Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

Cited by (287)

Items 101–200 of 287

1. Spatial genomics: mapping human steatotic liver disease
   Kylie P. Matchett, Jasmin Paris, Sarah Amalia Teichmann, Neil Cowan Henderson · 2024 · Nature Reviews Gastroenterology & Hepatology
2. Experience and the ever‐changing brain: What the transcriptome can reveal
   Todd G. Rubin, Jason D. Gray, Bruce S. McEwen · 2014 · BioEssays
3. Single-cell analysis: Advances and future perspectives
   Emir Hodzic · 2016 · Bosnian Journal of Basic Medical Sciences
4. Noninvasive Strategy Based on Real-Time in Vivo Cataluminescence Monitoring for Clinical Breath Analysis
   Runkun Zhang, Wanting Huang, Gongke Li · 2017 · Analytical Chemistry
5. Computational Tools for Stem Cell Biology
   Qin Bian, Patrick Cahan · 2016 · Trends in biotechnology
6. Integrating Imaging and Omics: Computational Methods and Challenges
   Jean-Karim Hèriché, Stephanie Alexander, Jan Ellenberg · 2019 · Annual Review of Biomedical Data Science
7. Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition
   Satoi Nagasawa, Yukie Kashima, Ayako Suzuki, Yutaka Suzuki · 2021 · Inflammation and Regeneration
8. NeuroSystematics and Periodic System of Neurons: Model vs Reference Species at Single-Cell Resolution
   Leonid L. Moroz · 2018 · ACS Chemical Neuroscience
9. Spatial molecular profiling: platforms, applications and analysis tools
   Minzhe Zhang, Thomas Y. Sheffield, Xiaowei Zhan, Qiwei Li, Donghan M. Yang, Yunguan Wang, Shidan Wang, Yang Xie, Tao Wang, Guanghua Xiao · 2020 · Briefings in Bioinformatics
10. Genome annotation: From human genetics to biodiversity genomics
    Roderic Guigó · 2023 · Cell Genomics
11. Single Cell Analysis: From Technology to Biology and Medicine
    Xinghua Pan · 2014 · Single Cell Biology
12. Quantitative approaches for investigating the spatial context of gene expression
    Je Hyuk Lee · 2016 · WIREs Systems Biology and Medicine
13. Efficient Synthesis of Light‐Triggered Circular Antisense Oligonucleotides Targeting Cellular Protein Expression
    Linlin Yang, Hyun Bum Kim, Jai‐Yoon Sul · 2018 · ChemBioChem
14. Integrating single-cell RNA-Seq with spatial transcriptomics in pancreatic ductal adenocarcinoma using multimodal intersection analysis
    Reuben Moncada, Florian Wagner, Marta Chiodin, Joseph C. Devlin, Maayan Baron, Cristina H. Hajdu, Diane M. Simeone, Itai Yanai · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
15. Multiplexed laser particles for spatially resolved single-cell analysis
    Sheldon J. J. Kwok, Nicola Martino, Paul H. Dannenberg, Seok Hyun Yun · 2019 · Light Science & Applications
16. A bead-based microfluidic approach to integrated single-cell gene expression analysis by quantitative RT-PCR
    Hao Ran Sun, Tim Olsen, Jing Zhu, Jianguo Tao, Brian Ponnaiya, Sally A. Amundson, David J. Brenner, Qiao Lin · 2014 · RSC Advances
17. Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapy
    Junsha An, Yajie Lu, Yuxi Chen, Yuling Chen, Zhaokai Zhou, Jianping Chen, Cheng Yun Peng, Ruizhen Huang, Fu Peng · 2024 · Frontiers in Immunology
18. An Overview of Single-Cell Isolation Techniques
    Qudsia Zeb, Ce Wang, Sarfraz Shafiq, Liangyu Liu · 2019 · Elsevier eBooks
19. Recent advances in mammalian reproductive biology
    Lu Wen, Qiang Liu, Jing-Jing Xu, Xixi Liu, Chao-Yi Shi, Zuwei Yang, Yili Zhang, Hong Xu, Jiang Liu, Hui Yang et al. · 2019 · Science China Life Sciences
20. Spatial mapping of cancer tissues by OMICS technologies
    Rashid Ahmed, Robin Augustine, Enrique Valera, Anurup Ganguli, Nasrin Mesaeli, Irfan S. Ahmad, Rashid Bashir, Anwarul Hasan · 2021 · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer
21. A practical guide to spatial transcriptomics
    Lukáš Valihrach, Daniel Žucha, Pavel Abaffy, Mikael Kubista · 2024 · Molecular Aspects of Medicine
22. Global and targeted approaches to single-cell transcriptome characterization
    Aleksandra A. Kolodziejczyk, Tapio Lönnberg · 2017 · Briefings in Functional Genomics
23. DNA Computing: NOT Logic Gates See the Light
    Cole Emanuelson, Anirban Bardhan, Alexander Deiters · 2021 · ACS Synthetic Biology
24. Spatial transcriptomics: recent developments and insights in respiratory research
    Wenjia Wang, Liuxi Chu, Liyong He, Ming‐Jing Zhang, Kaitong Dang, Chen Gao, Qinyu Ge, Zhouguang Wang, Xiangwei Zhao · 2023 · Military Medical Research
25. The Boechera Genus as a Resource for Apomixis Research
    Vladimir B. Brukhin, Jaroslaw V. Osadtchiy, Ana Marcela Florez‐Rueda, Dmitry Smetanin, Evgeny A. Bakin, Margarida Sofia Nobre, Ueli Grossniklaus · 2019 · Frontiers in Plant Science
26. Single cell sequencing approaches for complex biological systems
    Timour Baslan, James B Hicks · 2014 · Current Opinion in Genetics & Development
27. Precision toxicology based on single cell sequencing: an evolving trend in toxicological evaluations and mechanism exploration
    Boyang Zhang, Kunlun Huang, Liye Zhu, Yunbo Luo, Wentao Xu · 2017 · Archives of Toxicology
28. Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies
    Qiao Rui Xing, Nadia Omega Cipta, Kiyofumi Hamashima, Yih‐Cherng Liou, Cheng-Gee Koh, Yuin‐Han Loh · 2020 · Frontiers in Genetics
29. Cellular Deconstruction: Finding Meaning in Individual Cell Variation
    James H. Eberwine, Junhyong Kim · 2015 · Trends in Cell Biology
30. New Methods in Tissue Engineering: Improved Models for Viral Infection
    Vyas Ramanan, Margaret A. Scull, Timothy Patrick Sheahan, Charles M. Rice, Sangeeta N. Bhatia · 2014 · Annual Review of Virology
31. Technical Advances in Single-Cell RNA Sequencing and Applications in Normal and Malignant Hematopoiesis
    Xiangtao Huang, Xi Li, Peizhong Qin, Yao Zhu, Shuangnian Xu, Jieping Chen · 2018 · Frontiers in Oncology
32. In Situ Transcriptome Accessibility Sequencing (INSTA-seq)
    Daniel Fürth, Victor Hatini, Je Hyuk Lee · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
33. Development and application of transcriptomics technologies in plant science
    Han Wang, Yueting Xu, Zhizhong Zhang, Guoping Zhang, Cong Tan, Lingzhen Ye · 2024 · Crop Design
34. Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis
    Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Malavika Lingeswaran, Jeewan Ram Vishnoi, Puneet Pareek, Sanjeev Misra, Praveen Sharma · 2019 · Indian Journal of Clinical Biochemistry
35. Correlated gene modules uncovered by high-precision single-cell transcriptomics
    Alec R. Chapman, David F. Lee, Wenting Cai, Wenping Ma, Xiang Li, Wenjie Sun, Xiaoliang Sunney Xie · 2022 · Proceedings of the National Academy of Sciences
36. Integrated single cell data analysis reveals cell specific networks and novel coactivation markers
    Shila Ghazanfar, Adam J Bisogni, John T. Ormerod, David Ming Lin, Jean Yee Hwa Yang · 2016 · BMC Systems Biology
37. The Power of Single‐Cell Analysis for the Study of Liver Pathobiology
    Angela Chu, Joel D. Schilling, Kevin R. King, Ariel E. Feldstein · 2020 · Hepatology
38. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
    Jovan Tanevski, Thin Nguyen, Buu Minh Thanh Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu et al. · 2020 · Life Science Alliance
39. Single-cell RNA Sequencing in Immunology
    Yirui Cao, Yue Qiu, Guo-Wei Tu, Cheng Yang · 2020 · Current Genomics
40. Progress and Clinical Application of Single-Cell Transcriptional Sequencing Technology in Cancer Research
    Jian Liu, Tianmin Xu, Yuemei Jin, Bingyu Huang, Yan Zhang · 2021 · Frontiers in Oncology
41. Live single-cell laser tag
    Loïc Binan, Javier Mazzaferri, Karine Choquet · 2016 · Nature Communications
42. Optimal Destabilization of DNA Double Strands by Single‐Nucleobase Caging
    Patrick Seyfried, Marcel Heinz, György Pintér et al. · 2018 · Chemistry - A European Journal
43. Revealing allele-specific gene expression by single-cell transcriptomics
    Julio Aguila Benitez, Shangli Cheng, Qiaolin Deng · 2017 · The International Journal of Biochemistry & Cell Biology
44. Temporal and spatial omics technologies for 4D profiling
    David E. Reynolds, Yoon Ho Roh, Daniel Oh, Phoebe Vallapureddy, Rong Fan, Jina Ko · 2025 · Nature Methods
45. Identification of mi RNA s involved in DRG neurite outgrowth and their putative targets
    Dario Motti, Jessica K. Lerch, Matt C. Danzi, J. Gans, Frank Kuo, Tatiana I. Slepak, John L. Bixby, Vance Lemmon · 2017 · FEBS Letters
46. Single-Neuron RNA Modification Analysis by Mass Spectrometry: Characterizing RNA Modification Patterns and Dynamics with Single-Cell Resolution
    Kevin D. Clark, Stanislav S. Rubakhin, Jonathan V. Sweedler · 2021 · Analytical Chemistry
47. Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq
    TaeHyun Kim, Chae‐Seok Lim, Bong‐Kiun Kaang · 2015 · BMB Reports
48. Untangling Alzheimer’s disease with spatial multi-omics: a brief review
    Cody R. Marshall, Melissa A. Farrow, Katerina V. Djambazova, Jeffrey M. Spraggins · 2023 · Frontiers in Aging Neuroscience
49. Unravelling tumour spatiotemporal heterogeneity using spatial multimodal data
    Chunman Zuo, Junchao Zhu, Jiawei Zou, Luonan Chen · 2025 · Clinical and Translational Medicine
50. Spatial transcriptomics: new dimension of understanding biological complexity
    Zhuxia Li, Guangdun Peng · 2022 · Biophysics Reports
51. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight
    Eliah G. Overbey, Saswati Das, Henry Cope, Pedro Madrigal, Žaneta Andrusivová, Solène Frapard, Rebecca Klotz, Daniela Bezdan, Anjali E. Gupta, Ryan T. Scott et al. · 2022 · Cell Reports Methods
52. Application of spatial transcriptome technologies to neurological diseases
    Dongshan Ya, Yingmei Zhang, Qi Cui, Yanlin Jiang, Jiaxin Yang, Ning Tian, Wenjing Xiang, Xiaohui Lin, Qinghua Li, Rujia Liao · 2023 · Frontiers in Cell and Developmental Biology
53. Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput
    James H. Eberwine, Junhyong Kim, Ron C. Anafi, Steven S. Brem, Maja Bućan, Stephen A. Fisher, M. Sean Grady, Amy E. Herr, David Issadore, Hyejoong Jeong et al. · 2023 · Nature Methods
54. New discoveries in the field of metabolism by applying single-cell and spatial omics
    Baocai Xie, Dengfeng Gao, Biqiang Zhou, Shi Chen, Lianrong Wang · 2023 · Journal of Pharmaceutical Analysis
55. Dosage compensation in the process of inactivation/reactivation during both germ cell development and early embryogenesis in mouse
    Xiaoyong Li, Zhiqiang Hu, Xuelin Yu, Chen Zhang, Bin Ma, Lin He, Chaochun Wei, Ji Wu · 2017 · Scientific Reports
56. Site-specific gene expression analysis using an automated tissue micro-dissection punching system
    Takuya Yoda, Masahito Hosokawa, Kiyofumi Takahashi, Chikako Sakanashi, Haruko Takeyama, Hideki Kambara · 2017 · Scientific Reports
57. The role of single-cell genomics in human genetics
    Varun K. A. Sreenivasan, Saranya Balachandran, Malte Spielmann · 2022 · Journal of Medical Genetics
58. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution
    Sarah M. Mangiameli, Haiqi Chen, Andrew Earl, Julie A. Dobkin, Daniel Lesman, Jason Daniel Buenrostro, Fei Chen · 2023 · Nature Methods
59. Seeing is believing: new methods for in situsingle-cell transcriptomics
    Gal Avital, Tamar Hashimshony, Itai Yanai · 2014 · Genome biology
60. Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA)
    Sean B. Yeldell, Brittani K. Ruble, Ivan J. Dmochowski · 2017 · Organic & Biomolecular Chemistry
61. Dissecting stem cell differentiation using single cell expression profiling
    Victoria Moignard, Berthold Göttgens · 2016 · Current Opinion in Cell Biology
62. Conditionally Activated (“Caged”) Oligonucleotides
    Linlin Yang, Ivan J. Dmochowski · 2021 · Molecules
63. Single‐cell RNA sequencing: revealing human pre‐implantation development, pluripotency and germline development
    Sophie Petropoulos A, Sarita Panula, John Paul Schell, Fredrik Lanner · 2016 · Journal of Internal Medicine
64. Single‐Cell Transcriptomic Analysis
    Zhihong Zheng, Enguo Chen, Weiguo Lü, Gary Charles Mouradian, Matthew Robert Hodges, Mingyu Liang, Pengyuan Liu, Yan Lü · 2020 · Comprehensive physiology
65. Advances in Spatial Omics Technologies
    Tianxiao Hui, Jian Zhou, Muchen Yao, Ying Xie, Hu Zeng · 2025 · Small Methods
66. Fibroblasts in the tumor microenvironment: heterogeneity and dynamic interactions in tumor progression revealed by spatial transcriptomics
    Xiaoyu Ji, Xian Wu, Wei Sun, Hao Zhang · 2025 · Cellular Oncology
67. Single-cell sequencing and its applications in bladder cancer
    Wang Wei, Yuan Rong, Sanhe Liu, Chunxiu Yang, Erick Thokerunga, Diansheng Cui, Fubing Wang · 2022 · Expert Reviews in Molecular Medicine
68. Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing
    Peisen Zhao, Sudip Mondal, Chris Martin, Andrew DuPlissis, Shahab Chizari, Ke-Yue Ma, Rajani Maiya, Robert O. Messing, Ning Jenny Jiang, Adela Ben‐Yakar · 2023 · Nature Methods
69. Promise of spatially resolved omics for tumor research
    Yanhe Zhou, Xinyi Jiang, Xiangyi Wang, Jianpeng Huang, Tong Li, Hongtao Jin, Jiuming He · 2023 · Journal of Pharmaceutical Analysis
70. Next-Generation Sequencing-Based Spatial Transcriptomics: A Perspective from Barcoding Chemistry
    Weixiong Shi, Jing Zhang, Shanqing Huang, Qian Fan, Jiao Cao, Jun Zeng, Lingling Wu, Chaoyong James Yang · 2024 · JACS Au
71. The niche in single‐cell technologies
    Giacomo Donati · 2015 · Immunology and Cell Biology
72. Bridging scales: From cell biology to physiology using in situ single-cell technologies
    Maeve Patricia Nagle, Gabriela S. Tam, Evan Maltz, Zachary Hemminger, Roy Wollman · 2021 · Cell Systems
73. Mapping Gene Expression in the Spatial Dimension
    Yingwen Chen, Weizhou Qian, Li Lin, Linfeng Cai, Kun Yin, Shaowei Jiang, Jia Tao Song, Ray P. S. Han, Chaoyong James Yang · 2021 · Small Methods
74. Single cell RNA sequencing improves the next generation of approaches to AML treatment: challenges and perspectives
    Zahra Khosroabadi, Samaneh Azaryar, Hassan Dianat‐Moghadam, Zohreh Amoozgar, Mohammadreza Sharifi · 2025 · Molecular Medicine
75. Single neuron transcriptome analysis can reveal more than cell type classification
    Lise J. Harbom, William D. Chronister, Michael J. McConnell · 2016 · BioEssays
76. Application of Single-Cell Omics in Breast Cancer
    Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Malavika Lingeswaran, Jeewan Ram Vishnoi, Puneet Pareek, Praveen Sharma, Sanjeev Misra · 2019 · Elsevier eBooks
77. Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome
    Edward Saehong Oh, Richie Jeremian, Gabriel Oh, Daniel E. Groot, Miki Susic, KwangHo Lee, Kelly K. Foy, Peter W. Laird, Artūras Petronis, Viviane Labrie · 2017 · Scientific Reports
78. Bone mechanobiology in mice: toward single-cell in vivo mechanomics
    Ariane C. Scheuren, Esther Wehrle, Felicitas R. Flohr, Ralph Müller · 2017 · Biomechanics and Modeling in Mechanobiology
79. Visualization of cardiovascular development, physiology and disease at the single-cell level: Opportunities and future challenges
    Chen Yifan, Yang Fan, Jun Pu · 2020 · Journal of Molecular and Cellular Cardiology
80. Neuropsychiatric disorders: An immunological perspective
    Ernest Aw, Yingying Zhang, Esra Yalçın, U. Herrmann, Michael C. Carroll · 2021 · Advances in immunology
81. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology
    Sunaina Banerjee, Satyaghosh Maurya, Rahul Roy · 2018 · Journal of Biosciences
82. A journey to uncharted territory: new technical frontiers in studying tumor–stromal cell interactions
    Ian H. Guldner, Siyuan Zhang · 2014 · Integrative Biology
83. Photouncaged Sequence-specific Interstrand DNA Cross-Linking with Photolabile 4-oxo-enal-modified Oligonucleotides
    Jingjing Sun, Xinjing Tang · 2015 · Scientific Reports
84. Basic Research Advances on Pituitary Stem Cell Function and Regulation
    John P. Russell, Emily J. Lodge, Cynthia L. Andoniadou · 2018 · Neuroendocrinology
85. Correlated Gene Modules Uncovered by Single-Cell Transcriptomics with High Detectability and Accuracy
    Alec R. Chapman, David F. Lee, Wenting Cai, Wenping Ma, Xiang Li, Wenjie Sun, Xiaoliang Sunney Xie · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
86. Single-Cell Transcriptomic Characterization of Vertebrate Brain Composition, Development, and Function
    Bosiljka Tasic, Boaz P. Levi, Vilas Menon · 2017 · Springer eBooks
87. Photoactivatable Circular Caged Oligonucleotides for Transcriptome In Vivo Analysis (TIVA)
    Linlin Yang, Dora von Trentini, Hyun‐Bum Kim · 2021 · ChemPhotoChem
88. Accelerating a paradigm shift: The Common Fund Single Cell Analysis Program
    Ananda L. Roy, Richard Conroy, Jessica M. Smith, Yong Ming Yao, Andrea C. Beckel-Mitchener, James Melvin Anderson, Elizabeth L. Wilder · 2018 · Science Advances
89. Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics
    Marco Mignardi, Omer Ishaq, Xiaoyan Qian, Carolina Wählby · 2016 · Proceedings of the IEEE
90. The impact of single-cell genomics on the field of mycobacterial infection
    Inês Geraldes, Mónica Fernandes, Alexandra G. Fraga, Nuno Sampaio Osório · 2022 · Frontiers in Microbiology
91. Next‐generation spatial transcriptomics: unleashing the power to gear up translational oncology
    Nan Wang, Weifeng Hong, Yixing Wu, Zhe‐Sheng Chen, Minghua Bai, Weixin Wang, Ji Ye Zhu · 2024 · MedComm
92. Molecular tools for the characterization of seizure susceptibility in genetic rodent models of epilepsy
    José Ramón Bosque, Ricardo Gómez‐Nieto, Sebastián Hormigo, M. Javier Herrero-Turrión, María Elena Díaz-Casado, Consuelo Sancho, Dolores E. López · 2019 · Epilepsy & Behavior
93. Oligonucleotide Probe for Transcriptome in Vivo Analysis (TIVA) of Single Neurons with Minimal Background
    Sean B. Yeldell, Linlin Yang, Jaehee Lee, James H. Eberwine, Ivan J. Dmochowski · 2020 · ACS Chemical Biology
94. Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells
    Lauren A. Laboissonniere, Takuma Sonoda, Seul Ki Lee, Jeffrey M. Trimarchi, Tiffany M. Schmidt · 2017 · Journal of Visualized Experiments
95. RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
    Nicholas Owen, Mariya Moosajee · 2019 · Therapeutic Advances in Ophthalmology
96. The mechanisms shaping the single-cell transcriptional landscape
    Celia Pilar Martinez‐Jimenez, Duncan T. Odom · 2016 · Current Opinion in Genetics & Development
97. De Novo Gene Expression Reconstruction in Space
    Je Hyuk Lee · 2017 · Trends in Molecular Medicine
98. HDTD: analyzing multi-tissue gene expression data
    Anestis Touloumis, John C. Marioni, Simon Tavaré · 2016 · Bioinformatics
99. Live Cell Genomics: Cell-Specific Transcriptome Capture in Live Tissues and Cells
    Thomas J. Bell, James H. Eberwine · 2015 · Methods in molecular biology
100. Continuous collection and simultaneous detection of picoliter volume of nucleic acid samples using a mille-feuille probe
     Hidenori Ito, Motoki Tanaka, Yuanshu Zhou, Yuji Nashimoto, Yasufumi Takahashi, Kosuke Ino, Tomokazu Matsue, Hitoshi Shiku · 2016 · Analytical and Bioanalytical Chemistry