What is a cell type and how to define it?

Cited by (481)

Items 101–200 of 481

1. The adult ovary at single cell resolution: an expert review
   Ilmatar Rooda, Loren Méar, Jasmin Hassan, Pauliina Damdimopoulou · 2025 · American Journal of Obstetrics and Gynecology
2. Further refining the boundaries of the hippocampus CA2 with gene expression and connectivity: Potential subregions and heterogeneous cell types
   Michael S. Bienkowski · 2023 · Hippocampus
3. Connecting single-cell transcriptomes to projectomes in the mouse visual cortex
   Staci A. Sorensen, Nathan W. Gouwens, Yun Wang, Matthew Mallory, Agata Budzillo, Rachel A. Dalley, Brian Lee, Olga Gliko, Hsien-Chi Kuo, Xiuli Kuang et al. · 2026 · Nature
4. scTOP: physics-inspired order parameters for cellular identification and visualization
   Maria Yampolskaya, Michael J. Herriges, Laertis Ikonomou, Darrell N. Kotton, Pankaj Mehta · 2023 · Development
5. Movement-related increases in subthalamic activity optimize locomotion
   Joshua W. Callahan, Juan Carlos Morales, Jeremy F. Atherton, Dorothy T. Wang, Selena Kostic, Mark D. Bevan · 2024 · Cell Reports
6. Meta-analysis of single-cell RNA sequencing co-expression in human neural organoids reveals their high variability in recapitulating primary tissue
   Jonathan M. Werner, Jesse Gillis · 2024 · PLoS Biology
7. Accurate quantification of single-cell and single-nucleus RNA-seq transcripts using distinguishing flanking k-mers
   Kristján Eldjárn Hjörleifsson, Delaney K. Sullivan, Nikhila P. Swarna · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
8. Mapping the topography of spatial gene expression with interpretable deep learning
   Uthsav Chitra, Brian J. Arnold, Hirak Sarkar · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
9. Charting the spatial transcriptome of the human cerebral cortex at single-cell resolution
   Songren Wei, Meng Luo, Pingping Wang, Rui Chen, Xiyun Jin, Chang Xu, Chenyang Li, Xiaoyu Lin, Zhaochun Xu, Hongxin Liu et al. · 2025 · Nature Communications
10. The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution
    Arnau Sebé-Pedrós, Amos Tanay, Mara Lawniczak, Detlev Arendt, Stein Aerts, John M. Archibald, Maria Ina Arnone, Mark Blaxter, Phillip A. Cleves, Susana M. Coelho et al. · 2025 · Nature
11. Dissecting cell‐type‐specific pathways in medial entorhinal cortical‐hippocampal network for episodic memory
    Hisayuki Osanai, Indrajith R. Nair, 貴司 北村 · 2023 · Journal of Neurochemistry
12. Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing
    Oleksandr Dudchenko, José Ordovás-Montañés, Colin D. Bingle · 2023 · Biochemical Journal
13. Electrophysiological classification of human layer 2–3 pyramidal neurons reveals subtype-specific synaptic interactions
    Henrike Planert, Franz Xaver Mittermaier, Sabine Grosser, Pawel Fidzinski, Ulf Christoph Schneider, Helena Radbruch, Julia Onken, Martin Holtkamp, Dietmar Schmitz, Henrik Alle et al. · 2025 · Nature Neuroscience
14. Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation
    Victoria A. Sleight · 2023 · Briefings in Functional Genomics
15. ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution
    Matthias Flotho, Jérémy Amand, Pascal Hirsch, Friederike Grandke, Tony Wyss‐Coray, Andreas Keller, Fabian Kern · 2023 · Nucleic Acids Research
16. Parvalbumin and Somatostatin: Biomarkers for Two Parallel Tectothalamic Pathways in the Auditory Midbrain
    Mengting Liu, Yixiao Gao, Fengyuan Xin · 2024 · Journal of Neuroscience
17. Hox gene–specific cellular targeting using split intein Trojan exons
    Fengqiu Diao, Deeptha Vasudevan, Ellie S. Heckscher, Benjamin H. White · 2024 · Proceedings of the National Academy of Sciences
18. Lack of basic rationale in epithelial-mesenchymal transition and its related concepts
    Ying Cao · 2024 · Cell & Bioscience
19. Flexible and stretchable bioelectronics for organoids
    Jaeyong Lee, Jia Liu B · 2025 · Med-X
20. Recent advances in understanding neuronal diversity and neural circuit complexity across different brain regions using single-cell sequencing
    Yu Xing, Chunfang Zan, Lu Liu · 2023 · Frontiers in Neural Circuits
21. Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet
    G. Hoffman, Donghoon Lee, J. Bendl et al. · 2023 · Research Square
22. Transcriptomic and spatial GABAergic neuron subtypes in zona incerta mediate distinct innate behaviors
    Mengyue Zhu, Jieqiao Peng, Mi Wang, Shan Lin, Huiying Zhang, Yu Zhou, Xinyue Dai, Huiying Zhao, Yan‐Qin Yu, Li Shen et al. · 2025 · Nature Communications
23. The evolving definition of plant cell type
    Sahand Amini, Jeff J. Doyle, Marc Libault · 2023 · Frontiers in Plant Science
24. Analog epigenetic memory revealed by targeted chromatin editing
    Palacios, Sebastian, Bruno, Simone, Weiss, Ron, Salibi, Elia, Kane, Andrew, Ilia, Katherine, Del Vecchio, Domitilla · 2024
25. Roadmap for direct and indirect translation of optogenetics into discoveries and therapies for humans
    Christian Lüscher, Valentina Emiliani, Nita A. Farahany, Aryn H. Gittis, Viviana Gradinaru, Katherine A. High, Botond Roska, José‐Alain Sahel, Ofer Yizhar, Hongkui Zeng et al. · 2025 · Nature Neuroscience
26. A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans
    Yongbin Li, Siyu Chen, Weihong Liu, Di Zhao, Yimeng Gao, Shipeng Hu, Hanyu Liu, Yuanyuan Li, Lei Qu, Xiao Liu · 2024 · Nature Communications
27. Research progress of the inferior colliculus: from Neuron, neural circuit to auditory disease
    Mengting Liu, Yuyao Wang, Li Jiang, Xiaopeng Zhang, Chunrui Wang, Tianhong Zhang · 2024 · Brain Research
28. Molecular diversity and functional dynamics in the central amygdala
    Li-Feng Yeh, Shuzhen Zuo, Pin-Wu Liu · 2024 · Frontiers in Molecular Neuroscience
29. VIVIT: Resolving trans-scale volumetric biological architectures via ionic glassy tissue
    Yixiao Gao, Fengyuan Xin, Tao Wang, Chengjun Shao, Ying Hu, Zhuoya Chen, Yiwei Wang, Fenghua Xie, Tianyu Li, Sijie Li et al. · 2025 · Cell
30. Genetic approaches to elucidating cortical and hippocampal GABAergic interneuron diversity
    Robert P. Machold, Bernardo Rudy · 2024 · Frontiers in Cellular Neuroscience
31. Cell types or cell states? An investigation of adrenergic and mesenchymal cell phenotypes in neuroblastoma
    Anuraag Bukkuri, Stina Andersson, Marina S. Mazariegos, Joel S. Brown, Emma U. Hammarlund, Sofie Mohlin · 2024 · iScience
32. From Inhibition to Exciting Science
    György Buzsáki · 2024 · Hippocampus
33. Benchmarking strategies for cross-species integration of single-cell RNA sequencing data
    Yuyao Song, Zhichao Miao, Alvis Brāzma · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
34. Allometry of cell types in planarians by single cell transcriptomics
    Elena Emili, Alberto Pérez-Posada, Maria D. Christodoulou · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
35. Single-cell genomics and regulatory networks for 388 human brains
    Prashant S. Emani, Jason J. Liu, Declan Clarke et al. · 2024 · bioRxiv
36. Transcriptional programs underlying human monocyte differentiation and diversity
    Ravi K. Komaravolu, Daniel J. Araujo, Catherine C. Hedrick, Ahmad Alimadadi · 2025 · Journal of Leukocyte Biology
37. The new frontier in understanding human and mammalian brain development
    Tomasz Jan Nowakowski, Patricia R. Nano, Katherine S. Matho, Xiaoyin Chen, Emily K. Corrigan, Wubin Ding, Yuan Gao, Matthew G. Heffel, Jaikishan Jayakumar, Harris S. Kaplan et al. · 2025 · Nature
38. Laminar organization of pyramidal neuron cell types defines distinct CA1 hippocampal subregions
    Maricarmen Pachicano, Shipra Mehta, A Huete Hurtado, Tyler D. Ard, Jim Stanis, Bayla M Breningstall, Michael S. Bienkowski · 2025 · Nature Communications
39. Optimization of AAV vectors for transactivator-regulated enhanced gene expression within targeted neuronal populations
    Leo Kojima, Kaoru Seiriki, Hiroki Rokujo, Takanobu Nakazawa, Atsushi Kasai, Hitoshi Hashimoto · 2024 · iScience
40. Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System
    Matti Hoch, Jannik Rauthe, Konstantin Cesnulevicius, Myron Schultz, David Lescheid, Olaf Wolkenhauer A, Valerio Chiurchiù, Shailendra K. Gupta · 2023 · International Journal of Molecular Sciences
41. Linking brain activity across scales with simultaneous opto- and electrophysiology
    Adrian Hoffmann, Fritjof Helmchen · 2023 · Neurophotonics
42. Neuronal Spike Shapes (NSS): A straightforward approach to investigate heterogeneity in neuronal excitability states
    Lorenzo Martini, Gianluca Amprimo, Stefano Di Carlo, Gabriella Olmo, Claudia Ferraris, Alessandro Savino, Roberta Bardini · 2023 · Computers in Biology and Medicine
43. The Brain is not Mental! Coupling Neuronal and Immune Cellular Processing in Human Organisms
    Anna Ciaunica, Michael G. Levin · 2022
44. How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex
    Fabrizia Pipicelli, Ana Villalba, Simon Hippenmeyer · 2025 · Current Opinion in Neurobiology
45. Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq
    Delaney K. Sullivan, Kristján Eldjárn Hjörleifsson, Nikhila P. Swarna, Conrad G. Oakes, Guillaume Holley, Páll Melsted, Lior S. Pachter · 2024 · Nucleic Acids Research
46. Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses
    Alana I. Mendelsohn, Laudan Nikoobakht, Jay B. Bikoff, Rui M. Costa · 2025 · Cell Reports
47. Machine learning identification of enhancers in the rhesus macaque genome
    Jing He, BaDoi N. Phan, Willa G. Kerkhoff, Aydin Alikaya, Tao Hong, Olivia R Brull, J. Megan Fredericks, Morgan Sedorovitz, Chaitanya Srinivasan, Michael J. Leone et al. · 2025 · Neuron
48. Dynamical systems of fate and form in development
    Alex M. Plum, Mattia Serra · 2025 · Seminars in Cell and Developmental Biology
49. A data-intelligence-intensive bioinformatics copilot system for large-scale omics research and scientific insights
    Yang Liu, Rongbo Shen, Lu Zhou, Qingyu Xiao, Jiao Yuan, Yixue Li · 2025 · Briefings in Bioinformatics
50. Temporal controls over cortical projection neuron fate diversity
    Esther Klingler · 2023 · Current Opinion in Neurobiology
51. Bidirectional valence coding in amygdala intercalated clusters: A neural substrate for the opponent-process theory of motivation
    Kenta M. Hagihara, Andreas Lüthi · 2024 · Neuroscience Research
52. Defining ancestry, heritability and plasticity of cellular phenotypes in somatic evolution
    Joshua S. Schiffman, Andrew R. D’Avino, Tamara Prieto et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
53. The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output
    Alexandra J. Trevisan, Katie Han, Phillip Chapman, Anand Sunil Kulkarni, Jennifer M. Hinton, Cody Ramirez, Ines Klein, Graziana Gatto, Mariano I. Gabitto, Vilas Menon et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
54. Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development
    Yuan Gao, Cindy T. J. van Velthoven, Changkyu Lee, Emma D. Thomas, Darren Bertagnolli, Daniel Carey, Tamara Casper, Anish Bhaswanth Chakka, Rushil Chakrabarty, Michael Clark et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
55. Using combined single-cell gene expression, TCR sequencing and cell surface protein barcoding to characterize and track CD4+ T cell clones from murine tissues
    Annekathrin Silvia Nedwed, Sara Salome Helbich, Kathrin Luise Braband, Michael Volkmar, Michael Delacher, Fédérico Marini · 2023 · Frontiers in Immunology
56. Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery
    Abdur Rahman M. A. Basher, Caleb Hallinan, Kwonmoo Lee · 2025 · Nature Communications
57. Allometry of cell types in planarians by single-cell transcriptomics
    Elena Emili, Alberto Pérez-Posada, Virginia Vanni, David A. Salamanca-Díaz, Dianalí Ródriguez-Fernández, Maria D. Christodoulou, Jordi Solana · 2025 · Science Advances
58. Aging in mice alters regionally enriched striatal astrocytes
    Kay E. Linker, Violeta Durán‐Laforet, Matthias Ollivier, Xinzhu Yu, Dorothy P. Schafer, Baljit S. Khakh · 2025 · Nature Communications
59. Mapping human brain pathways: challenges and opportunities in the integration of scales
    C. Charvet · 2023 · Brain, Behavior and Evolution
60. Diversity-induced trivialization and resilience of neural dynamics
    Axel Hutt, Daniel Trotter, Aref Pariz, Taufik A. Valiante, Jérémie Lefebvre · 2024 · Chaos An Interdisciplinary Journal of Nonlinear Science
61. Distribution, development, and identity of retinal ganglion cells labeled in the Sert‐Cre reporter mouse
    Jianmin Su, Lillian I.J. Byer, Yanping Liang, Michael A. Fox · 2024 · The Journal of Comparative Neurology
62. The promising role of proteomes and metabolomes in defining the single‐cell landscapes of plants
    Christopher Anderton, R. Glen Uhrig · 2024 · New Phytologist
63. Deciphering Drug Targets and Actions with Single-Cell and Spatial Resolution
    Zhengyuan Pang, Benjamin F. Cravatt, Ye Li · 2023 · The Annual Review of Pharmacology and Toxicology
64. Algorithms for a Commons Cell Atlas
    A. Sina Booeshaghi, Ángel Gálvez-Merchán, Lior S. Pachter · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
65. Uncertainty-aware single-cell annotation with a hierarchical reject option
    Lauren Theunissen, Thomas Mortier, Yvan Saeys, Willem Waegeman · 2024 · Bioinformatics
66. Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis
    Menghan Wang, Ana Di Pietro-Torres, Christian Feregrino, Maëva Luxey, Chloé Moreau, Sabrina Fischer, Antoine Fages, Danilo Ritz, Patrick Tschopp · 2025 · Nature Communications
67. Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet
    Gabriel E. Hoffman, Donghoon Lee, Jaroslav M. Bendl, N. M. Prashant, Aram Hong, Clara Casey, Marcela Alvia, Zhiping Shao, Stathis Argyriou, Karen Therrien et al. · 2026 · Nature Communications
68. The role of post-transcriptional modifications during development
    Renáta Hamar, Máté Varga · 2022 · Biologia Futura
69. The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide
    Michael Hawrylycz, Maryann Elizabeth Martone, Patrick R. Hof, Ed S. Lein, Aviv Regev, Giorgio A. Ascoli, Jan Gunnar Bjaalie, Hong‐Wei Dong, Satrajit Ghosh, Jesse A Gillis et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
70. Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells
    Roozbeh Dehghannasiri, George Henderson, Rob Bierman, Tavor Z. Baharav, Kaitlin Chaung, Peter Lincoln Wang, Julia Salzman · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
71. Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution
    Tzu‐Chiao Lu, Maria Brbić, Ye-Jin Park et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
72. Preservation of co-expression defines the primary tissue fidelity of human neural organoids
    Jonathan M. Werner, Jesse A Gillis · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
73. A Developmental Atlas of the Drosophila Nerve Cord Uncovers a Global Temporal Code for Neuronal Identity
    Sebastian Cachero, Myrto Mitletton, Isabella R. Beckett, Elizabeth C. Marin, Laia Serratosa Capdevila, Marina Gkantia, Jelly HM Soffers, Haluk Lacin, Gregory S.X.E. Jefferis, Erika Doná · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
74. Single-cell phylotranscriptomics of developmental and cell type evolution
    Fuqiang Ma, Chaogu Zheng · 2024 · Trends in Genetics
75. Future projections for mammalian whole-brain simulations based on technological trends in related fields
    Jun Igarashi · 2024 · Neuroscience Research
76. Fascial Manual Medicine: The Concept of Fascial Continuum
    Bruno Bordoni, Allan R Escher · 2025 · Cureus
77. That Stinging Sensation: Modularity and the Origin of the Stinging Cell
    Leslie S. Babonis · 2025 · Integrative and Comparative Biology
78. A mechanism for adaptive genome regulation in cancer
    Gustavo S. França, Itai Yanai · 2026 · Nature
79. Computational Tools for Neuronal Morphometric Analysis: A Systematic Search and Review
    Jéssica Leite, Fabiano Nhoatto, António Chingombe Jacob, Roberto Santana, Fábio M. F. Lobato · 2024 · Neuroinformatics
80. Cell differentiation controls iron assimilation in the choanoflagellate Salpingoeca rosetta
    Fredrick Leon, Jesus M. Espinoza-Esparza, Vicki Deng, Maxwell C. Coyle, Sarah G. Espinoza, David Scott Booth · 2025 · mSphere
81. A brain flatmap data visualization tool for mouse, rat, and human
    Joel D. Hahn, Chloe Duckworth · 2023 · The Journal of Comparative Neurology
82. Heterogeneity of Thalamic Input Landscapes
    László Acsády · 2023 · Oxford University Press eBooks
83. Sensation and Perception
    Iuliia Kotseruba, John K. Tsotsos · 2025 · Oxford University Press eBooks
84. Single-cell analysis of the nervous system at small and large scales with instant partitions
    Paul W. Frazel, K Fricano-Kugler, AA May-Zhang, Michael R. O’Dea, P Prakash, NM Desmet, H Lee, RH Meltzer, Kristina M. Fontanez, Pabodha Hettige et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
85. Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data
    Tara Chari, Gennady Gorin, Lior S. Pachter · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
86. Cattle Cell Atlas: a multi-tissue single cell expression repository for advanced bovine genomics and comparative biology
    Lingzhao Fang, Bo Han, Houcheng Li et al. · 2024 · Research Square
87. Fast, flexible analysis of differences in cellular composition with crumblr
    Gabriel E. Hoffman, Panos Roussos · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
88. Mitotyping – An integrative framework to quantify mitochondrial specialization and plasticity
    Anna Sophia Monzel, Jack Devine, Darshana Kapri, Gabriel Sturm, Caroline Trumpff, Vilas Menon, Philip L. De Jager, Jose Antonio Enriquez, Martin Picard · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
89. Single Nucleus Profiling Highlights the All-Brain Echinoderm Nervous System
    Periklis Paganos, Jack Ullrich-Lüter, Alba Almazán et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
90. Cell Decoder: decoding cell identity with multi-scale explainable deep learning
    Jun Zhu, Zeyang Zhang, Yujia Xiang, Beini Xie, Xinwen Dong, Linhai Xie, Peijie Zhou, Rongyan Yao, Li Yang, Yang Li et al. · 2025 · Genome biology
91. Single-nucleus profiling highlights the all-brain echinoderm nervous system
    Periklis Paganos, Jack Ullrich-Lüter, Alba Almazán, Danila Voronov, Jil Carl, Anne-C. Zakrzewski, Berit Zemann, Maria Lorenza Rusciano, Tiphaine Sancerni, Maria Schauer et al. · 2025 · Science Advances
92. A competition model of multilineage priming and cell-fate decisions
    Tobias Steinschaden, Louis Faure, Ruslan Soldatov, Igor I. Adameyko · 2025 · Cell Reports
93. Embeddings from language models are good learners for single-cell data analysis
    Tianyu Liu, Tianqi Chen, Wangjie Zheng, Xiao Luo, Yiqun T. Chen, Hongyu Zhao · 2026 · Patterns
94. Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities
    Huasen Jiang, Xiaoyu Huang, Xiangpeng Bi, Wenjian Ma, Haibo Ni, Zhiqiang Wei, Pin Sun, Henggui Zhang, Shugang Zhang · 2026 · Briefings in Bioinformatics
95. Multiomics approaches to cardiovascular disease: technological innovations and clinical translation
    Binte Zehra, Nidhina Vinod, Shuhd Bineshaq, Inna Aleksandrova, Richa Tambi, Muhammed Faizan, Samah Alasrawi, Mohamed Almarri, Martina K. Brueckner, Wolfgang Michael Kuebler et al. · 2026 · American Journal of Physiology-Heart and Circulatory Physiology
96. Sexual dimorphism in the complete Drosophila male central nervous system connectome
    Stuart Berg, Isabella R. Beckett, Marta Costa, Schlegel Philipp, Michał Januszewski, Elizabeth C. Marin, Aljoscha Nern, Stephan Preibisch, Wei Qiu, Shin-ya Takemura et al. · 2026 · Cell
97. Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model
    Haoxiang Gao, Kui Hua, Xinze Wu, Lei Wei, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang · 2024 · Communications Biology
98. Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development
    Huawei Feng, Wenjuan Fan, Min Liu · 2025 · BMC Genomics
99. Organizational Principles of the Primate Cerebral Cortex at the Single‐Cell Level
    Renrui Chen, Pengxing Nie, Liangxiao Ma, Guang‐Zhong Wang · 2025 · Advanced Science
100. Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS
     Yeganeh M. Marghi, Rohan Gala, Fahimeh Baftizadeh, Uygar Sümbül · 2024 · Nature Computational Science