata Rao Vantaku, Sareh Parangi, Vamsi K. Mootha · 2024 · Nature
  41. 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
  42. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms
    Zidong Zhang, Michel Zamojski, Gregory R. Smith, Thea L. Willis, Val Yianni, Natalia Mendelev, Hanna Pinças, Nitish Seenarine, Mary Anne S. Amper, Mital Vasoya et al. · 2022 · Cell Reports
  43. FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells
    Ziang Zhu, Guohua Lou, Xiao-Lu Teng, Haixia Wang, Ying Luo, Wangke Shi, Kiddist D. Yihunie, Shumeng Hao, Kole DeGolier, Chengheng Liao et al. · 2023 · Nature Immunology
  44. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis
    Sneha Mitra, Ro Malik, Wilfred Wong, Afsana Rahman, Alexander J. Hartemink, Yuri Pritykin, Kushal K. Dey, Christina S. Leslie · 2024 · Nature Genetics
  45. 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
  46. Single-cell analysis enters the multiomics age
    Jeffrey M. Perkel · 2021 · Nature
  47. Single-cell multiplex chromatin and RNA interactions in ageing human brain
    Xingzhao Wen, Zhifei Luo, Wenxin Zhao, Riccardo Calandrelli, Tri C. Nguyen, Xueyi Wan, John Lalith Charles Richard, Sheng Zhong · 2024 · Nature
  48. Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
    Saori Sakaue, Kathryn Weinand, Shakson Isaac, Kushal K. Dey, Karthik A. Jagadeesh, Masahiro Kanai, Gerald F. M. Watts, Zhu Zhu, Accelerating Medicines Partnership® RA/SLE Program and Network, Jennifer Albrecht et al. · 2024 · Nature Genetics
  49. GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks
    Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Nila H. Servaas, Maksim M. Kholmatov, Neha Daga, Daria Nogina, Sophia Müller‐Dott, Armando Reyes‐Palomares et al. · 2023 · Molecular Systems Biology
  50. scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders
    Yichuan Cao, Xiamiao Zhao, Songming Tang, Qun Jiang, Sijie Li, Siyu Li, Shengquan Chen · 2024 · Nature Communications
  51. Mapping genotypes to chromatin accessibility profiles in single cells
    Franco Izzo, Robert M. Myers, Saravanan Ganesan, Levan Mekerishvili, Sanjay Kottapalli, Tamara Prieto, Elliot O. Eton, Theo Botella, Andrew Jeffrey Dunbar, Robert L. Bowman et al. · 2024 · Nature
  52. Multiscale footprints reveal the organization of cis-regulatory elements
    Hu Yan, Max A. Horlbeck, Ruochi Zhang, Sai Ma, Rojesh Shrestha, Vinay K. Kartha, Fabiana M. Duarte, Conrad Hock, Rachel E. Savage, Ajay S. Labade et al. · 2025 · Nature
  53. SMILE: mutual information learning for integration of single-cell omics data
    Yang Xu, Priyojit Das, Rachel Patton McCord · 2021 · Bioinformatics
  54. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system
    Philipp Sven Lars Schäfer, Daniel Dimitrov, Eduardo J. Villablanca, Julio Sáez-Rodríguez · 2024 · Nature Immunology
  55. Aging of the Hematopoietic Stem Cell Niche: New Tools to Answer an Old Question
    Francesca Matteini, Medhanie Assmelash Mulaw, Maria Carolina Florian · 2021 · Frontiers in Immunology
  56. Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data
    Michelle Y. Y. Lee, Klaus H. Kaestner, Mingyao Li · 2023 · Genome biology
  57. Current Bioinformatics Tools in Precision Oncology
    Tesfaye Wolde, Vipul Bhardwaj, Vijay Pandey · 2025 · MedComm
  58. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
    Peter Orchard, Nandini Manickam, Arushi Varshney, Swarooparani Vadlamudi, Charles Burant, Stephen C.J. Parker, Jeremy Kaplan, Claudia Lalancette, Karen L. Mohlke, Katherine Gallagher et al. · 2021 · Genome Research
  59. Single-cell joint profiling of multiple epigenetic proteins and gene transcription
    Haiqing Xiong, Qianhao Wang, Chen C. Li, Aibin He · 2024 · Science Advances
  60. The chromatin landscape of Th17 cells reveals mechanisms of diversification of regulatory and pro-inflammatory states
    Thakore, Pratiksha I., Schnell, Alexandra, Zhao, Maryann, Huang, Linglin, Hou, Yu, Christian, Elena, Zaghouani, Sarah, Wang, Chao, Singh, Vasundhara, Ma, Sai et al. · 2022
  61. Emerging artificial intelligence applications in Spatial Transcriptomics analysis
    Yijun Li, Stefan Stanojevic, Lana Xia Garmire · 2022 · Computational and Structural Biotechnology Journal
  62. 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
  63. Gene regulation on extrachromosomal DNA
    King L. Hung, Paul S. Mischel, Howard Y. Chang · 2022 · Nature Structural & Molecular Biology
  64. NF-κB dynamics in the language of immune cells
    Mohammad Aqdas, Myong‐Hee Sung · 2022 · Trends in Immunology
  65. Single-Cell RNA Sequencing Technology Landscape in 2023
    Hui‐Qi Qu, Charlly Kao, Hakon H. Hakonarson · 2023 · Stem Cells
  66. Stem cell‐intrinsic mechanisms regulating adult hair follicle homeostasis
    Seon A Lee, Kefei Nina Li, Tudorita Tumbar · 2020 · Experimental Dermatology
  67. Single-Cell Multiomics Techniques: From Conception to Applications
    Maria A. Dimitriu, Irina Lazar-Contes, Martin Roszkowski, Isabelle M. Mansuy · 2022 · Frontiers in Cell and Developmental Biology
  68. 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
  69. Applications of Single-Cell Omics in Tumor Immunology
    Junwei Liu, Saisi Qu, Tongtong Zhang, Yufei Gao, Hongyu Shi, Kaichen Song, Wei Chen, Weiwei Yin · 2021 · Frontiers in Immunology
  70. Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems
    Fides Lea Zenk, Jonas Simon Fleck, Sophie Martina Johanna Jansen, Bijan Kashanian, Benedikt Eisinger, Małgorzata Santel, Jean-Samuel Dupré, J. Gray Camp, Barbara Treutlein · 2024 · Nature Neuroscience
  71. Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumours
    Samarth Hegde, Bruno Giotti, Brian Y. Soong, László Halász, Jessica Le Bérichel, Maximilian M. Schaefer, Benoit Kloeckner, Raphaël Mattiuz, Matthew D. Park, Assaf Magen et al. · 2025 · Nature
  72. Spatial multiomic landscape of the human placenta at molecular resolution
    Johain R. Ounadjela, Ke Zhang, Koseki J. Kobayashi-Kirschvink, Kang Jin, Andrew J. C. Russell, Andreas Ian Lackner, Claire Callahan, Francesca Viggiani, Kushal K. Dey, Karthik A. Jagadeesh et al. · 2024 · Nature Medicine
  73. Tracking cell-type-specific temporal dynamics in human and mouse brains
    Ziyu Lu, Melissa Zhang, Jasper Lee, Andras Sziraki, Sonya Anderson, Zehao Zhang, Zihan Xu, Weirong Jiang, Shaoyu Ge, Peter T. Nelson et al. · 2023 · Cell
  74. Spatial integration of multi-omics single-cell data with SIMO
    Penghui Yang, Kaiyu Jin, Yue Yao, Lijun Jin, Xin Shao, Chengyu Li, Xiaoyan Lu, Xiaohui Fan · 2025 · Nature Communications
  75. 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)
  76. Mapping cells through time and space with moscot
    Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Aimée Bastidas-Ponce, Marta Tarquis-Medina et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  77. Intricacies of single-cell multi-omics data integration
    Pia Rautenstrauch, Anna Hendrika Cornelia Vlot, Sepideh Saran, Uwe Ohler · 2021 · Trends in Genetics
  78. The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
    Seth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt et al. · 2022 · Nucleic Acids Research
  79. Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies
    M. Joaquina Delàs, Christos M. Kalaitzis, Tamara Fawzi, Madeleine Demuth, Isabel Zhang, Hannah T. Stuart, Elena Costantini, Kenzo Ivanovitch, Elly Margaret Tanaka, James Briscoe · 2022 · Developmental Cell
  80. Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens
    Jordan E. Otto, Oana Ursu, Alexander P. Wu, Evan B. Winter, Michael S. Cuoco, Sai Ma, Kristin Qian, Brittany C. Michel, Jason D. Buenrostro, Bonnie Berger et al. · 2023 · Molecular Cell
  81. Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data
    Chuxi Xiao, Yixin Chen, Qiuchen Meng, Lei Wei, Xuegong Zhang · 2024 · Briefings in Bioinformatics
  82. Pharmacological activation of STAT1-GSDME pyroptotic circuitry reinforces epigenetic immunotherapy for hepatocellular carcinoma
    Yalin Tu, Haoran Wu, Chengpeng Zhong, Yan Liu, Zhewen Xiong, Siyun Chen, Jing Wang, Patrick Pak-Chun Wong, Weiqin Yang, Zhixian Liang et al. · 2024 · Gut
  83. Retrotransposons as a Source of DNA Damage in Neurodegeneration
    Eugénie Pezé-Heidsieck, Tom Bonnifet, Rania Znaidi, Camille Ravel‐Godreuil, Olivia Massiani-Beaudoin, Rajiv L. Joshi, Julia Fuchs · 2022 · Frontiers in Aging Neuroscience
  84. Benchmarking single-cell multi-modal data integrations
    Shaliu Fu, Shu-Guang Wang, Duanmiao Si, Gaoyang Li, Yawei Gao, Qi Liu · 2025 · Nature Methods
  85. Current Methodological Challenges of Single-Cell and Single-Nucleus RNA-Sequencing in Glomerular Diseases
    Dries Deleersnijder, Jasper Callemeyn, Ingrid Arijs, Maarten Naesens, Amaryllis H. Van Craenenbroeck, Diether Lambrechts, Ben Sprangers · 2021 · Journal of the American Society of Nephrology
  86. Virus Infection Variability by Single-Cell Profiling
    Maarit Suomalainen, Urs F. Greber · 2021 · Viruses
  87. siVAE: interpretable deep generative models for single-cell transcriptomes
    Yongin Choi, Ruoxin Li, Gerald Quon · 2023 · Genome biology
  88. Microtechnologies for single-cell and spatial multi-omics
    Yanxiang Deng, Zhiliang Bai, Rong Fan · 2023 · Nature Reviews Bioengineering
  89. Clonally heritable gene expression imparts a layer of diversity within cell types
    Jeff Eron Mold, Martin H. Weissman, Michael Ratz, Michael Hagemann-Jensen, Joanna Hård, Carl‐Johan Eriksson, Hosein Toosi, Joseph Berghenstråhle, Christoph Ziegenhain, Leonie von Berlin et al. · 2024 · Cell Systems
  90. A single-nuclei paired multiomic analysis of the human midbrain reveals age- and Parkinson’s disease–associated glial changes
    Levi Adams, Min Kyung Song, Samantha Yuen, Yoshiaki Tanaka, Yoon‐Seong Kim · 2024 · Nature Aging
  91. scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell–cell interactions
    Hechen Li, Ziqi Zhang, Michael Squires, Xi Xian Chen, Xiuwei Zhang · 2025 · Nature Methods
  92. Inferring gene regulation from stochastic transcriptional variation across single cells at steady state
    Anika Gupta, Jorge Diego Martin-Rufino, Thouis R. Jones, Vidya Subramanian, Xiaojie Qiu, Emanuelle I. Grody, Alex Bloemendal, Chen Weng, Sheng-Yong Niu, Kyung Hoi Min et al. · 2022 · Proceedings of the National Academy of Sciences
  93. Progress in single-cell multimodal sequencing and multi-omics data integration
    Xuefei Julie Wang, Xinchao Wu, Ni Hong, Wenfei Jin · 2023 · Biophysical Reviews
  94. Graph neural networks for single-cell omics data: a review of approaches and applications
    Li, Sijie, Hua, Heyang, Chen, Shengquan · 2025 · Briefings in Bioinformatics
  95. Tracking single-cell evolution using clock-like chromatin accessibility loci
    Yu Xiao, Wan Jin, Lingao Ju, Jie Fu, Gang Wang, Mengxue Yu, Fangjin Chen, Kaiyu Qian, Xinghuan Wang, Yi Zhang · 2024 · Nature Biotechnology
  96. Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome
    Eli Metzner, Kaden M. Southard, Thomas M. Norman · 2024 · Cell Systems
  97. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq
    Haikuo Li, Shuozhen Bao, Negin Farzad, Xiaoyu Qin, Anthony A. Fung, Di Zhang, Zhiliang Bai, Bo Tao, Rong Fan · 2025 · Nature Protocols
  98. Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
    Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong · 2022 · Genome biology
  99. Single-cell analysis of cis-regulatory elements
    Alexandre P. Marand, Robert J. Schmitz · 2021 · Current Opinion in Plant Biology
  100. JSNMF enables effective and accurate integrative analysis of single-cell multiomics data
    Yuanyuan Ma, Zexuan Sun, Pengcheng Zeng, Wenyu Zhang, Zhixiang Lin · 2022 · Briefings in Bioinformatics