Spatial reconstruction of single-cell gene expression data

Cited by (1,061)

Items 801–900 of 1,061

1. Single‐cell transcriptomics of LepR‐positive skeletal cells reveals heterogeneous stress‐dependent stem and progenitor pools
   Chunyang Mo, Jingxin Guo, Jiachen Qin, Xiaoying Zhang, Yuxi Sun, Hanjing Wei, Dandan Cao, Yiying Zhang, Chengchen Zhao, Yanhong Xiong et al. · 2021 · The EMBO Journal
2. Vitessce: integrative visualization of multimodal and spatially resolved single-cell data
   Mark S. Keller, Ilan Gold, Chuck McCallum, Trevor Manz, Peter V. Kharchenko, Nils Gehlenborg · 2024 · Nature Methods
3. Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development
   Ryan M. J. Genga, Eric M. Kernfeld, Krishna Mohan Parsi, Teagan J. Parsons, Michael J. Ziller, René Maehr · 2019 · Cell Reports
4. CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution
   Wenjun Kong, Brent A. Biddy, Kenji Kamimoto, Junedh Amrute, Emily G. Butka, Samantha A. Morris · 2020 · Nature Protocols
5. Hypothalamic oestrogen receptor alpha establishes a sexually dimorphic regulatory node of energy expenditure
   J. Edward van Veen, Laura G. Kammel, Patricia Bunda, Michaël Shum, Michelle Reid, Megan G. Massa, Douglas V. Arneson, Jae W. Park, Zhi Zhang, Anitta Joseph et al. · 2020 · Nature Metabolism
6. A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells
   Vasilios Zachariadis, Huaitao Cheng, Nathanael Andrews, Martin Enge · 2020 · Molecular Cell
7. Contrastive self-supervised clustering of scRNA-seq data
   Madalina Ciortan, Matthieu Defrance · 2021 · BMC Bioinformatics
8. Ductal Ngn3-expressing progenitors contribute to adult β cell neogenesis in the pancreas
   Christopher Gribben, Christopher Lambert, Hendrik A. Messal, Ella-Louise Hubber, Chloe L. Rackham, Ian M. Evans, Harry Heimberg, Peter M. Jones, Rocı́o Sancho, Axel Behrens · 2021 · Cell stem cell
9. A systematic performance evaluation of clustering methods for single-cell RNA-seq data
   Angelo Duò, Mark D. Robinson, Charlotte Soneson · 2018 · F1000Research
10. Spatiotemporal Dynamics of the Molecular Expression Pattern and Intercellular Interactions in the Glial Scar Response to Spinal Cord Injury
    Leilei Gong, Yun Gu, Xiaoxiao Han, Chengcheng Luan, Chang Liu, Xinghui Wang, Yufeng Sun, Mengru Zheng, Mengya Fang, Shuhai Yang et al. · 2022 · Neuroscience Bulletin
11. Interleukin‐18 signaling promotes activation of hepatic stellate cells in mouse liver fibrosis
    Jana Knorr, Benedikt K. Kaufmann, María Eugenia Inzaugarat, Theresa Maria Holtmann, Lukas Jonathan Geisler, Jana Hundertmark, Marlene Sophia Kohlhepp, Laela M. Boosheri, Daisy Chilin-Fuentes, Amanda Birmingham et al. · 2022 · Hepatology
12. TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics
    Simon Mages, Noa Moriel, Inbal Avraham‐Davidi, Evan M. Murray, Jan Watter, Fei Chen, Orit Rozenblatt–Rosen, Johanna Klughammer, Aviv Regev, Mor Nitzan · 2023 · Nature Biotechnology
13. Single-cell transcriptomics suggest distinct upstream drivers of IL-17A/F in hidradenitis versus psoriasis
    Jaehwan Kim, Jongmi Lee, Xuan Li, Hyun Soo Lee, Katherine Kim, Vasuma Chaparala, William J. Murphy, Wei Zhou, Junyue Cao, Michelle Anne Lowes et al. · 2023 · Journal of Allergy and Clinical Immunology
14. Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids
    Agnieszka Rybak‐Wolf, Emanuel Wyler, Tancredi Massimo Pentimalli, Ivano Legnini, Anna Oliveras, Petar Glažar, Anna Loewa, Seung Joon Kim, Benedikt B. Kaufer, Andrew Woehler et al. · 2023 · Nature Microbiology
15. High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
    Matthew A. Lalli, Denis R. Avey, Joseph D. Dougherty, Jeffrey Milbrandt, Robi David Mitra · 2020 · Genome Research
16. Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans
    Muñoz, José F., Delorey, Toni, Ford, Christopher B., Li, Bi Yu, Thompson, Dawn A., Rao, Reeta P., Cuomo, Christina A. · 2019 · Nature Communications
17. Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal–foetal interface during pregnancy
    Andy Nelson, Arne W. Mould, Elizabeth K. Bikoff, Elizabeth J. Robertson · 2016 · Nature Communications
18. Combinatorial prediction of marker panels from single‐cell transcriptomic data
    Conor Delaney, Alexandra Schnell, Louis V. Cammarata, Aaron Yao-Smith, Aviv Regev, Vijay Kumar Kuchroo, Meromit Singer · 2019 · Molecular Systems Biology
19. In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription
    Amjad Askary, Luis Óscar Sánchez-Guardado, James M. Linton, Duncan M. Chadly, Mark W. Budde, Long Cai, Carlos Lois, Michael B. Elowitz · 2019 · Nature Biotechnology
20. High expression of ACE2 and TMPRSS2 and clinical characteristics of COVID-19 in colorectal cancer patients
    Chao Liu, Kai Wang, Min Zhang, Xiaoyu Hu, Tian Hu, Yumei Liu, Qinyong Hu, Shikai Wu, Jinbo Yue · 2021 · npj Precision Oncology
21. Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
    Vassilis Glaros, René Rauschmeier, Artem V. Artemov, Annika Reinhardt, Sebastian Ols, Aikaterini Emmanouilidi, Charlotte Gustafsson, Yuanyuan You, Claudio Mirabello, Åsa K. Björklund et al. · 2021 · Immunity
22. Unravelling glioblastoma heterogeneity by means of single-cell RNA sequencing
    Ana Hernández Martínez, Rodrigo Madurga, Noemí Garcia‐Romero, Ángel Ayuso‐Sacido · 2021 · Cancer Letters
23. Loss of chromosome Y in primary tumors
    Meifang Qi, Jiali Pang, Irene Rin Mitsiades, Andrew A. Lane, Esther Rheinbay · 2023 · Cell
24. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines
    Qionghua Zhu, Xin Zhao, Yuanhang Zhang, Yanping Li, Shang Liu, Jingxuan Han, Zhiyuan Sun, Chunqing Wang, Daqi Deng, Yisen Tang et al. · 2023 · Nature Communications
25. Biologically Relevant Heterogeneity: Metrics and Practical Insights
    Albert Gough, Andrew M. Stern, John Maier, Timothy R. Lezon, Tongying Shun, Chakra Chennubhotla, Mark E. Schurdak, Steven A. Haney, D. Lansing Taylor · 2017 · SLAS DISCOVERY
26. Single-cell RNA sequencing unveils an IL-10-producing helper subset that sustains humoral immunity during persistent infection
    Gang Xin, Ryan Zander, David Schauder, Chen Yao, Jason S. Weinstein, William R. Drobyski, Vera L. Tarakanova, Joseph E. Craft, Weiguo Cui · 2018 · Nature Communications
27. Disentangling glial diversity in peripheral nerves at single-nuclei resolution
    Aldrin Kay‐Yuen Yim, Peter L. Wang, John R. Bermingham, Amber R. Hackett, Amy M. Strickland, Timothy M. Miller, Cindy V. Ly, Robi David Mitra, Jeffrey Milbrandt · 2022 · Nature Neuroscience
28. Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism
    Bo Wang, Jiawei Luo, Ying Liu, Wanwan Shi, Zehao Xiong, Cong Shen, Yahui Long · 2023 · Briefings in Bioinformatics
29. Dynamic zonation of liver polyploidy
    Tanami, Sivan, Ben-Moshe, Shani, Elkayam, Anat, Mayo, Avi, Bahar Halpern, Keren, Itzkovitz, Shalev · 2017 · Cell and Tissue Research
30. Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
    Saikia, Mridusmita, Burnham, Philip, Keshavjee, Sara H., Wang, Michael F. Z., Heyang, Michael, Moral-Lopez, Pablo, Hinchman, Meleana M., Danko, Charles G., Parker, John S. L., De Vlaminck, Iwijn · 2019 · Nature Methods
31. PD-1 blockade-unresponsive human tumor-infiltrating CD8+ T cells are marked by loss of CD28 expression and rescued by IL-15
    Kyung Hwan Kim, Hong Kwan Kim, Hyung‐Don Kim, Chang Gon Kim, Hoyoung Lee, Ji Won Han, Seong Jin Choi, Seongju Jeong, Minwoo Jeon, Hyunglae Kim et al. · 2020 · Cellular and Molecular Immunology
32. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies
    Wilton B. Williams, Robert Ryan Meyerhoff, Robert J. Edwards, Hui Li, Kartik Manne, Nathan I. Nicely, Rory C. Henderson, Ye Zhou, Katarzyna Janowska, Katayoun Mansouri et al. · 2021 · Cell
33. XGBoost-based and tumor-immune characterized gene signature for the prediction of metastatic status in breast cancer
    Qingqing Li, Hui Yang, Peipei Wang, Xiaocen Liu, Kun Lv, Mingquan Ye · 2022 · Journal of Translational Medicine
34. Modeling human multi-lineage heart field development with pluripotent stem cells
    Donghe Yang, Juliana Gomez-Garcia, Shunsuke Funakoshi, Thinh Ngoc Tran, Ian M. Fernandes, Gary D. Bader, Michael A. Laflamme, Gordon M. Keller · 2022 · Cell stem cell
35. Multi-omics analysis of human mesenchymal stem cells shows cell aging that alters immunomodulatory activity through the downregulation of PD-L1
    Yuchen Gao, Ying Chi, Yunfei Chen, Wentian Wang, Huiyuan Li, Wenting Zheng, Ping Zhu, Jinying An, Yanan Duan, Ting Sun et al. · 2023 · Nature Communications
36. An AI Agent for Fully Automated Multi‐Omic Analyses
    Juexiao Zhou, Bin Zhang, Guowei Li, Xiuying Chen, Haoyang Li, Xiaopeng Xu, Siyuan Chen, Wenjia He, Chencheng Xu, Liwei Liu et al. · 2024 · Advanced Science
37. A single-cell atlas of the developing Drosophila ovary identifies follicle stem cell progenitors
    Maija Slaidina, Torsten U. Banisch, Selena Gupta, Ruth Lehmann · 2020 · Genes & Development
38. BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking clusterin expression in cancer associated fibroblasts with HSF1 signaling
    Shaashua, Lee, Ben-Shmuel, Aviad, Pevsner-Fischer, Meirav, Friedman, Gil, Levi-Galibov, Oshrat, Nandakumar, Subhiksha, Barki, Debra, Nevo, Reinat, Brown, Lauren E., Zhang, Wenhan et al. · 2022 · Nature Communications
39. Kinetics of adult hematopoietic stem cell differentiation in vivo
    Samik Upadhaya, Catherine M. Sawai, Efthymia Papalexi, Ali Rashidfarrokhi, Geunhyo Jang, Pratip K. Chattopadhyay, Rahul Satija, Boris Reizis · 2018 · The Journal of Experimental Medicine
40. Self-assembling manifolds in single-cell RNA sequencing data
    Alexander J. Tarashansky, Yuan Xue, Pengyang Li, Stephen R. Quake, Bo Wang · 2019 · eLife
41. Dysregulated adaptive immune response contributes to severe COVID-19
    Kuai Yu, 吴永坚, Jingjing He, Xuefei Liu, Bo Wei, Wen Wen, Xiaofeng Wen, Wenxiong Xu, Xingjun Dong, Yue Yan et al. · 2020 · Cell Research
42. Colorectal Cancer Stem Cell States Uncovered by Simultaneous Single‐Cell Analysis of Transcriptome and Telomeres
    Hua Wang, Peng Gong, Tong Chen, Shan Gao, Zhenfeng Wu, Xiaodong Wang, Jie Li, Sadie L. Marjani, José C. Costa, Sherman M. Weissman et al. · 2021 · Advanced Science
43. GNN-based embedding for clustering scRNA-seq data
    Madalina Ciortan, Matthieu Defrance · 2021 · Bioinformatics
44. Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis
    Quinn T. Easter, Bruno Fernandes Matuck, Germán Beldorati Stark, Catherine L. Worth, Alexander V. Predeus, Brayon J. Fremin, Khoa Huynh, Vaishnavi Nattar Ranganathan, Zhi Feng Ren, Diana Pereira et al. · 2024 · Nature Communications
45. Genetic regulation of gene expression across multiple tissues in chickens
    Dailu Guan, Zhonghao Bai, Xiaoning Zhu, Conghao Zhong, Yali Hou, Di Zhu, Houcheng Li, Fangren Lan, Shuqi Diao, Yuelin Yao et al. · 2025 · Nature Genetics
46. High Throughput Single Cell RNA Sequencing, Bioinformatics Analysis and Applications
    Xiaoyun Huang, Shiping Liu, Liang Li Wu, Miaomiao Jiang, Yong Hou · 2018 · Advances in experimental medicine and biology
47. Spatial Transcriptional Mapping of the Human Nephrogenic Program
    Nils O. Lindström, Rachel S. G. Sealfon, Xi Chen, Riana K. Parvez, Andrew Ransick, Guilherme De Sena Brandine, Jinjin Guo, Bill Hill, Tracy Tran, Albert D. Kim et al. · 2020 · Developmental Cell
48. Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells
    Thi Xuan Ai Pham, Amitesh Panda, Harunobu Kagawa, San Kit To, Cankat Ertekin, Grigorios Georgolopoulos, Sam Samuel Franciscus Allegonda van Knippenberg, Ryan Allsop, Alexandre Bruneau, Jonathan Sai‐Hong Chui et al. · 2022 · Cell stem cell
49. Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
    Candace C. Liu, Noah F. Greenwald, Alex Kong, Erin McCaffrey, Ke Xuan Leow, Dunja Mrdjen, Bryan J. Cannon, Josef Lorenz Rumberger, Sricharan Reddy Varra, Michael Angelo · 2023 · Nature Communications
50. PD-1 blockade increases the self-renewal of stem-like CD8 T cells to compensate for their accelerated differentiation into effectors
    Amanda L. Gill, Peter H. Wang, Judong Lee, William H. Hudson, Satomi Ando, Koichi Araki, Yinghong Hu, Andreas Wieland, Se Jin Im, Autumn A. Gavora et al. · 2023 · Science Immunology
51. Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review
    Xue Yang, Kexin Huang, Dewei Yang, Weiling Zhao, Xiaobo Zhou · 2023 · Global Challenges
52. Predicting cellular responses to perturbation across diverse contexts with State
    Adduri, Abhinav K., Gautam, Dhruv, Bevilacqua, Beatrice, Naghipourfar, Mohsen, Imran, Alishba, Shah, Rohan, Teyssier, Noam, Verma, Rishi, Carpenter, Christopher, Eraslan, Basak et al. · 2026 · Cell
53. Gene expression atlas of a developing tissue by single cell expression correlation analysis
    Josephine Bageritz, Philipp Willnow, Erica Valentini, Svenja Leible, Michael Boutros, Aurelio A. Teleman · 2019 · Nature Methods
54. Mesoderm specification and diversification: from single cells to emergent tissues
    Elisabetta Ferretti, Anna‐Katerina Hadjantonakis · 2019 · Current Opinion in Cell Biology
55. Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy
    Sara De Biasi, Lara Gibellini, Domenico Lo Tartaro, Simone Puccio, Claudio Rabacchi, Emilia Maria Cristina Mazza, Jolanda Brummelman, Brandon Williams, Kelly A. Kaihara, Mattia Forcato et al. · 2021 · Nature Communications
56. Statistical and machine learning methods for spatially resolved transcriptomics with histology
    Jian Hu, Amelia R. Schroeder, Kyle Coleman, Chixiang Chen, Benjamin J. Auerbach, Mingyao Li · 2021 · Computational and Structural Biotechnology Journal
57. Single‐cell RNA‐sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent
    Moonyoung Kang, Yuri Choi, Hyeonjin Kim, Sang‐Gyu Kim · 2022 · New Phytologist
58. A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
    Manuel Neumann, Xiaocai Xu, Cezary Smaczniak, Julia Schumacher, Wenhao Yan, Nils Blüthgen, Thomas Greb, Henrik Jönsson, Jan A. Traas, Kerstin Kaufmann et al. · 2022 · Nature Communications
59. Gasdermin D licenses MHCII induction to maintain food tolerance in small intestine
    Kaixin He, Tingting Wan, Decai Wang, Ji Hu, Tingyue Zhou, Wanyin Tao, Zheng Wei, Lu Qiao, Rongbin Zhou, Zhigang Tian et al. · 2023 · Cell
60. Expansion of hedgehog disrupts mesenchymal identity and induces emphysema phenotype
    Chaoqun Wang, Nabora Reyes de Mochel, Stephanie A. Christenson, Monica Cassandras, Rebecca H. Moon, Alexis N. Brumwell, Lauren E. Byrnes, Alfred Li, Yasuyuki Yokosaki, Peiying Shan et al. · 2018 · Journal of Clinical Investigation
61. Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT
    Bushra Raj, James A. Gagnon, Alexander F. Schier · 2018 · Nature Protocols
62. EndoDB: a database of endothelial cell transcriptomics data
    Shawez Khan, Federico Taverna, Kateřina Rohlenová, Lucas Treps, Vincent Geldhof, Laura P. M. H. de Rooij, Liliana Sokol, Andreas Pircher, Lena‐Christin Conradi, Joanna Maria Kalucka et al. · 2018 · Nucleic Acids Research
63. Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses
    Mélanie Durand, Thomas Walter, Tiphène Pirnay, Thomas Naessens, Paul Gueguen, Christel Goudot, Sonia Lameiras, Qing Chang, Nafiseh Talaei, Olga Ornatsky et al. · 2019 · The Journal of Experimental Medicine
64. Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor-resistant HER2-positive breast cancer
    Qingfei Wang, Ian H. Guldner, Samantha M. Golomb, Longhua Sun, Jack A. Harris, Xin Lü, Siyuan Zhang · 2019 · Nature Communications
65. Revealing dynamics of gene expression variability in cell state space
    Dominic Grün · 2019 · Nature Methods
66. Pathogenic Potential of Hic1-Expressing Cardiac Stromal Progenitors
    Soliman, Hesham, Paylor, Ben, Scott, R. Wilder, Lemos, Dario R., Chang, ChihKai, Arostegui, Martin, Low, Marcela, Lee, Christina, Fiore, Daniela, Braghetta, Paola et al. · 2020 · Cell Stem Cell
67. In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy
    Kolja Becker, Holger Klein, Eric Simon, Coralie Viollet, Christian Haslinger, Germán Leparc, Christian Schultheis, Victor N. Chong, Markus H. Kuehn, Francesc Fernández-Albert et al. · 2021 · Scientific Reports
68. Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation
    Laura Serrano-Ron, Pablo Pérez-García, Álvaro Sánchez-Corrionero, Inmaculada Gude, Javier Cabrera, Pui-Leng Ip, Kenneth D. Birnbaum, Miguel Á. Moreno-Risueno · 2021 · Molecular Plant
69. Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations
    Zhao-Zhe Hao, Jia-Ru Wei, Dongchang Xiao, Rui-Feng Liu, Nana Xu, Lei Tang, Meng-Hung Huang, Yu-Hui Shen, Chang-Sheng Xing, Wanjing Huang et al. · 2022 · Nature Neuroscience
70. Microfluidics for Neuronal Cell and Circuit Engineering
    Rouhollah Habibey, Jesús Eduardo Rojo Arias, Johannes Striebel, Volker Busskamp · 2022 · Chemical Reviews
71. Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation
    Milena Petkova, Marle Kraft, Simon Stritt, Inés Martínez‐Corral, Henrik Ortsäter, Ying Sun, Michael Vanlandewijck, Bojana Jakic, Eulàlia Baselga, Sandra D. Castillo et al. · 2023 · The Journal of Experimental Medicine
72. Transcription factor PagMYB31 positively regulates cambium activity and negatively regulates xylem development in poplar
    Yanhui Zhang, Song Chen, Ling‐Hua Xu, Shimin Chu, Xiaojing Yan, Lanying Lin, Jia‐Long Wen, Bo Zheng, Su Chen, Quanzi Li · 2024 · The Plant Cell
73. Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy
    Camelia Y. J. Quek, Aditya Pratapa, Xinyu Bai, Ghamdan Al‐Eryani, Inês Pires da Silva, Aaron T. Mayer, Nenad Bartoniček, Kate Harvey, Nigel Gordon Maher, Jordan W. Conway et al. · 2024 · Cell Reports
74. Systems Immunology: Learning the Rules of the Immune System
    Alexandra–Chloé Villani, Siranush Sarkizova, Nir Hacohen · 2018 · Annual Review of Immunology
75. Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation
    Jonathan S. Packer, Cole Trapnell · 2018 · Trends in Genetics
76. Single-cell transcriptome-based multilayer network biomarker for predicting prognosis and therapeutic response of gliomas
    Ji Zhang, Meige Guan, Qianliang Wang, Jiajun Zhang, Tianshou Zhou, Xiaoqiang Sun · 2019 · Briefings in Bioinformatics
77. The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution
    Hong Li, Kenneth L. Jones, Joan E. Hooper, Trevor Williams · 2019 · Development
78. Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling
    Neha Shrestha, Tongyu Liu, Yewei Ji, Rachel B. Reinert, Mauricio Torres, Xin Li, Maria Zhang, Chih-Hang Anthony Tang, Chih‐Chi Andrew Hu, Chengyang Liu et al. · 2020 · Journal of Clinical Investigation
79. Tuft Cells Inhibit Pancreatic Tumorigenesis in Mice by Producing Prostaglandin D2
    Kathleen E. DelGiorno, Chi‐Yeh Chung, Vera Vavinskaya, H. Carlo Maurer, Sammy Weiser Novak, Nikki K. Lytle, Zhibo Ma, Rajshekhar R. Giraddi, Dezhen Wang, Linjing Fang et al. · 2020 · Gastroenterology
80. Inflammatory molecular endotypes of nasal polyps derived from White and Japanese populations
    Tsuguhisa Nakayama, Ivan T. Lee, Wei Le, Yasuhiro Tsunemi, Nicole A. Borchard, David Zarabanda, Sachi S. Dholakia, Philip A. Gall, Angela Yang, Dayoung Kim et al. · 2021 · Journal of Allergy and Clinical Immunology
81. NFkB ‐signaling promotes glial reactivity and suppresses Müller glia‐mediated neuron regeneration in the mammalian retina
    Isabella Palazzo, Levi J. Todd, Thanh V. Hoang, Thomas A. Reh, Seth Blackshaw, Andy J. Fischer · 2022 · Glia
82. TNF is a potential therapeutic target to suppress prostatic inflammation and hyperplasia in autoimmune disease
    Renee E. Vickman, LaTayia Aaron, Renyuan Zhang, Nadia A. Lanman, Brittany R. Lapin, Victoria Gil, Max Greenberg, Takeshi Sasaki, Gregory M. Cresswell, Meaghan Maureen Broman et al. · 2022 · Nature Communications
83. SIMBA: single-cell embedding along with features
    Huidong Chen, Jayoung Ryu, Michael E. Vinyard, Adam K. Lerer, Luca Pinello · 2023 · Nature Methods
84. Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer
    Antti Kiviaho, Sini K. Eerola, Heini M. L. Kallio, Maria K. Andersen, Miina Hoikka, Aliisa M. Tiihonen, Iida Salonen, Xander Spotbeen, Alexander Giesen, Charles T. A. Parker et al. · 2024 · Nature Communications
85. Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology
    Michael J. Ziller, Juan Alberto Ortega, Katharina A. Quinlan, David P. Santos, Hongcang Gu, Eric J. Martin, Christina Galonska, Ramona Pop, Susanne Maidl, Alba Di Pardo et al. · 2018 · Cell stem cell
86. The translational regulation of maternal mRNA s in time and space
    Cecilia Lanny Winata, Vladimir P. Korzh · 2018 · FEBS Letters
87. Tet inactivation disrupts YY1 binding and long-range chromatin interactions during embryonic heart development
    Shao-Hai Fang, Jia Li, Yang Xiao, Minjung Lee, Lei Guo, Wei Han, Tingting Li, Matthew C. Hill, Ting-Ting Hong, W. Mo et al. · 2019 · Nature Communications
88. Sampling time-dependent artifacts in single-cell genomics studies
    Ramon Massoni-Badosa, Giovanni Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Doménica Marchese, Javier Rodríguez‐Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal et al. · 2020 · Genome biology
89. Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala
    Timothy P. O’Leary, Kaitlin E. Sullivan, Lihua Wang, Jody Clements, Andrew L. Lemire, Mark S. Cembrowski · 2020 · eLife
90. Exploring intermediate cell states through the lens of single cells
    Adam L. MacLean, Tian Hong, Qing Hua Nie · 2018 · Current Opinion in Systems Biology
91. Personalized neoantigen vaccine combined with PD-1 blockade increases CD8+ tissue-resident memory T-cell infiltration in preclinical hepatocellular carcinoma models
    Hengkai Chen, Zhenli Li, Liman Qiu, Xiuqing Dong, Geng Chen, Yingjun Shi, Linsheng Cai, Wenhan Liu, Honghao Ye, Yang Zhou et al. · 2022 · Journal for ImmunoTherapy of Cancer
92. Differentiation trajectories and biofunctions of symbiotic and un-symbiotic fate cells in root nodules of Medicago truncatula
    Qinyi Ye, Fugui Zhu, Fanghao Sun, Tai-Cheng Wang, Jiale Wu, Peng Liu, Chen Shen, Jiangli Dong, Tao Wang · 2022 · Molecular Plant
93. Targeted alveolar regeneration with Frizzled-specific agonists
    Ahmad N. Nabhan, Joshua D. Webster, Jarrett Adams, Levi L. Blazer, Christine Everrett, Céline Eidenschenk, Alexander Arlantico, Isabel Fleming, Hans D. Brightbill, Paul J. Wolters et al. · 2023 · Cell
94. Super-enhancer RNA m6A promotes local chromatin accessibility and oncogene transcription in pancreatic ductal adenocarcinoma
    Rui Li, Hongzhe Zhao, Xudong Huang, Jialiang Zhang, Ruihong Bai, Lisha Zhuang, Shujuan Wen, Shaojia Wu, Quanbo Zhou, Mei Li et al. · 2023 · Nature Genetics
95. Integrated analysis of single cell transcriptomic data across conditions, technologies, and species
    Butler, Andrew, Satija, Rahul · 2017
96. Brainstem Organoids From Human Pluripotent Stem Cells
    Nobuyuki Eura, Takeshi K. Matsui, Joachim Luginbühl, Masaya Matsubayashi, Hitoki Nanaura, Tomo Shiota, Kaoru Kinugawa, Naohiko Iguchi, Takao Kiriyama, Canbin Zheng et al. · 2020 · Frontiers in Neuroscience
97. Single‐cell RNA sequencing redefines the mesenchymal cell landscape of mouse endometrium
    Phoebe M. Kirkwood, Douglas A Gibson, James R. Smith, John R. Wilson‐Kanamori, Olympia Kelepouri, Arantza Esnal‐Zufiaurre, Ross Dobie, Neil Cowan Henderson, Philippa T. K. Saunders · 2021 · The FASEB Journal
98. DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data
    Bobby Ranjan, Wenjie Sun, Jinyu Park, Kunal Mishra, Florian Schmidt, Ronald Xie, Fatemeh Alipour, Vipul Singhal, Ignasius Joanito, Mohammad Amin Honardoost et al. · 2021 · Nature Communications
99. Genetic, parental and lifestyle factors influence telomere length
    Sergio Andreu‐Sánchez, Geraldine Aubert, Aida Ripoll-Cladellas, Sandra Henkelman, Daria V. Zhernakova, Trishla Sinha, Alexander Kurilshikov, María Carmen Cénit, Marc Jan Bonder, Lifelines Cohort Study et al. · 2022 · Communications Biology
100. Molecular subtypes of ALS are associated with differences in patient prognosis
     Jarrett Eshima, Samantha A. O’Connor, Ethan Marschall, Robert P. Bowser, Christopher L. Plaisier, Barbara S. Smith · 2023 · Nature Communications