Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

Fang, Rongxin, Xia, Chenglong, Close, Jennie L., Zhang, Meng, He, Jiang, Huang, Zhengkai, Halpern, Aaron R., Long, Brian, Miller, Jeremy A., Lein, Ed S., Zhuang, Xiaowei·2022·Science
DOI 10.1126/science.abm1741

Cited by (274)

Items 201–274 of 274

  1. The left amygdala is genetically sexually-dimorphic: multi-omics analysis of structural MRI volumes
    Yuanyuan Gui, Geyu Zhou, Shuya Cui, Hongyu Li, Hui Juan Lu, Hongyu Zhao · 2025 · Translational Psychiatry
  2. Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex
    Juan Meng, Cheng Chen, Zhiyong Zhu, Yongkang Sun, Yiming Huang, Jiqiang Fu, Luyan Wu, Ling Li, Ling Li, Yiqin Bai et al. · 2026 · Nature Communications
  3. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining
    Kun Wang, Xiao Zhang, Hansen Cheng, Wenhao Ma, Guangchao Bao, Liting Dong, Yixiong Gou, Jian Yang, Haoyang Cai · 2023 · BMC Bioinformatics
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    Miao Liu, Shengyan Jin, Sherry S. Agabiti, Tyler B Jensen, Tianqi Yang, Jonathan S. D. Radda, Christian Felipe Ruiz, Gabriel Baldissera, Moein Rajaei, Jeffrey P. Townsend et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  5. SpaRx: Elucidate single-cell spatial heterogeneity of drug responses for personalized treatment
    Ziyang Tang, Xiang Liu, Zuotian Li, Tonglin Zhang, Baijian Yang, Jing Su, Qianqian Song · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  6. Comparative single-cell regulome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis
    Yuting Liu, Xin Luo, Yiming Sun, Kaimin Chen, Ting Hu, Benhui You, Jiahao Xu, Fengyun Zhang, Xiaoyu Meng, Xiang Li et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Spatial transcriptomics in adult Drosophila reveals new cell types in the brain and identifies subcellular mRNA patterns in muscles
    Jasper Janssens, Pierre J.J. Mangeol, Nikolai Hecker, Gabriele Partel, Katina I. Spanier, Joy N. Ismail, Gert J. Hulselmans, Stein Aerts, Frank Schnorrer · 2024 · eLife
  8. A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex
    Lei Han, Zhen Liu, Lifang Wang, Yuxuan Liu, Yanrong Wei, Jianyun Ma, Youzhe He, Yichen Zuo, Jiao Fang, Hui Yang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  9. Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization
    Bereket T Berackey, Zhiqun Tan, Ginny Wu, Sujan Chandra Das, Li Ren, Benjamin Esser, Qiao Ye, Mahsa Nafisi, Samuel S. Park, Pedro Adolfo Sequeira Mendieta et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  10. Progenitor Diversity and Architecture of the Human Ganglionic Eminences Shaping the Basal Ganglia
    Clara Siebert, Mengyi Song, Juan Moriano, Zhenmeiyu Li, Arantxa Cebrián‐Silla, Miranda Walker, Songcang Chen, Jennifer Baltazar, Lílian Gomes de Oliveira, Merut Shankar et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  11. Molecularly defined cellular atlas of the entire mouse brain with isotropic single-cell resolution
    Mengting Zhao, Jiandong Zhou, Tao Jiang, Miao Ren, Chuhao Dou, Lingyi Cai, Shengda Bao, Xueyan Jia, Zhaoyang Meng, Feifang Tang et al. · 2025 · Nature Communications
  12. A Single-Cell Omics Technical Guide for Advancing Neuropsychiatric Research
    Kayleigh Casmey, Maria Zimmermann, Yuxin Xie, Sierra A. Codeluppi-Arrowsmith, Gustavo Turecki · 2025 · Genes
  13. Synaptic transmission in supragranular layers of the human cortex – comparative review of structure, function, and plasticity
    Amelie Eichler, Pia Kruse, Charlotte Schob, Maximilian Lenz · 2025 · Frontiers in Synaptic Neuroscience
  14. HCN channels reveal conserved and divergent physiology in supragranular pyramidal neurons in primate species
    Cristina Radaelli, Matthew T. Schmitz, Xiao-Ping Liu, Scott Sawchuk, Ximena Opitz-Araya, Mark Hudson, Naz Taskin, Darren Bertagnolli, Jeff Goldy, Andrew Lin Ko et al. · 2026 · Communications Biology
  15. Enhancer dynamics and cellular architecture in the human spinal cord
    Elena K. Kandror, Anqi Wang, Mathieu Carriere, Alexis Peterson, Will Liao, Andreas Tjärnberg, Jun Hou Fung, Krishnaa T. A. Mahbubani, Jackson Loper, William Pangburn et al. · 2026 · Neuron
  16. Spatial multiomics dissects the SARS-CoV-2-induced disruption of cell adhesion and immune dynamics in the human hippocampus
    Hui Wei, Zhongman Jin, Caiyun Zhu, Pengsheng You, Jiaping Sui, Lian Huang, N N Liu, Wanwan Zhu, Qi Xu · 2026 · Journal of Neuroinflammation
  17. Phagocytosis and neuroinflammation: orchestrating central nervous system homeostasis, repair, and the resolution of inflammation
    Andrew D. Gaudet, Laura K. Fonken · 2026 · Trends in Neurosciences
  18. From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science
    Youzhe He, Yanrong Wei, Jingxi Zhi, C J Huang, Lei Han, Shiping Liu, Lifang Wang · 2026 · GigaScience
  19. Gene expression profiling enables refined parcellation of cortical layers in the heterogeneous human cerebral cortex
    Yanrong Wei, Youzhe He, Yuyang Liu, Langjian Zhu, Tiannan Feng, Zhiming Shen, Wu Wei, Longqi Liu, Lei Han, Lifang Wang · 2026 · Genome Medicine
  20. Decoding the lung-brain axis in influenza: from pulmonary infection to central nervous system injury
    Xindan Liang, X Wang, Zhibin Wang, Chunjing Chen, Li Li, Fangguo Lu · 2026 · Journal of Neuroinflammation
  21. Human genetics across levels of biological organization
    Diederik S. Laman Trip, Pedro Beltrão · 2026 · Nature Reviews Genetics
  22. q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics
    Myrl G. Marmarelis, Russell Littman, Francesca Battaglin, Donna Niedzwiecki, Alan Paul Venook, José Luis Ambite, Aram Galstyan, Heinz‐Josef Lenz, Greg Ver Steeg · 2024 · Communications Biology
  23. A complementary approach for neocortical cytoarchitecture inspection with cellular resolution imaging at whole brain scale
    Zhixiang Liu, Zhao Feng, Guangcai Liu, Anan Li, Hui Gong, Xiaoquan Yang, Xiangning Li · 2024 · Frontiers in Neuroanatomy
  24. The cytoarchitectonic landscape revealed by deep learning method facilitated precise positioning in mouse neocortex
    Zhixiang Liu, Anan Li, Hui Gong, Xiaoquan Yang, Qingming Luo, Zhao Feng, Xiangning Li · 2024 · Cerebral Cortex
  25. Tilted thick light-sheet microscopy with context-aware 3D localization for RNA imaging in intact 50 μm-thick sections
    Lin Cai, Qihang Song, Dongjian Cao, Qihuan Li, Wendi Wu, Yinghao Xiao, Xingguang Chen, Shu‐Jing Huang, Jie Yang, Yingjun Zhang et al. · 2025 · Optics Express
  26. Spatially Resolved Gene Expression is Not Necessary for Identifying Spatial Domains
    Senlin Lin, Yi Chen Zhao, Zhiyuan Yuan · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  27. Unveiling the Spatiotemporal Diversity of the Endothelium in Development: A Multi-Omics Approach
    Roy Jung, Chinmay M. Trivedi · 2024 · Circulation Research
  28. Three-dimensional single-cell transcriptome imaging of thick tissues
    Rongxin Fang, Aaron R. Halpern, Mohammed Mostafizur Rahman, Zhengkai Huang, Zhiyun Lei, Sebastian J Hell, Catherine G. Dulac, Xiaowei Zhuang · 2024 · eLife
  29. Efficient coding in biophysically realistic excitatory-inhibitory spiking networks
    Veronika Koren, Simone Blanco Malerba, Tilo Schwalger, Stefano Panzeri · 2025 · eLife
  30. Spatial transcriptomics in the adult Drosophila brain and body
    Jasper Janssens, Pierre J.J. Mangeol, Nikolai Hecker, Gabriele Partel, Katina I. Spanier, Joy N. Ismail, Gert J. Hulselmans, Stein Aerts, Frank Schnorrer · 2025 · eLife
  31. Long-Range Input to Cortical Microcircuits Shapes EEG-BOLD Correlation
    Vincent S.C. Chien, Stanislav Jiříček, Thomas R. Knösche, Jaroslav Hlinka, HELMUT J. SCHMIDT · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Multimodal spatial transcriptomics redefines cortical pathology in Huntington’s disease
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  33. Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain
    Yang Xie, Lei Chang, Guojie Zhong, Jonathan A. Rink, Tatiana Baez-Becerra, Ethan J. Armand, Wubin Ding, Kai Li, Éric Bonne, Anita Lie et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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  35. Laws for Glia Organization Conserved Across Mammals
    António Pinto‐Duarte, Katharine Bogue, Terrence J. Sejnowski A B, Shyam Srinivasan · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Genes, neurons and cortical architecture supporting human cognitive ability
    Djai B. Heyer · 2023
  37. [Advances of spatial omics in the individualized diagnosis and treatment of head and neck cancer].
    Chenyang Xu, Yin Wang, Dongmin Wei, Wenming Li, Ye Qian, Xinliang Pan, Dapeng Lei · 2023 · PubMed Central
  38. Comparative neuroimaging of sex differences in human and mouse brain anatomy
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  39. Structural characterization of a polymorphic repeat at the CACNA1C schizophrenia locus
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  40. SEQUENCING OF SINGLE CELLS: APPLICATION AND PERSPECTIVES
    Неряхин Александр Дмитриевич, Adis A. Tukhbatullin, G.R. Khannanova, Рафикова Гузель Альбертовна, Kadriia Enikeeva · 2024 · Molekulyarnaya Meditsina (Molecular medicine)
  41. Pathogenic variants associated with speech/cognitive delay and seizures affect genes with expression biases in excitatory neurons and microglia in developing human cortex
    Jeffrey B. Russ, Alexa C. Stone, Kayli Maney, Lauren C. Morris, Caroline Fiona Wright, Jillian H. Hurst, Jennifer L. Cohen · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  42. Visual analysis of spatial transcriptomics data with RedeViz
    Dehe Wang, Xianwen Ren · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  43. Cellular self-organization in hydrogels
    Yubing Xie · 2024 · Scientia Sinica Chimica
  44. Exploration of Alzheimers Disease
    Siying Bi · 2024 · Journal of Food Science Nutrition and Health
  45. Efficient coding in biophysically realistic excitatory-inhibitory spiking networks
    Veronika Koren, Simone Blanco Malerba, Tilo Schwalger, Stefano Panzeri · 2025 · eLife
  46. Spatial transcriptomics
    Ilya Belalov, Ye Wang, Anton A. Buzdin, Xinmin Li · 2025 · Elsevier eBooks
  47. Oblique Thick Light-Sheet Microscopy with Spatiotemporal 3D Localization for RNA Imaging in Intact 50 μm-Thick Sections
    Lin Cai, Qihang Song, Dongjian Cao, Qihuan Li, Wendi Wu, Yinghao Xiao, Xingguang Chen, Shu‐Jing Huang, Jie Yang, Yingjun Zhang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  48. Cytosplore EvoViewer: Visual Analytics of Conserved Evolutionary Patterns in multi-species single-cell sequencing data
    Soumyadeep Basu, Morgan E. Wirthlin, Jeroen Eggermont, Thomas Kroes, Boudewijn P. F. Lelieveldt, Ed S. Lein, Trygve E. Bakken, Thomas Höllt · 2025 · IEEE Pacific Visualization Conference (PacificVis)
  49. Gene expression changes in human brain evolution
    Stefano Berto, Soojin V. Yi, Geneviève Konopka · 2025 · Elsevier eBooks
  50. scMOBA: A conversational single-cell Multi-Omics Brain Agent across species
    Ran Wei, Ziyao Zhang, Jianle Sun, Yongkang Sun, Juan Meng, Peng Zheng, Chaoqi Liang, Fanyi Meng, Wanli Ouyang, Lei Bai et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Additional file 1 of SingleScan: a comprehensive resource for single-cell sequencing data processing and mining
    Wang, Kun, Zhang, Xiao, Cheng, Hansen, Ma, Wenhao, Guangchao Bao, Liting Dong, Yixiong Gou, Yang, Jian, Cai, Haoyang · 2023 · Figshare
  52. Additional file 1 of Glioblastoma cells have increased capacity to repair radiation-induced DNA damage after migration to the olfactory bulb
    Charlotte Degorre, Ian C. Sutton, Lehman, Stacey L., Uma T. Shankavaram, Kevin A. Camphausen, Philip J. Tofilon · 2023 · Figshare
  53. Genetic associations of externalising and internalising symptoms with brain imaging and cell types among autistic individuals and the general population
    Adeniran Okewole, Yuanjun Gu, Amir Ebneabbasi, Marcin A. Radecki, Laramie E. Duncan, Hadar Segal‐Gavish, Gizem Hazal Senturk, Nicholas J. Bray, Simon Braschi, Eden Hymanson et al. · 2025 · medRxiv
  54. A new cell type drove human brain complexity
    Antonela Bonafina, Laurent Nguyen · 2026 · Science
  55. Multi-Omics Reveals Activated Fibroblasts with Dual Functional Roles in Repair and Negative Barrier in the CD8 + T Cell Cytotoxic Niche for Lung Cancer Neoadjuvant Therapy
    Ruihan Zhou, Chaoxin Xiao, Ping Zhou, Ouying Yan, Banglei Yin, Xiaohong Yao, Jiaxin Liu, Xuexue Wu, WW Hou, Yulin Wang et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Single-molecule microscopy for precision medicine and diagnostics
    Yachen Ying, Yijun Liu, Songlin Liu, Li Li, Bochen Ma, Liang Yuan, Xilin Dou, Qin Shentu, Rui Ai, Jiao Lei et al. · 2026 · TrAC Trends in Analytical Chemistry
  57. Microbiome depletion rejuvenates the aging brain
    Caterina Gasperini, Kristina M. Holton, Francesco Limone, Mahitha Juttu, Cristina C. DeMeo, Kristina Kekrtova, Sayalee Patankar, Kaylee M Wells, Richard M. Giadone, Laura Ben Driss et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  58. Layer-specific cellular composition of mouse primary somatosensory and human temporal cortex: a direct 3D confocal counting approach
    Sergio Plaza‐Alonso, Lidia Alonso‐Nanclares, Silvia Tapia‐González, Laura Fernández‐García, Asta Kastanauskaite, Javier DeFelipe · 2026 · Frontiers in Neuroanatomy
  59. Density-Aware Spatial Randomization (DenSR) generates realistic null models for object-based colocalization analysis
    Sudharsan Kannan, Taylor L. Voelker, Benjamin S Snyder, Gail A. Robertson · 2026 · Molecular Biology of the Cell
  60. STAID: A Self‐Refining Deep Learning Framework for Spatial Cell‐Type Deconvolution with Biologically Informed Modeling
    Jixin Liu, Shuli Sun, Zhengliang Lv, X Q Liu, Yihua Wang, Bingqiang Liu · 2026 · Advanced Science
  61. Decoding spatial transcriptomics across multicellular and subcellular resolutions
    Chongyue Zhao, Tianhao Liu, Leigh M. Miller, Hongdou Li, Hanqiu Zhao, Daniel Barnett, Ruizhi Yuan, Hua Zhang, Qian Wang, Taylor John Eddens et al. · 2026 · Nature Communications
  62. Molecular Technologies for Intracellular mRNA Imaging and Their Recent Biological Applications
    Ke Xia, Xiangnan Wang, Zhenkun Wu, Xia Chu · 2026 · Chemical & Biomedical Imaging
  63. A framework for comparative analysis of human and mouse cortical neuron dendrites in corresponding brain regions
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  64. CTMAP: an adversarial cross-modal learning framework for accurate and robust cell-type annotation in single-cell resolution spatial transcriptomics
    Ying Wang, Jinyue Zhao, Mingming Guan, Duanchen Sun · 2026 · Briefings in Bioinformatics
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  66. STGAT: spatial domain identification of consecutive slices based on graph contrastive learning
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  67. A massively parallel CRISPR-based screening platform for modifiers of neuronal depolarization
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  74. Spatiotemporal Resolution for Neurodegenerative Diseases: Linking Proteinopathy, Cellular Vulnerability, and Disease Trajectories
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