Disentangling neural cell diversity using single-cell transcriptomics

Poulin, Jean-Francois, Tasic, Bosiljka, Hjerling-Leffler, Jens, Trimarchi, Jeffrey M, Awatramani, Rajeshwar·2016·Nature Neuroscience
DOI 10.1038/nn.4366

Cited by (296)

Items 201–296 of 296

  1. Development of a surgical procedure for removal of a placentome from a pregnant ewe during gestation
    Colleen A. Lambo, Ashley K Edwards, Fuller W. Bazer, Kathrin Anson Dunlap, Michael Carey Satterfield · 2020 · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology
  2. Using Induced Pluripotent Stem Cells to Investigate Complex Genetic Psychiatric Disorders
    Stephanie J. Temme, Brady J. Maher, Kimberly M. Christian · 2016 · Current Behavioral Neuroscience Reports
  3. Inferring causal trajectories from spatial transcriptomics using CASCAT
    Yingying Yu, Wan Nie, Qianqian Zhang, Shuai Cheng Li · 2025 · Nucleic Acids Research
  4. Revisit the Cellular Transmission and Emerging Techniques in Understanding the Mechanisms of Proteinopathies
    Jinwen Jiang, Yu Liu, Qihui Wu · 2021 · Frontiers in Neuroscience
  5. Applications of single‐cell multi‐omics sequencing in deep understanding of brain diseases
    Xu Zhang, Ping Lü, Xiaorong Shen · 2022 · Clinical and Translational Discovery
  6. Characterizing RNA modifications in the central nervous system and single cells by RNA sequencing and liquid chromatography–tandem mass spectrometry techniques
    Arya Patel, Kevin D. Clark · 2023 · Analytical and Bioanalytical Chemistry
  7. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application
    Shivai Gupta, Richard Witas, Alexandria Voigt, Touyana Semenova, Cuong Quoc Nguyen · 2020 · Advances in experimental medicine and biology
  8. Translatome Analyses Using Conditional Ribosomal Tagging in GABAergic Interneurons and Other Sparse Cell Types
    Vivek Mahadevan, Areg Peltekian, Chris J. McBain · 2020 · Current Protocols in Neuroscience
  9. A Novel Single Vector Intersectional AAV Strategy for Interrogating Cellular Diversity and Brain Function
    Alex C. Hughes, Brittany G. Pollard, Beisi Xu, Jesse W. Gammons, Phillip Chapman, Jay B. Bikoff, Lindsay A. Schwarz · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  10. The Mouse Visual System and Visual Perception
    Laura Busse · 2018 · Handbook of behavioral neuroscience
  11. The Interneuron Class Struggle
    Jacob M Ratliff, Renata Batista‐Brito · 2020 · Cell
  12. Moore's Law in Single Cell Transcriptomics
    Valentine Svensson, Roser Vento‐Tormo, Sarah Amalia Teichmann · 2017 · arXiv (Cornell University)
  13. Strategies to decipher neuron identity from extracellular recordings in the cerebellum of behaving non-human primates
    David J. Herzfeld, Nathan J. Hall, Stephen G. Lisberger · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Interpretable modality-aware mapping of gene regulation in single-cell multiomics with scMAGCA
    Yunhe Wang, Zhou, Wei Liu, Peiru Zhang, Yue Cheng, Yanchi Su, Fuzhou Wang, Ka‐Chun Wong, Xiangtao Li · 2026 · Nature Communications
  15. Strategies to Decipher Neuron Identity from Extracellular Recordings in Behaving Nonhuman Primates
    David J. Herzfeld, Nathan J. Hall, Stephen G. Lisberger · 2025 · Journal of Neuroscience
  16. Progress towards a cellularly resolved mouse mesoconnectome is empowered by data fusion and new neuroanatomy techniques
    Nestor Timonidis, Paul H. E. Tiesinga · 2021 · Neuroscience & Biobehavioral Reviews
  17. Gene expression and chromatin conformation differs between worker bees performing different tasks
    Fang Fang, Huanhuan Zhou, Xiaojuan Feng, Xiasang Chen, Zhen Wang, Shuhong Zhao, Xiang Olivia Li · 2022 · Genomics
  18. deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data
    Alexis Germán Murillo Carrasco, Tatiane Katsue Furuya, Miyuki Uno, Tharcísio Citrângulo Tortelli, Roger J. Chammas · 2023 · BMC Bioinformatics
  19. Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq)
    Anirban Paul, Z. Josh Huang · 2018 · Journal of Visualized Experiments
  20. Values of Single-Cell RNA Sequencing in Development of Cerebral Cortex
    Enqiang Chang, Xiaoguo Ruan, Ruilou Zhu, Yangyang Wang, Jiaqiang Zhang · 2020 · Advances in experimental medicine and biology
  21. A Novel Single-Cell RNA Sequencing Data Feature Extraction Method Based on Gene Function Analysis and Its Applications in Glioma Study
    Jujuan Zhuang, Changjing Ren, Dan Ren, Yu’ang Li, Danyang Liu, Lingyu Cui, Geng Tian, Jiasheng Yang, Jingbo Liu · 2021 · Frontiers in Oncology
  22. A common framework for mouse hypothalamic cell atlases
    Alexander C. Jackson · 2022 · Nature Metabolism
  23. Circuit mechanisms to transform neural population dynamics for motor control
    David J. Herzfeld, Stephen G. Lisberger · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  24. The Golgi apparatus: adaptations to neuronal shape and functions
    Aygul Subkhangulova, Marina Mikhaylova · 2025 · The EMBO Journal
  25. scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data
    Meng Liu, Wenhao Chen, Jianping Zhao, Chun-Hou Zheng, Feilong Guo · 2023 · Current Bioinformatics
  26. Deciphering brain cellular and behavioral mechanisms: Insights from single‐cell and spatial RNA sequencing
    Renrui Chen, Pengxing Nie, Jing Wang, Guang‐Zhong Wang · 2024 · Wiley Interdisciplinary Reviews - RNA
  27. Single-cell Clustering Based on Word Embedding and Nonparametric Methods
    Tianyu Wang, Sheida Nabavi · 2018 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  28. Isolation and Quantification Brain Region-Specific and Cell Subtype-Specific Histone (De)Acetylation in Cognitive Neuroepigenetics
    Craig Myrum, Peter R. Rapp · 2019 · Methods in molecular biology
  29. Single-Cell Transcriptomics: Technology and Applications
    Ota Fuchs · 2019 · Elsevier eBooks
  30. Detection of Cell Separation-Induced Gene Expression Through a Penalized Deconvolution Approach
    An‐Shun Tai, Chun‐Chao Wang, Wen‐Ping Hsieh · 2022 · Statistics in Biosciences
  31. Extracting new insights from bulk transcriptomics
    Vilas Menon · 2018 · Nature Neuroscience
  32. Molecular Profiling to Infer Neuronal Cell Identity: Lessons from small ganglia of the Crab Cancer borealis
    Adam J. Northcutt, Daniel Robert Kick, Adriane G. Otopalik, Benjamin M. Goetz, Rayna M. Harris, Joseph M. Santin, Hans A. Hofmann, Eve E. Marder, David J. Schulz · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Enhanced Aversive Signals During Classical Conditioning in Dopamine Axons in Medial Prefrontal Cortex
    Kenta Abe, Yuki Kambe, Kei Majima, Zijing Hu, Makoto Ohtake, Ali Momennezhad, Hideki Izumi, Takuma Tanaka, Ashley Matunis, Emma Stacy et al. · 2023 · eLife
  34. scGRIP: a graph-based explainable AI framework for single-cell multi-omics Gene Regulatory Inference with Prior Knowledge
    Wenqi Dong, Manqi Zhou, Fang Wang, Yue Li · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Exome Sequencing Starting from Single Cells
    Ioanna Andreou, Markus Storbeck, Peter F. Hahn, Samuel J. Rulli, Eric Lader · 2024 · Current Protocols
  36. From gene regulatory networks to social networks: integrative sociogenomics from single cell to superorganism
    Jesse L. Huisken, Sandra M. Rehan · 2025 · Insectes Sociaux
  37. Vitamin D Regulates Olfactory Function via Dual Transcriptional and mTOR‐Dependent Translational Control of Synaptic Proteins
    Pengcheng Ren, Renhe Cao, Xiaoshan Ye, Wenbin Pang, Qingshang Bi, Meihui Huang, Qionglin Zhou, Dan Ye, Wei Xiang, Le Xiao · 2025 · Advanced Science
  38. Transcriptional Profiling of Identified Circuit Elements in Invertebrates
    Marta Morey · 2017 · Springer eBooks
  39. Strength in numbers from integrated single-cell neuroscience
    Rahul Satija · 2018 · Nature Biotechnology
  40. From single cells to neural circuits
    Michael A. Skinnider · 2023 · Science
  41. Neuron identity switches in response to the gradient gene expression pathway
    Gustavo Guzmán, Omar Paredes, Rebeca Romo‐Vázquez, Hugo A. Vélez-Pérez, J. Alejandro Morales · 2025 · Frontiers in Cellular Neuroscience
  42. Deciphering the adult brain development complexity by single-cell transcriptome analysis—a review
    Shahid Mehmood, Muhammad Bilal, R. Manzoor, Hafiz M.N. Iqbal · 2019 · Materials Today Chemistry
  43. The new technologies of high-throughput single-cell RNA sequencing
    Ekaterina A. Vodiasova, Elina S. Chelebieva, О. Н. Кулешова · 2019 · Vavilov Journal of Genetics and Breeding
  44. Single-Cell RNA Sequencing of Somatosensory Neurons
    Martin Häring, Jussi Kupari · 2022 · Neuromethods
  45. Genetic Single Neuron Anatomy reveals fine granularity of cortical interneuron subtypes
    Xiaojun Wang, Jason Tucciarone, Siqi Jiang, Fangfang Yin, Bor‐Shuen Wang, Dingkang Wang, Jia Yao, Xueyan Jia, Yuxin Li, Tao Yang et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Hypothalamic Nutrient Sensing
    Nicholas Heeley · 2018 · Apollo (University of Cambridge)
  47. Agonist-induced Functional Analysis and Cell Sorting, a novel tool to select and analyze neurons: Fragile X as a proof of concept
    Sara Castagnola, Julie Cazareth, Kévin Lebrigand, Marielle Jarjat, Virginie Magnone, Sébastien Delhaye, Frédéric Brau, Barbara Bardoni, Thomas Maurin · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  48. A critical assessment of single-cell transcriptomes sampled following patch-clamp electrophysiology
    Shreejoy J. Tripathy, Lilah Toker, Claire Bomkamp, Burak Ogan Mancarci, Manuel Belmadani, Paul Pavlidis · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  49. Receptive field organization of motion computation in the fly: a study of cell types and their variability
    L. López · 2020
  50. Loss or Gain of Function? Effects of Ion Channel Mutations on Neuronal Firing Depend on the Cell Type
    Nils A. Koch, Lukas Sonnenberg, Ulrike B. S. Hedrich, Stephan Lauxmann, Jan Benda · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Electrical diversity of neurons in sensory cortices
    Niccolò Calcini, Fleur Zeldenrust, Tansu Celikel · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  52. A quantitative spatial atlas of transcriptomic, morphological, and electrophysiological cell type densities in the mouse brain
    Csaba Verasztó, Yann Roussel, Lida Kanari, Henry Markram, Daniel X. Keller · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Methodological Challenges in Functional Investigation and Therapeutic Use of microRNAs
    Federica Marinaro, Meritxell Pons‐Espinal, Davide De Pietri Tonelli · 2017 · Elsevier eBooks
  54. Studying BDNF/TrkB Signaling: High-Throughput Microfluidic Gene Expression Analysis from Rare or Limited Samples of Adult and Aged Central Neurons
    Arup R. Nath, Roy Drissen, Fei Guo, Claus Nerlov, Liliana Minichiello · 2017 · Neuromethods
  55. Faculty of 1000 evaluation for Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.
    Siddharth S. Dey, Alex Chialastri · 2018 · F1000 - Post-publication peer review of the biomedical literature
  56. A new diffusely infiltrating glioma mouse model reveals neuronal alterations in the brain tumor microenvironment
    Daniela Torres · 2018
  57. Generation of Neural Diversity
    Dan H. Sanes, Thomas A. Reh, William A. Harris, Matthias Landgraf · 2019 · Elsevier eBooks
  58. Using cell type-specific methods to understand molecular processes in the brain
    Rajput, Ashish · 2019
  59. Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems
    Duygu Dikicioǧlu · 2019 · Methods in molecular biology
  60. The molecular underpinnings of neuronal cell identity in the stomatogastric ganglion of cancer borealis
    Adam J. Northcutt · 2019
  61. Single-cell RNAseq Imputation Based on Matrix Completion with Side Information
    Tianyu Wang, Sheida Nabavi · 2019 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  62. Single-cell analysis of mRNA splicing variants
    Jacob L. Potts · 2020
  63. Coupling, membrane conductance, and ion channel mRNA profiles in the establishment and maintenance of network activity in the crustacean cardiac ganglion
    Daniel Robert Kick · 2021
  64. Single cell transcriptomics and epigenomics methods provide high resolution genomics profiling of brain disorders
    Kevin Miyashiro, James H. Eberwine · 2021 · Elsevier eBooks
  65. Revisit the Cellular Transmission and Emerging Techniques in Proteinopathies
    Jingwen Jiang, Yu Liu, Qihui Wu · 2021 · Preprints.org
  66. Advancing the Characterization of Neuronal Cyto-Architecture by X-ray Phase-Contrast Tomography
    Marina Eckermann · 2021 · Göttingen series in x-ray physics
  67. Faculty Opinions recommendation of Dorsolateral septum somatostatin interneurons gate mobility to calibrate context-specific behavioral fear responses.
    Amy L. Milton · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  68. Faculty Opinions recommendation of Dorsolateral septum somatostatin interneurons gate mobility to calibrate context-specific behavioral fear responses.
    Sreedharan Sajikumar, Radha Raghuraman · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  69. Faculty Opinions recommendation of Studies of cortical connectivity using optical circuit mapping methods.
    James Duffin · 2017 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  70. Uncovering the transcriptional signatures of hub connectivity in neural networks
    Aurina Arnatkevičiūtė, Ben Fulcher, Alex Fornito · 2018
  71. Neuro-urology research: a comprehensive overview
    Anne M.J. Verstegen · 2023 · Elsevier eBooks
  72. eLife Assessment: Enhanced Aversive Signals During Classical Conditioning in Dopamine Axons in Medial Prefrontal Cortex
    Joshua P. Johansen · 2023 · eLife
  73. UNVEILING CELLULAR DIVERSITY: A COMPREHENSIVE GUIDE TO CELL CLUSTERING METHODS
    Paxton Steven · 2022 · EPH - International Journal of Applied Science
  74. UNVEILING CELLULAR DIVERSITY: A COMPREHENSIVE GUIDE TO CELL CLUSTERING METHODS
    Paxton Steven, Zane Kaleb · 2022 · EPH - International Journal of Business & Management Science
  75. An Approach to Cellular Diversity in the Human Brain
    Gustavo Guzmán, Omar Paredes, Hugo A. Vélez-Pérez, Rebeca Romo‐Vázquez, J. Alejandro Morales · 2023 · IEEE EMBS R9 Conference
  76. More is better: A simple antibody-based strategy for recovering all major mouse brain cell types from multiplexed single-cell RNAseq samples
    Federico Pratesi, Laura K. Hamilton, Jessica Avila Lopez, Anne Aumont, Mariano Avino, Nishita Singh, Ihor Arefiev, Marie A. Brunet, Karl J. L. Fernandes · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  77. Vitamin D regulates olfactory function via dual transcriptional and mTOR-dependent translational control of synaptic proteins
    Ren Pengcheng, Cao Renhe, Xiayan Ye, Pang Wenbin, Qingshang Bi, Meihui Huang, Qionglin Zhou, Dan Ye, Xiang Wei, Le Xiao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Cell types and neuronal genetic architecture in the rat CSF-contacting nucleus and the role of 5-HT in this nucleus in mediating morphine addiction through the brain–CSF circuit
    Ying Li, Bin Gui, Yijun Zhang, Licai Zhang · 2025 · Frontiers in Neuroscience
  79. Molecular heterogeneity of midbrain dopamine neurons
    Rajeshwar Awatramani, Jean-Francois Poulin · 2025 · Handbook of behavioral neuroscience
  80. The Metacontinuum: Bridging cellular composition to cognitive functions in brain organization
    Gustavo Guzmán, Elsa Magaña-Cuevas, Rocío Hernández-Rizo, Lorena Malinalli López-Medina, Omar Cano-Garcia, Omar Paredes · 2025 · Biosystems
  81. Structure-guided integrative soft deep clustering analysis of scRNA-seq and scATAC-seq data
    Jiang Xingzuo, Chenyuan Wang, Yao Jiaxi, Wang Chengyuan · 2025 · Frontiers in Microbiology
  82. Cell Type Proportion Inference Over Human Neurodevelopment
    Gustavo Guzmán, J. Alejandro Morales, Omar Paredes · 2025 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  83. Additional file 1 of Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues
    Jia, Erteng, Huajuan Shi, Wang, Ying, Zhou, Ying, Liu, Zhiyu, Min Pan, Bai, Yunfei, Zhao, Xiangwei, Ge, Qinyu · 2021 · Figshare
  84. Additional file 2 of Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues
    Jia, Erteng, Huajuan Shi, Wang, Ying, Zhou, Ying, Liu, Zhiyu, Min Pan, Bai, Yunfei, Zhao, Xiangwei, Ge, Qinyu · 2021 · Figshare
  85. Additional file 1 of deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data
    Murillo Carrasco, Alexis Germán, Tatiane Katsue Furuya, Miyuki Uno, Citrangulo Tortelli, Tharcisio, Roger J. Chammas · 2024 · Figshare
  86. Additional file 1 of Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data
    Pelin Gundogdu, Carlos Loucera, Inmaculada Álamo-Álvarez, Dopazo, Joaquin, Isabel Nepomuceno · 2022 · DIGITAL.CSIC (Spanish National Research Council (CSIC))
  87. Benchmarking of single nuclei RNA-seq methods on human post-mortem brain tissue
    Kasra Nikouei, Elin Lundin, Fatima Memic, Craig A. Stockmeier, Jens Hjerling‐Leffler · 2025 · Genomics
  88. A multimodal spatial atlas of transcriptomic, morphological, and electrophysiological cell type densities in the mouse brain
    Csaba Verasztó, Yann Roussel, Lida Kanari, Sébastien Piluso, Henry Markram, Daniel X. Keller · 2026 · PLoS Computational Biology
  89. The role of intrinsic neuronal excitability for Prelimbic network function
    Rafael De Sa · 2019 · theses.fr (ABES)
  90. Rôle de la phosphodiestérase 2A dans la physiopathologie du syndrome de l’X fragile
    Sébastien Delhaye · 2021 · theses.fr (ABES)
  91. Identity crisis: exploring the boundaries of cell type identification in the age of single-cell transcriptomics
    Seulkee Yang, Sudeeksha Tyagi, Christian Rosenmund, Melissa A. Herman · 2026 · Frontiers in Cellular Neuroscience
  92. Nmur1 and Cckar fail to support functional genetic access in adult dopamine neurons and challenge GPCR atlas assignments
    Moueez Shah, Renqi Wu, Qiao Ye, Raluca Bugescu, Andrew Villa, Justine T. Wong, Fernando Garcia, Zhiqun Tan, Xiangmin Xu, Gina M. Leinninger et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  93. The transcriptional cortical response to daily torpor in Phodopus sungorus
    Lukas Can Bal, Marcel S. Woo, Nicola Rothammer, Elena Haugg, Christina Mayer, Annika Herwig, Manuel Alexander Friese · 2026 · Life Science Alliance
  94. A knockin Ntsr1Flp driver enables intersectional and systemic targeting of heterogeneous midbrain dopamine circuits
    Fernando Garcia, Andrew P. Villa, Justine T. Wong, Renqi Wu, Priscilla Coriano, Lief E. Fenno, Gina M. Leinninger, Andrew D. Steele · 2026 · Cell Reports Methods
  95. Traumatic brain injury induces cell-type-specific remodelling of the proteostasis network
    Jonathan Lefkowitz, Milo Taylor, Aditya Kumar, Ruchira Menka Jha, Dhivyaa Rajasundaram, Prajwal Ciryam · 2026 · Philosophical Transactions of the Royal Society B Biological Sciences
  96. Selective autophagy pathways in ageing and neurodegeneration: Emerging roles for mitophagy and nucleophagy
    Maria Markaki, Nektarios Tavernarakis · 2026 · FEBS Journal