Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

Shekhar, Karthik, Lapan, Sylvain W., Whitney, Irene E., Tran, Nicholas M., Macosko, Evan Z., Kowalczyk, Monika, Adiconis, Xian, Levin, Joshua Z. +6 more·2016·Cell
DOI 10.1016/j.cell.2016.07.054

Cited by (1,000)

Items 101–200 of 1,000

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  2. Inhibition decorrelates visual feature representations in the inner retina
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  5. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs
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  10. Establishing neuronal diversity in the spinal cord: a time and a place
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  12. Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis
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  15. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data
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  16. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes
    Armand, Ethan J., Li, Junhao, Xie, Fangming, Luo, Chongyuan, Mukamel, Eran A. · 2021 · Neuron
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  21. The diversity of GABAergic neurons and neural communication elements
    Huang, Z. Josh, Paul, Anirban · 2019 · Nature Reviews Neuroscience
  22. Origins and Proliferative States of Human Oligodendrocyte Precursor Cells
    Wei Huang, Aparna Bhaduri, Dmitry Velmeshev, Shaohui Wang, Li Wang, Catherine A. Rottkamp, Arturo Álvarez-Buylla, David H. Rowitch, Arnold R. Kriegstein · 2020 · Cell
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  26. Phenotypic convergence: distinct transcription factors regulate common terminal features
    Konstantinides, Nikolaos, Kapuralin, Katarina, Fadil, Chaimaa, Barboza, Luendreo, Satija, Rahul, Desplan, Claude · 2018 · Cell
  27. Quantifying the effect of experimental perturbations at single-cell resolution
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  29. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
    Lafzi, Atefeh, Moutinho, Catia, Picelli, Simone, Heyn, Holger · 2018 · Nature Protocols
  30. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
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  34. Neuronal specification in space and time
    Isabel Holguera, Claude Desplan · 2018 · Science
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    Yinqing Li, Violeta G. López-Huerta, Xian Adiconis, Kirsten M. Levandowski, Soonwook Choi, Sean Simmons, Mario A. Arias-García, Baolin Guo, Annie Y. Yao, Timothy R. Blosser et al. · 2020 · Nature
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  39. Introduction to Single‐Cell RNA Sequencing
    Thale Kristin Olsen, Ninib Baryawno · 2018 · Current Protocols in Molecular Biology
  40. Decoding molecular and cellular heterogeneity of mouse nucleus accumbens
    Chen, Renchao, Blosser, Timothy R., Djekidel, Mohamed N., Hao, Junjie, Bhattacherjee, Aritra, Chen, Wenqiang, Tuesta, Luis M., Zhuang, Xiaowei, Zhang, Yi · 2021 · Nature Neuroscience
  41. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
    Jellert T. Gaublomme, Bo Li, Cristin Aubin, Abigail Knecht, Yiming Yang, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Ashley Dionne, Lan Nguyễn et al. · 2019 · Nature Communications
  42. Connectivity map of bipolar cells and photoreceptors in the mouse retina
    Christian Behrens, Timm Schubert, Silke Haverkamp, Thomas Euler, Philipp Berens · 2016 · eLife
  43. Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development
    Nowakowski, Tomasz J., Rani, Neha, Golkaram, Mahdi, Zhou, Hongjun R., Alvarado, Beatriz, Huch, Kylie, West, Jay A., Leyrat, Anne, Pollen, Alex A., Kriegstein, Arnold R. et al. · 2018 · Nature Neuroscience
  44. Hippo Signaling Plays an Essential Role in Cell State Transitions during Cardiac Fibroblast Development
    Yang Xiao, Matthew C. Hill, Min Zhang, Thomas J. Martin, Yuka Morikawa, Suya Wang, Alexander R. Moise, Joshua D. Wythe, James F. Martin · 2018 · Developmental Cell
  45. Cell types and cell circuits in human and non-human primate retina
    Ulrike Grünert, Paul R. Martin · 2020 · Progress in Retinal and Eye Research
  46. Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids
    Sangbae Kim, Albert Lowe, Rachayata Dharmat, Seung‐Hoon Lee, Leah A. Owen, Jun Wang, Akbar Shakoor, Yumei Li, Denise J. Morgan, Andre A. Hejazi et al. · 2019 · Proceedings of the National Academy of Sciences
  47. Detection of differentially abundant cell subpopulations in scRNA-seq data
    Zhao, Jun, Jaffe, Ariel, Li, Henry, Lindenbaum, Ofir, Sefik, Esen, Jackson, Ruaidhrí, Cheng, Xiuyuan, Flavell, Richard A., Kluger, Yuval · 2021 · Proceedings of the National Academy of Sciences
  48. Guided construction of single cell reference for human and mouse lung
    Minzhe Guo, Michael P. Morley, Cheng Jiang, Yixin Wu, Guangyuan Li, Yina Du, Shuyang Zhao, Andrew F. Wagner, Adnan Cihan Cakar, Michal Kouril et al. · 2023 · Nature Communications
  49. Diversity amongst trigeminal neurons revealed by high throughput single cell sequencing
    Minh Quang Nguyen, Youmei Wu, Lauren S. Bonilla, Lars J. von Buchholtz, Nicholas J. P. Ryba · 2017 · PLoS ONE
  50. Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing
    Elisabetta Furlanis, Peter Scheiffele · 2018 · Annual Review of Cell and Developmental Biology
  51. Effector TH17 Cells Give Rise to Long-Lived TRM Cells that Are Essential for an Immediate Response against Bacterial Infection
    Maria Carolina Amezcua Vesely, Paris Pallis, Piotr Bielecki, Jun Siong Low, Jun Zhao, Christian C. D. Harman, Lina Kroehling, Ruaidhrí P. Jackson, Will Bailis, Paula Licona-Limón et al. · 2019 · Cell
  52. Single-cell atlases: shared and tissue-specific cell types across human organs
    Rasa Elmentaite, Cecilia Domínguez Conde, Lu Yang, Sarah Amalia Teichmann · 2022 · Nature Reviews Genetics
  53. Removal of batch effects using distribution-matching residual networks
    Uri Shaham, Kelly Patrick Stanton, Jun Zhao, Huamin Li, Khadir Raddassi, Ruth R. Montgomery, Yuval Kluger · 2017 · Bioinformatics
  54. Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq
    Hu, Peng, Fabyanic, Emily, Kwon, Deborah Y., Tang, Sheng, Zhou, Zhaolan, Wu, Hao · 2017 · Molecular Cell
  55. Single-Cell Landscapes of Primary Glioblastomas and Matched Organoids and Cell Lines Reveal Variable Retention of Inter- and Intra-Tumor Heterogeneity
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  56. Single-cell transcriptomic evidence for dense intracortical neuropeptide networks
    Smith, Stephen J, Sümbül, Uygar, Graybuck, Lucas T, Collman, Forrest, Seshamani, Sharmishtaa, Gala, Rohan, Gliko, Olga, Elabbady, Leila, Miller, Jeremy A, Bakken, Trygve E et al. · 2019 · eLife
  57. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney
    Rajasree Menon, Edgar A. Otto, Austin Kokoruda, Jian Zhou, Zidong Zhang, Euisik Yoon, Yu‐Chih Chen, Olga G. Troyanskaya, Jason R. Spence, Matthias Kretzler et al. · 2018 · Development
  58. openTSNE: a modular Python library for t-SNE dimensionality reduction and embedding
    Pavlin G. Poličar, Martin Stražar, Blaž Zupan · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Single-Cell RNA Sequencing: Unraveling the Brain One Cell at a Time
    Dimitry Ofengeim, Νικόλαος Γιαγτζόγλου, Dann Huh, Chengyu Zou, Junying Yuan · 2017 · Trends in Molecular Medicine
  60. Efficient Algorithms for t-distributed Stochastic Neighborhood Embedding
    George C. Linderman, Manas Rachh, Jeremy G. Hoskins, Stefan Steinerberger, Yuval Kluger · 2017 · arXiv (Cornell University)
  61. Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq
    Shristi Pandey, Karthik Shekhar, Aviv Regev, Alexander F. Schier · 2018 · Current Biology
  62. Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing
    Andrew P. Voigt, S. Scott Whitmore, Miles J. Flamme‐Wiese, Megan J. Riker, Luke A. Wiley, Budd A. Tucker, Edwin M. Stone, Robert F. Mullins, Todd E. Scheetz · 2019 · Experimental Eye Research
  63. Immature excitatory neurons develop during adolescence in the human amygdala
    Shawn F. Sorrells, Mercedes F. Paredes, Dmitry Velmeshev, Vicente Herranz‐Pérez, Kadellyn Sandoval, Simone Mayer, Edward F. Chang, Ricardo Insausti, Arnold R. Kriegstein, John L.R. Rubenstein et al. · 2019 · Nature Communications
  64. Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data
    Tian Tian, Jie Zhang, Xiang Lin, Zhi Wei, Hakon H. Hakonarson · 2021 · Nature Communications
  65. Inferring relevant cell types for complex traits by using single-cell gene expression
    Calderon, Diego, Bhaskar, Anand, Knowles, David A., Golan, David, Raj, Towfique, Fu, Audrey Q., Pritchard, Jonathan K. · 2017 · The American Journal of Human Genetics
  66. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis
    Semir Beyaz, Charlie Chung, Haiwei Mou, Khristian Erich Bauer-Rowe, Michael E. Xifaras, Ilgin Ergin, Lenka Dohnalová, Moshe Biton, Karthik Shekhar, Onur Eskiocak et al. · 2021 · Cell stem cell
  67. Deep soft K-means clustering with self-training for single-cell RNA sequence data
    Liang Chen, Weinan Wang, Yuyao Zhai, Minghua Deng · 2020 · NAR Genomics and Bioinformatics
  68. A cell atlas of the chick retina based on single-cell transcriptomics
    Masahito Yamagata, Wenjun Yan, Joshua R. Sanes · 2021 · eLife
  69. Ensembles of endothelial and mural cells promote angiogenesis in prenatal human brain
    Elizabeth Erin Crouch, Aparna Bhaduri, Madeline G. Andrews, Arantxa Cebrián‐Silla, Loukas N. Diafos, Janeth O. Birrueta, Kaylee Wedderburn-Pugh, Edward J. Valenzuela, Neal K. Bennett, Ugomma C. Eze et al. · 2022 · Cell
  70. Impact of similarity metrics on single-cell RNA-seq data clustering
    Kim, Taiyun, Chen, Irene Rui, Lin, Yingxin, Wang, Andy Yi-Yang, Yang, Jean Yee Hwa, Yang, Pengyi · 2019 · Briefings in Bioinformatics
  71. Classification of Mouse Retinal Bipolar Cells: Type-Specific Connectivity with Special Reference to Rod-Driven AII Amacrine Pathways
    Yoshihiko Tsukamoto, Naoko Omi · 2017 · Frontiers in Neuroanatomy
  72. Neural circuits in the mouse retina support color vision in the upper visual field
    Klaudia P. Szatko, Maria M. Korympidou, Yanli Ran, Philipp Berens, Deniz Dalkara, Timm Schubert, Thomas Euler, Katrin Franke · 2020 · Nature Communications
  73. Enteric glial cell heterogeneity regulates intestinal stem cell niches
    Meryem B. Baghdadi, Arshad Ayyaz, Sabrina Coquenlorge, Bonnie Chu, Sandeep Kumar, Catherine Streutker, Jeffrey L. Wrana, Tae-Hee Kim · 2021 · Cell stem cell
  74. True S-cones are concentrated in the ventral mouse retina and wired for color detection in the upper visual field
    Francisco Manuel Nadal-Nicolás, Vincent P Kunze, John M Ball, Brian T Peng, Akshay Krisnan, Gao-Hui Zhou, Lijin Dong, Wei Li · 2020 · eLife
  75. K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data
    Florian Wagner, Yun Yan, Itai Yanai · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  76. Manifold learning-based methods for analyzing single-cell RNA-sequencing data
    Kevin R. Moon, Jay S. Stanley, Daniel B. Burkhardt, David van Dijk, Guy Wolf, Smita Krishnaswamy · 2017 · Current Opinion in Systems Biology
  77. Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis
    Yuqiong Hu, Xiaoye Wang, Boqiang Hu, Yunuo Mao, Yidong Chen, Liying Yan, Jun Yong, Ji Dong, Yuan Wei, Wei Wang et al. · 2019 · PLoS Biology
  78. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling
    Qingnan Liang, Rachayata Dharmat, Leah A. Owen, Akbar Shakoor, Yumei Li, Sangbae Kim, Albert T. Vitale, Ivana K. Kim, Denise J. Morgan, Shaoheng Liang et al. · 2019 · Nature Communications
  79. Differential Encoding in Prefrontal Cortex Projection Neuron Classes Across Cognitive Tasks
    Jan H. Lui, Nghia D. Nguyen, Sophie M. Grutzner, Spyros Darmanis, Diogo Peixoto, Mark J. Wagner, William E. Allen, Justus M. Kebschull, Ethan B. Richman, Jing Ren et al. · 2020 · Cell
  80. Cell type ontologies of the Human Cell Atlas
    David Osumi-Sutherland, Chuan Xu, Maria Keays, Adam P. Levine, Peter V. Kharchenko, Aviv Regev, Ed Lein, Sarah Amalia Teichmann · 2021 · Nature Cell Biology
  81. Satb1 regulates Contactin 5 to pattern dendrites of a mammalian retinal ganglion cell
    Yi-Rong Peng, Nicholas M. Tran, A. Krishnaswamy, D. Kostadinov, Emily M. Martersteck, J. Sanes · 2017 · Neuron
  82. Efficient Generation of Transcriptomic Profiles by Random Composite Measurements
    Cleary, Brian, Cong, Le, Cheung, Anthea, Lander, Eric S., Regev, Aviv · 2017 · Cell
  83. Benchmarking principal component analysis for large-scale single-cell RNA-sequencing
    Koki Tsuyuzaki, Hiroyuki Sato, Kenta Sato, Itoshi Nikaido · 2020 · Genome biology
  84. Spinal macrophages resolve nociceptive hypersensitivity after peripheral injury
    Jesse K. Niehaus, Bonnie Taylor‐Blake, Lipin Loo, Jeremy M. Simon, Mark J. Zylka · 2021 · Neuron
  85. CaSTLe – Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments
    Yuval Lieberman, Lior Rokach, Tal Shay · 2018 · PLoS ONE
  86. Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea
    De‐Quan Li, Sangbae Kim, Jinmiao Li, Qianmiao Gao, Jongsu Choi, Fang Bian, Jiaoyue Hu, Yun Zhang, Jin Li, Rong Lu et al. · 2020 · The Ocular Surface
  87. Lung endothelial cells regulate pulmonary fibrosis through FOXF1/R-Ras signaling
    Fenghua Bian, Ying‐Wei Lan, Shuyang Zhao, Zicheng Deng, Samriddhi Shukla, Anusha Acharya, Johnny Donovan, Tien T. Le, David Milewski, Matthew D. Bacchetta et al. · 2023 · Nature Communications
  88. VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics
    Seninge, Lucas, Anastopoulos, Ioannis, Ding, Hongxu, Stuart, Joshua · 2021 · Nature Communications
  89. Spectacle: An interactive resource for ocular single-cell RNA sequencing data analysis
    Andrew P. Voigt, S. Scott Whitmore, Nicholas D. Lessing, Adam P. DeLuca, Budd A. Tucker, Edwin M. Stone, Robert F. Mullins, Todd E. Scheetz · 2020 · Experimental Eye Research
  90. Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in <i>Drosophila</i>
    Schlegel, Philipp, Yin, Yijie, Bates, Alexander S., Dorkenwald, Sven, Eichler, Katharina, Brooks, Paul, Han, Daniel S., Gkantia, Marina, dos Santos, Marcia, Munnelly, Eva J. et al. · 2023
  91. Heparan Sulfate Proteoglycans as Emerging Players in Synaptic Specificity
    Giuseppe Condomitti, Joris de Wit · 2018 · Frontiers in Molecular Neuroscience
  92. Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
    Miao Liu, Yanfang Lu, Bing Yang, Yanbo Chen, Jonathan S. D. Radda, Mengwei Hu, Samuel G. Katz, Siyuan Wang · 2020 · Nature Communications
  93. Benchmarking strategies for cross-species integration of single-cell RNA sequencing data
    Yuyao Song, Zhichao Miao, Alvis Brāzma, Irene Papatheodorou · 2023 · Nature Communications
  94. Droplet-based single cell RNAseq tools: a practical guide
    Salomon, Robert, Kaczorowski, Dominik, Valdes-Mora, Fatima, Nordon, Robert E., Neild, Adrian, Farbehi, Nona, Bartonicek, Nenad, Gallego-Ortega, David · 2019 · Lab on a Chip
  95. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
    Ariel A. Hippen, Matías Marín Falco, Lukas M. Weber, Erdoğan Pekcan Erkan, Kaiyang Zhang, Jennifer A. Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks · 2021 · PLoS Computational Biology
  96. Regenerative and restorative medicine for eye disease
    Russell Neil Van Gelder, Michael F. Chiang, Michael A. Dyer, Thomas N. Greenwell, Leonard A. Levin, Rachel Wong, Clive Niels Svendsen · 2022 · Nature Medicine
  97. Single-Cell Transcriptomic Analysis Identifies a Unique Pulmonary Lymphangioleiomyomatosis Cell
    Minzhe Guo, Jane J. Yu, Anne‐Karina T. Perl, Kathryn A. Wikenheiser‐Brokamp, Matthew Riccetti, Erik Y. Zhang, Parvathi Sudha, Mike Adam, Andrew Potter, Elizabeth J. Kopras et al. · 2020 · American Journal of Respiratory and Critical Care Medicine
  98. De novo gene signature identification from single‐cell RNA‐seq with hierarchical Poisson factorization
    Hanna Mendes Levitin, Jinzhou Yuan, Yim Ling Cheng, Francisco J. R. Ruiz, Erin C. Bush, Jeffrey N. Bruce, Peter Canoll, Antonio Iavarone, Anna Lasorella, David M. Blei et al. · 2019 · Molecular Systems Biology
  99. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior
    Yvonne Kölsch, Joshua Hahn, Anna Sappington, Manuel Stemmer, António M. Fernandes, Thomas O. Helmbrecht, Shriya Lele, Salwan Butrus, Eva Laurell, Irene Arnold-Ammer et al. · 2020 · Neuron
  100. Systematic comparative analysis of single cell RNA-sequencing methods
    Jiarui Ding, Xian Adiconis, Sean Simmons, Monika S. Kowalczyk, Cynthia C. Hession, Nemanja Despot Marjanovic, Travis K. Hughes, Marc H. Wadsworth, Tyler Burks, Lan Nguyễn et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)