A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Yao, Zizhen, van Velthoven, Cindy T.J., Nguyen, Thuc Nghi, Goldy, Jeff, Sedeno-Cortes, Adriana E., Baftizadeh, Fahimeh, Bertagnolli, Darren, Casper, Tamara, Chiang, Megan, Crichton, Kirsten, Ding, Song-Lin, Fong, Olivia, Garren, Emma, Glandon, Alexandra, Gouwens, Nathan W., Gray, James, Graybuck, Lucas T., Hawrylycz, Michael J., Hirschstein, Daniel, Kroll, Matthew, Lathia, Kanan, Lee, Changkyu, Levi, Boaz, McMillen, Delissa, Mok, Stephanie, Pham, Thanh, Ren, Qingzhong, Rimorin, Christine, Shapovalova, Nadiya, Sulc, Josef, Sunkin, Susan M., Tieu, Michael, Torkelson, Amy, Tung, Herman, Ward, Katelyn, Dee, Nick, Smith, Kimberly A., Tasic, Bosiljka, Zeng, Hongkui·2021·Cell
DOI 10.1016/j.cell.2021.04.021

Cited by (998)

Items 701–800 of 998

  1. A toolbox for genetic targeting of the claustrum
    Joël Tuberosa, Madlaina Boillat, Julien Dal Col, Leonardo Marconi, Julien Codourey, Loris Mannino, Elena Georgiou, Marc Menoud, Alan Carleton, Iván Rodríguez · 2024 · eLife
  2. High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution
    Dennis J. Eastburn, Kevin S. White, Nathan D. Jayne · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Delta opioid receptors engage multiple signaling cascades to differentially modulate prefrontal GABA release with input and target specificity
    Ryan P.D. Alexander, Kevin J. Bender · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Molecular states underlying neuronal cell type development and plasticity in the whisker cortex
    Salwan Butrus, Hannah R. Monday, Christopher J. Yoo · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Mapping the Cellular Etiology of Schizophrenia and Diverse Brain Phenotypes
    2024
  6. Myeloid-derived β-hexosaminidase is essential for neuronal health and lysosome function: implications for Sandhoff disease
    Kate Inman Tsourmas, Claire Ann Butler, Nellie E. Kwang, Zachary R. Sloane, Koby J. G. Dykman, Ghassan O. Maloof, Christiana A. Prekopa, Robert P. Krattli, Sanad M. El-Khatib, Vivek Swarup et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Discovery of neuronal cell types by pairing whole cell reconstructions with RNA expression profiles
    Tiago Ferreira, Mark Eddison, Monique Copeland, Mary L. Lay, Monet Weldon, Judith Baka, Emily Tenshaw, Alyssa K. Stark, David Schauder, Donald J. Olbris et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  8. Cell-type specific transcriptional modulation by psilocybin induces sustained plasticity in mouse medial prefrontal cortex
    Heike Schuler, Delong Zhou, Chloé Savignac, Vedrana Cvetkovska, Yiu-Chung Tse, Juliet Meccia, Joëlle Lopez, Ashot S. Harutyunyan, Jiannis Ragoussis, Danilo Bzdok et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  9. Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity
    Renjie Liao, Defeng Fu, Zaoxu Xu, Han Liang, Xiaoran Zhou, Yiling Elaine Chen, Xue‐Qi Liu, Ji Cheng, Ruidong Guo, Li Chen et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  10. Diverse activity in prefrontal projections promotes temporal control of action
    Xin Ding, Matthew A. Weber, Trevor C. Butler, Alexandra S. Bova, Stephanie Guerrero, Christopher Hunter, Rachel C. Cole, Hannah R Stutt, Madison S. McMurrin, Mackenzie M. Spicer et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  11. Learning induces persistent chromatin loops underlying robust gene expression during memory recall
    Peibo Xu, Keerthivasan Raanin Chandradoss, Bradley J. Lukasak, Alekh Paranjapye, Abraham J. Waldman, Kenneth Pham, Han-Seul Ryu, Constin Liu, Katelyn R. Titus, Rahul Sureka et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  12. Human Neocortical Glutamatergic Neurons Revealed Through Multimodal Profiling
    Rachel A. Dalley, Sarah Walling-Bell, Jeremy A. Miller, Femke Waleboer, Julian Thijssen, Audrey McCutcheon, Emily C. Gelfand, Matthew Mallory, Cristina Radaelli, Xiao-Ping Liu et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  13. Opto-juxtacellular interrogation of neural circuits in freely moving mice
    Lingjun Ding, Giuseppe Balsamo, Maria Diamantaki, Patricia Preston‐Ferrer, Andrea Burgalossi · 2023 · Nature Protocols
  14. Spatially resolved transcriptomic signatures of hippocampal subregions and Arc-expressing ensembles in active place avoidance memory
    Isaac Vingan, Shwetha Phatarpekar, Victoria Sook Keng Tung, Alejandro Ivan Hernandez, Oleg Vadimovich Evgrafov, Juan Marcos Alarcón · 2024 · Frontiers in Molecular Neuroscience
  15. STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution
    Bo Wang, Yahui Long, Yuting Bai, Jiawei Luo, Chee Keong Kwoh · 2024 · Briefings in Bioinformatics
  16. Autistic behavior is a common outcome of biallelic disruption of PDZD8 in humans and mice
    Andreea Pantiru, Stijn Van de Sompele, Clémence Ligneul, Camille Chatelain, Christophe Barrea, Jason P. Lerch, B Filippi, Serpil Alkan, Elfride B. W. De Baere, Jamie Johnston et al. · 2025 · Molecular Autism
  17. The sodium leak channel NALCN is regulated by neuronal SNARE complex proteins
    Samuel Usher, Estelle Toulmé, Roberta Florea, Stanislau Yatskevich, Christine C. Jao, Luuk Robin Hoegen Dijkhof, Janne M. Colding, Prajakta Joshi, Inna Zilberleyb, Thorsten Trimbuch et al. · 2025 · Science Advances
  18. Diminished angiogenic capacity in the hippocampus compared to the cortex indicates regional vulnerability
    Xiaojie Li, Nanjing Li, Yao He, J. Zu, Qixing Zhong, Zhihui Zhong · 2025 · Scientific Reports
  19. Smg5 Enhances Oligodendrocyte Differentiation via Nonsense-Mediated mRNA Decay of Hnrnpl Variant Transcripts
    Min Jiang, Conghui Li, Binghua Xie, Tangliang Li, Zhong‐Min Dai, Mengsheng S. Qiu · 2025 · Journal of Neuroscience
  20. Distinct Layer 6b transcriptomic subtypes parcellate the cortical mantle
    Margarita Kapustina, Brianna N. Bristow, Mark S. Cembrowski · 2025 · Progress in Neurobiology
  21. Proliferation of Plastic Packaging and Its Environmental Impacts at the Commune of Agoè-Nyivé 4 in Togo
    Ibrahim Batcham, Djiwonou Koffi Adjalo, Koko Zébéto Houedakor, Komlan Kounon Etienne Tede, Kossiwa Zinsou-Klassou · 2025 · Waste
  22. Single-cell resolution spatial transcriptomic signature of the retrosplenial cortex during memory consolidation
    Savannah Bliese, Budhaditya Basu, Stacy E. Beyer, Muhammad Elsadany, Jacob J. Michaelson, Snehajyoti Chatterjee · 2025 · Molecular Psychiatry
  23. SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics
    Jinming Cheng, Pierce K. H. Chow, Nan Liu · 2026 · NAR Genomics and Bioinformatics
  24. Epilepsy Treatment through Genetic Intervention of GABAergic Interneurons: Promises and Challenges
    Oleg V. Podgorny, Elena O. Petukhova, Vsevolod Vadimovich Belousov · 2025 · ACS Chemical Neuroscience
  25. stSCI: A multi-task learning framework for integrative analysis of single-cell and spatial transcriptomics data
    Han Shu, Chen Jing, Jialu Hu, Ruifen Zhang, Yongtian Wang, Jiajie Peng, Dan Xu, Xuequn Shang, Zhiyuan Yuan, Tao Wang · 2025 · The Innovation
  26. Functional KCC2 expression marks an evolutionarily conserved population of early-maturing interneurons in the perinatal cortex
    Rakenduvadhana Szrinivasan, Kalevi Trontti, Rémi Mathieu, Tangra Draia-Nicolau, Geneviève Chazal, Säde Loukasmäki, Silvana Bodington-Celma, Kaia Achim, Pavel Uvarov, Stanislav Khirug et al. · 2025 · Nature Communications
  27. Evolutionary convergence and divergence of hippocampal cytoarchitecture between rodents and primates revealed by single-cell spatial transcriptomics
    Tianyi Fei, Yu Dong, Xiaojuan Gou, Jiahao Zhang, Guangling Wang, Nini Yuan, Zhenkun Zhuang, Duoyuan Chen, Zihan Wu, Lijie Zhan et al. · 2025 · National Science Review
  28. Unlocking single-cell level and continuous whole-slide insights in spatial transcriptomics with PanoSpace
    Hua He, Pai Peng, Yang Shi-Tong, Meng-Guo Wang, Xiao-Fei Zhang, Luonan Chen · 2026 · Nature Computational Science
  29. Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice
    Zohreh Farsi, Ally A. Nicolella, Sean Simmons, Wangyong Shin, Muwon Kang, Gina Lee, Min Jee Kwon, Kira S. Brenner, Inès Picard, Nate Shepard et al. · 2026 · iScience
  30. Uncovering the molecular logic of cortical wiring between neuronal subtypes across development through ligand–receptor inference
    R. Mathieu, Tangra Draia-Nicolau, Léa Corbières, Annousha Devi Govindan, Vianney Bensa, Emilie Pallesi‐Pocachard, Lucas Silvagnoli, Alfonso Represa, Carlos Cardoso, Ludovic Telley et al. · 2026 · Nature Communications
  31. The Smarcal1-Usp37 locus modulates glycogen aggregation in astrocytes of the aged hippocampus
    Alicia Gómez-Pascual, Dow Michael Glikman, Hui Xin Ng, James E. Tomkins, Lu Lu, Ying Xu, David George Ashbrook, Catherine Cook Kaczorowski, Gerd Kempermann, JOHN T. KILLMAR et al. · 2026 · Cell Systems
  32. A silent Kv channel subunit shapes PV neuron action potential waveform and short-term synaptic plasticity during high-frequency firing
    Sanika Ganesh, Theresa M. Canty, Bernardo Luis Sabatini · 2026 · Proceedings of the National Academy of Sciences
  33. Reducing methylation of histone 3.3 lysine 4 in the medial ganglionic eminence and hypothalamus recapitulates neurodevelopmental disorder phenotypes
    Jianing Li, Anthony F. Tanzillo, Giusy Pizzirusso, Adam Caccavano, Ramesh Chittajallu, Mira Sohn, Daniel T. Abebe, Yajun Zhang, Kenneth A. Pelkey, Ryan Dale et al. · 2026 · Nature Communications
  34. The E3 Ubiquitin Ligase UBE3B Regulates Synaptic Development and Cortical Network Activity
    Shayal Vashisth, Aleya Shedd, Ariel Aiken, Solmi Cheon, Josh Bandopadhay, Kiran J. Kaur, Kimberly M. Huber, Maria H. Chahrour · 2026 · Autism Research
  35. Adaptive evolution of gene regulatory networks in mammalian neocortex
    Zhuo Li, Navjot Kaur, Gabriel Santpere, Sydney Keaton Muchnik, Suvimal Kumar Sindhu, Cai Qi, Mikihito Shibata, Olivier Clément, Thomas Klarić, Xabier de Martin et al. · 2026 · Nature
  36. Photocaged Oxytocin and Vasopressin Probes to Decipher Neuropeptide Signalling With High Spatiotemporal Resolution
    Konstantin Raabe, Predrag Kalaba, Xuan Ling Hilary Yong, Greta Crudeli, Sarah Melzer, Erik Keimpema, Victor Anggono, Markus Muttenthaler · 2026 · Angewandte Chemie International Edition
  37. Srrm2 haploinsufficiency drives SynGAP-γ reduction, Agap3 mis-splicing, and oligodendrocyte deficits in a genetic mouse model of schizophrenia
    Sameer Aryal, Chuhan Geng, Margaret A. Yin, Min Jee Kwon, Zohreh Farsi, Nathaniel Goble, Ahmet S. Asan, Kira S. Brenner, Nate Shepard, Ana Geller et al. · 2026 · Cell Reports
  38. The glucocorticoid-mediated genomic stress response
    Matthew D. B. Claydon, Becky L. Conway-Campbell · 2022 · Current Opinion in Endocrine and Metabolic Research
  39. Development and Developmental Disorders of the Cerebral Cortex
    Hans J. ten Donkelaar, Lana Vasung, Zoltán Molnár, Eleonora Aronica, Martin M. Y. Lammens, Hans van Bokhoven, Karin Kamphuis-van Ulzen, Akira Hori · 2023 · Springer eBooks
  40. Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits
    Diek W. Wheeler, Jeffrey D. Kopsick, Nate M. Sutton, Carolina Tecuatl, Alexander O. Komendantov, Kasturi Nadella, Giorgio A. Ascoli · 2024 · eLife
  41. BrainTACO: an explorable multi-scale multi-modal brain transcriptomic and connectivity data resource
    Florian Ganglberger, Dominic Kargl, Markus Töpfer, Julien Hernandez-Lallement, Nathan Lawless, Francesc Fernández-Albert, Wulf E. Haubensak, Katja Bühler · 2024 · Communications Biology
  42. The Brain–Heart Network of Syncope
    Sailen Barik, Thomas Riddell · 2024 · International Journal of Molecular Sciences
  43. Transcriptomic Correlates of State Modulation in GABAergic Interneurons: A Cross-Species Analysis
    Joram Keijser, Loreen Hertäg, Henning Sprekeler · 2024 · Journal of Neuroscience
  44. All-optical reporting of inhibitory receptor driving force in the nervous system
    Joshua S Selfe, Teresa J. S. Steyn, Eran Frank Shorer et al. · 2024 · Nature Communications
  45. FOXR2 Targets LHX6+/DLX+ Neural Lineages to Drive Central Nervous System Neuroblastoma
    Selin Jessa, Antonella De Cola, Bhavyaa Chandarana, Michael McNicholas, Steven Hébert, Adam Ptack, Damien Faury, Jessica W. Tsai, Andrey Korshunov, Timothy N. Phoenix et al. · 2024 · Cancer Research
  46. Modulation by serotonin reveals preferred recurrent excitatory connectivity in layer II of rat neocortex
    Fransiscus Adrian Agahari, Christian Stricker · 2025 · Cerebral Cortex
  47. A Role for δ Subunit-Containing GABA A Receptors on Parvalbumin-Positive Neurons in Maintaining Electrocortical Signatures of Sleep States
    Peter M. Lambert, Sofia V. Salvatore, Xinguo Lu, Hong‐Jin Shu, Ann M. Benz, Nicholas R. Rensing, Carla M. Yuede, Michael Wong, Charles F. Zorumski, Steven J. Mennerick · 2025 · Journal of Neuroscience
  48. Neuronal lipofuscinosis caused by Kufs disease/CLN4 DNAJC5 mutations but not by a CSPα/DNAJC5 deficiency
    Santiago López-Begines, Nozha Borjini, Ángela Lavado-Roldán, Cristina Mesa-Cruz, Fabiola Mavillard, Vera I. Wiersma, Fátima Rubio-Pastor, Emanuela Tumini, Carmen Paradela‐Leal, María L. Chiclana-Valcárcel et al. · 2025 · Science Advances
  49. Advances in approaches to study cell-type specific cortical circuits throughout development
    Meretta A. Hanson, Jason C. Wester · 2022 · Frontiers in Cellular Neuroscience
  50. RETRACTED: Dynamics of Stochastic Integrate-and-Fire Networks
    Gabriel Koch Ocker · 2022 · Physical Review X · Retracted
  51. LINCs Are Vulnerable to Epileptic Insult and Fail to Provide Seizure Control via On-Demand Activation
    Bethany J. Stieve, Madison Smith, Esther I. Krook-Magnuson · 2023 · eNeuro
  52. A cell type atlas of the lamprey brain
    Elias Gumnit, Maria Antonietta Tosches · 2023 · Nature Ecology & Evolution
  53. Learning Ultrametric Trees for Optimal Transport Regression
    Samantha Chen, Puoya Tabaghi, Yusu Wang · 2024 · Proceedings of the AAAI Conference on Artificial Intelligence
  54. Cell-type-specific contributions to theta-gamma coupled rhythms in the hippocampus
    Spandan Sengupta, Afroditi Talidou, Jérémie Lefebvre, Frances K. Skinner · 2024 · Network Neuroscience
  55. Functional and structural features of L2/3 pyramidal cells continuously covary with pial depth in mouse visual cortex
    Simon Weiler, Drago Guggiana-Nilo, Tobias Bonhoeffer · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Identifying common and novel cell types in single-cell RNA-sequencing data using FR-Match
    Yun Zhang, B. Aevermann, Rohan Gala · 2021 · bioRxiv
  57. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
    Fangming Xie, Ethan J. Armand, Zizhen Yao et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  58. Detection of allele-specific expression in spatial transcriptomics with spASE
    Luli S. Zou, Tongtong Zhao, Dylan M. Cable, Evan M. Murray, Martin J. Aryee, Fei Chen, Rafael A. Irizarry · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Goal-directed motor actions drive acetylcholine dynamics in sensory cortex
    Jing Zou, Jan Willem de Gee, Zakir Mridha, Simon Trinh, Andrew Erskine, Miao Jing, Jennifer Z. Yao, Stefanie Walker, Yulong Li, Matthew J. McGinley et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  60. Hypothalamic gene network dysfunction is associated with cognitive decline and body weight loss in Alzheimer’s disease mice
    Yanchao Dai, Amy R. Dunn, N Hadad, J-G Zhang, OB Poirion, AC Korgan, BS White, VM Philip, SM Neuner, Kristen M. S. O’Connell et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  61. Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution
    Nelson Johansen, Gerald Quon · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  62. Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding
    Rongbo Shen, Lin Liu, Zihan Wu et al. · 2022 · Research Square
  63. Sex-biasing influence of autism-associated Ube3a gene overdosage at connectomic, behavioral and transcriptomic levels
    Caterina Montani, Marco Pagani, A. Elizabeth de Guzman et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  64. scTOP: physics-inspired order parameters for cellular identification and visualization
    Maria Yampolskaya, Michael J. Herriges, Laertis Ikonomou · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  65. Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology
    Robert Cahill, Yu Wang, Rui Patrick Xian, Alex J. Lee, Hongkui Zeng, Bin Yu, Bosiljka Tasic, Reza Abbasi-Asl · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  66. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Aixin Zhang, Lei Jin, Shenqin Yao, Makoto Matsuyama, Cindy T. J. van Velthoven, Heather A. Sullivan, Na Sun, M Kellis, Bosiljka Tasic, Ian R. Wickersham et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  67. Single Cell Transcriptome of Stress Vulnerability Network in mouse Prefrontal Cortex
    Benjamin Wen Qing Hing, Sara B. Mitchell, Maureen Eberle et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  68. Applying high-resolution spatial transcriptomics to characterize the amyloid plaque cell niche in Alzheimer’s Disease
    Anna Mallach, Magdalena Zielonka, Veerle van Lieshout et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  69. Disease modification upon brief exposure to tofacitinib during chronic epilepsy
    Olivia R. Hoffman, Jennifer L. Koehler, Jose Ezekiel Clemente Espina, Anna M. Patterson, Emily S. Gohar, Emanuel M. Coleman, Barry A. Schoenike, Claudia Espinosa‐García, Felipe Paredes, Nicholas H. Varvel et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  70. Morpho-electric and computational properties of three types of human hippocampal CA1 pyramidal neurons
    Eline Jasmijn Mertens, Yoni Leibner, Jean L. Pie, Anna A. Galakhova, Femke Waleboer, Julia Meijer, Tim S. Heistek, René Wilbers, Djai B. Heyer, Natalia A. Goriounova et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  71. The Pgb1 locus controls glycogen aggregation in astrocytes of the aged hippocampus without impacting cognitive function
    Alicia Gómez-Pascual, Dow Michael Glikman, H. X. Ng, James E. Tomkins, Lu Lu, Ying Xu, David George Ashbrook, Catherine Cook Kaczorowski, Gerd Kempermann, JOHN T. KILLMAR et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Aixin Zhang, Lei Jin, Shenqin Yao, Makoto Matsuyama, Cindy T. J. van Velthoven, Heather A. Sullivan, Na Sun, M Kellis, Bosiljka Tasic, Ian R. Wickersham et al. · 2024 · eLife
  73. Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex
    Nafiseh Atapour, Marcello G. P. Rosa, Shi Bai · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  74. Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability
    George D. Dalton, Stephen K. Siecinski, Viktoriya D. Nikolova · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  75. Emergence of neocortical function in heterotopic neurons
    Sergi Roig‐Puiggros, Maëlle Guyoton, Dmitrii Suchkov, Aurélien Fortoul, Sabine Fièvre, Giulio Matteucci, Emma Maino, Charlie G. Foucher, Daniel Fuciec, Esther Klingler et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  76. Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes
    Xiaona Lu, Pengyu Ni, Paola Suárez-Meade · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  77. Synaptic proteome diversity is shaped by the levels of glutamate receptors and their regulatory proteins
    Rita Reig‐Viader, Diego del Castillo-Berges, Albert Burgas-Pau et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Brain-wide monosynaptic single-neuron connectivity with ROInet-seq
    Zhige Lin, Osnat Ophir, Thorsten Trimbuch, Bettina Brokowski, Muhammad Tibi, Hermann Schmidt, Christian Rosenmund, Hannah Hochgerner, Amit Zeisel · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  79. Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression
    Osman Sharifi, Viktoria Haghani, Kari E. Neier · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  80. Control of innate olfactory valence by segregated cortical amygdala circuits
    James R. Howe, Chung-Lung Chan, Donghyung Lee, Marlon Blanquart, James H. Lee, Laurine Decoster, Haylie K. Romero, Abigail N Zadina, Mackenzie Lemieux, Fergil Mills et al. · 2026 · eLife
  81. Transcriptomically-measured gene expression predicts physiological variation across single neurons in humans and mice
    Rennie M. Kendrick, Scott W. Linderman, Scott F. Owen · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  82. Unique Transcriptomic Cell Types of the Granular Retrosplenial Cortex are Preserved Across Mice and Rats Despite Dramatic Changes in Key Marker Genes
    Isla A. W. Brooks, Izabela Jedrasiak‐Cape, Chloe Rybicki-Kler · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  83. Hippocampal γCaMKII dopaminylation promotes synaptic-to-nuclear signaling and memory formation
    Andrew Francis Stewart, Sasha L. Fulton, Romain Durand-de Cuttoli, Robert E. Thompson, Peng‐Jen Chen, Elizabeth Brindley, Bulent Cetin, Lorna A. Farrelly, Rita Futamura, Sarah M. Claypool et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  84. Human Neuron and Mouse Models Reveal Synaptic Imbalance in Kabuki Syndrome
    Anna Wenninger, James Knopp, Steven Frye, Alexander Weaver, Neil McAdams, Sean Miller, Toshihiro Nomura, Ava Whitlark, Jack Swantkowski, Alexandra Noble et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Spatial single-cell mapping of transcriptional differences across genetic backgrounds in mouse brains
    Zachary Hemminger, Gabriela Sanchez-Tam, Haley De Ocampo, Aihui Wang, Thomas J Underwood, Fangming Xie, Qiuying Zhao, Dongyuan Song, Jingyi Jessica Li, Hong‐Wei Dong et al. · 2026 · Nature Methods
  86. Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling
    Emily R. Feierman, Alekh Paranjapye, Steven Su · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  87. In Search of Transcriptomic Correlates of Neuronal Firing-Rate Adaptation across Subtypes, Regions and Species: A Patch-seq Analysis
    John Hongyu Meng, Yijie Kang, Alan Lai, Michael Feyerabend, Wataru Inoue, Julio Martínez-Trujillo, Bernardo Rudy, Xiao‐Jing Wang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  88. Single cell approaches define the murine leptomeninges:cortical brain interface as a distinct cellular neighborhood comprised of neural and nonneural cell types
    2025
  89. Annotation Comparison Explorer (ACE): connecting brain cell types across studies of health and Alzheimer’s Disease
    Jeremy A. Miller, Kyle J. Travaglini, Tain Luquez, Rachel E. Hostetler, Aaron Oster, Scott F. Daniel, Bosiljka Tasic, Vilas Menon · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  90. Single-cell transcriptome of developing inhibitory neurons reveals expanding and contracting modes of diversification
    Minhui Liu, Facundo Ferrero Restelli, Elia Micoli, Giulia Barbiera, Rani Moors, Evelien Nouboers, Malou Reverendo, Jessica Xinyun Du, Hannah Bertels, Dimitris Konstantopoulos et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  91. Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum
    Jennifer C Chan, Giuseppina Di Salvo, Ashley M. Cunningham, Sohini Dutta, Elizabeth Brindley, Benjamin H. Weekley, Ethan Wan, Cindy Zhang, Naguib Mechawar, Gustavo Turecki et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  92. Harnessing the Power of Single-Cell Large Language Models with Parameter Efficient Fine-Tuning using scPEFT
    Fei He, Ruixin Fei, Jordan Edward Krull et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  93. A new mouse mutant with a discrete mutation in Pcdhgc5 reveals that the Protocadherin γC5 isoform is not essential for dendrite arborization in the cerebral cortex
    Camille M. Hanes, David M. Steffen, George C. Murray · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  94. Early postnatal CA3 hyperexcitability drives hippocampal development and epileptogenesis in SCN2A developmental and epileptic encephalopathy
    Yana Reva, Katharina Ulrich, Xian Xin, Yuanyuan Liu, Michaela Barboni, Daniil Kirianov, Nima Mojtahedi, Sarah Schoeb, Hanna Oelßner, Daria Savitska et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  95. SpaceSequest: A unified pipeline for spatial transcriptomics data analysis
    Yu Huining Sun, Sarbottam Piya, Zhengyu Ouyang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  96. Establishing a continuum of cell types in the visual cortex
    Juyoun Yoo, Fangming Xie, Salwan Butrus, Runzhe Xu, Zhiqun Tan, Ryan C. Gorzek, Parmis Mirshahidi, Elaine Tring, Sanjana Suresh, Jinho Kim et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  97. 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)
  98. Robust Integration of Sparse Single-Cell Alternative Splicing and Gene Expression Data with SpliceVI
    Smriti Vaidyanathan, Keren Isaev, Aaron Zweig, David A. Knowles · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  99. Multimodal alignments of in vivo imaging and spatial biology datasets at cellular resolution
    L. Wang, Xiqian Jiang, Xiaochen Sun, Gaurav Chattree, Ali H. Cetin, Xiaochun Cai, Elijah Paul, Radosław Chrapkiewicz, Oscar Hernandez, Yuxi Ke et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  100. Multiregional single-cell profiling reveals shared and specialized cellular vulnerability in Alzheimer’s disease
    Kyle J. Travaglini, Mariano I. Gabitto, Yi Ding, Anamika Agrawal, Nadia O. Postupna, Joseph T. Mahoney, Eitan S Kaplan, Erica J. Melief, Jeff Goldy, Anish Bhaswanth Chakka et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)