17 papers · ranked by Valyu relevance
Cameron G. Williams, Hyun Jae Lee, Takahiro Asatsuma, Roser Vento-Tormo + 1 more
'Roser Vento-Tormo' 'Ashraful Haque'] Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over the past decade, particularly in developmental biology, cancer, immunology, and neuroscience. Most commercially available scRNA-seq protocols require cells to be recovered intact and viable…
Linlin Zhang, Dongsheng Chen, Dongli Song, Xiaoxia Liu + 3 more
'Xun Xu' 'Xiangdong Wang'] The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with molecular alterations, defining in situ intercellular molecular communications and knowledge on spatiotemporal…
Boxiang Liu, Yanjun Li, Liang Zhang
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of spatial information. Spatial transcriptomics is a recent technological innovation…
Benjamin L. Walker, Zixuan Cang, Honglei Ren, Eric Bourgain-Chang + 1 more
'Qing Nie'] The rapid development of spatial transcriptomics (ST) techniques has allowed the measurement of transcriptional levels across many genes together with the spatial positions of cells. This has led to an explosion of interest in computational methods and techniques for harnessing both spatial and…
Teia Noel, Qingbo S. Wang, Anna Greka, Jamie L. Marshall
Spatial transcriptomic technologies capture genome-wide readouts across biological tissue space. Moreover, recent advances in this technology, including Slide-seqV2, have achieved spatial transcriptomic data collection at a near-single cell resolution. To-date, a repertoire of computational tools has been developed to…
Xiaoxia Liu, Yujia Jiang, Dongli Song, Linlin Zhang + 12 more
'Rui Hou' 'Yong Zhang' 'Jian Chen' 'Yunfeng Cheng' 'Longqi Liu' 'Xun Xu' 'Gang Chen' 'Duojiao Wu' 'Tianxiang Chen' 'Ao Chen' 'Xiangdong Wang'] Title: Abstract Spatial transcriptomics is considered as an important part of spatiotemporal molecular images to bridge molecular information with clinical images. Of those…
Dario Righelli, Lukas M Weber, Helena L Crowell, Brenda Pardo + 6 more
Spatially-resolved transcriptomics (SRT) refers to a new set of high-throughput technologies, which measure up to transcriptome-wide gene expression along with the spatial coordinates of the measurements. Technological platforms differ in terms of the number of measured genes (from hundreds to full transcriptome) and…
Jun Du, Yu-Chen Yang, Zhi-Jie An, Ming-Hui Zhang + 4 more
'Zou-Fang Huang' 'Ye Yuan' 'Jian Hou'] Spatial transcriptomics technologies developed in recent years can provide various information including tissue heterogeneity, which is fundamental in biological and medical research, and have been making significant breakthroughs. Single-cell RNA sequencing (scRNA-seq) cannot…
Zhiwei Fan, Yangyang Luo, Huifen Lu, Tiangang Wang + 4 more
'Weiling Zhao' 'Pora Kim' 'Xiaobo Zhou'] Title: Abstract In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location…
Yang Jin, Yuanli Zuo, Gang Li, Wenrong Liu + 5 more
'Xin Fu' 'Xiaojun Yao' 'Yong Peng'] Malignant tumors have increasing morbidity and high mortality, and their occurrence and development is a complicate process. The development of sequencing technologies enabled us to gain a better understanding of the underlying genetic and molecular mechanisms in tumors. In recent…
Quynh Nguyen, Lin Wei Tung, Bruce Lin, Raam Sivakumar + 11 more
Spatial transcriptomics has transformed our understanding of gene expression by preserving the spatial context within tissues. This review focuses on the application of spatial transcriptomics in human cardiac tissues, exploring current technologies with a focus on commercially available platforms. We also highlight…
Chase Holdener, Shaowen Jiang, Danica M. Sutherland, Kira A. Griswold + 3 more
The morbidity and mortality associated with viral diseases in plants, animals, and humans are significant concerns. Understanding how viruses cause disease and identifying the viral and host factors that determine the outcome of infection are essential to develop new antiviral therapeutics and strategies to induce…
Bin Duan, Shaoqi Chen, Xiaojie Cheng, Qi Liu
With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo, a tool for multi-slice spatial domain analysis, including modules for multi-slice spatial domain detection…
Hao Duan, Qingchen Zhang, Feifei Cui, Quan Zou + 2 more
'Jean Fan'] Spatial transcriptome technology can parse transcriptomic data at the spatial level to detect high-throughput gene expression and preserve information regarding the spatial structure of tissues. Identifying spatial domains, that is identifying regions with similarities in gene expression and histology, is…
Linbu Liao, Esha Madan, António M. Palma, Hyobin Kim + 10 more
'Praveen Bhoopathi' 'Robert Winn' 'Jose Trevino' 'Paul Fisher' 'Cord Herbert Brakebusch' 'Gahyun Kim' 'Junil Kim' 'Rajan Gogna' 'Kyoung Jae Won'] Background Understanding cellular heterogeneity within tissues hinges on knowledge of their spatial context. However, it is still challenging to accurately map cells to their…
Ce Chen, Yining Ge, Lingli Lu
Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information.…
Haoyu Wang, Peng Cheng, Juan Wang, Hongzhi Lv + 4 more
'Zhiyong Hou' 'Ren Xu' 'Wei Chen'] While bulk RNA sequencing and single-cell RNA sequencing have shed light on cellular heterogeneity and potential molecular mechanisms in the musculoskeletal system in both physiological and various pathological states, the spatial localization of cells and molecules and intercellular…