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Technical Advances and Applications of Spatial Transcriptomics [PDF]

, 2023
Transcriptomics is one of the largest areas of research in biological sciences. Aside from RNA expression levels, the significance of RNA spatial context has also been unveiled in the recent decade, playing a critical role in diverse biological processes,
Guohao Liang, Hong Yin, Fangyuan Ding, Ding, Fangyuan, Yin, Hong, Liang, Guohao   +5 more
core   +1 more source

Identifying spatial domain by adapting transcriptomics with histology through contrastive learning

, 2023
Recent advances in spatial transcriptomics have enabled measurements of gene expression at cell/spot resolution meanwhile retaining both the spatial information and the histology images of the tissues.
Yin, Rui, Luo, Mai, Yu, Weijiang, Pan, Zixiang, Chen, Jianing, Lu, Yutong, Zeng, Yuansong, Yang, Yuedong   +7 more
core   +1 more source

Introduction to Transcriptomics

, 2021
Slide deck for a presentation on transcriptomics, delivered on 25.06.2021 during a training session entitled 'Beginner's Guide to Bioinformatics,' organized by Helix Biogen Institute in ...
Ahmad, Umar
core   +1 more source

Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks

, 2022
The rapid development of spatial transcriptomics allows the measurement of RNA abundance at a high spatial resolution, making it possible to simultaneously profile gene expression, spatial locations of cells or spots, and the corresponding hematoxylin ...
Tang, Zhonghui, Li, Bingling, Yin, Rui, Wei, Zhuoyi, Yu, Weijiang, Lu, Yutong, Zeng, Yuansong, Yuan, Yuchen, Yang, Yuedong   +8 more
core   +1 more source

A unified pipeline for FISH spatial transcriptomics [PDF]

, 2023
High-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and its effects on cellular function.
Cisar, Cecilia, Ruffalo, Mathew, Benedict Paten, Nicholas Keener, Paten, Benedict, Cecilia Cisar, Mathew Ruffalo, Keener, Nicholas   +7 more
core   +1 more source

Effective Data Management and Spatial Analytics

, 2021
This webinar introduced the implementations of effective data management and spatial analytics by academic and industry leaders of the field, and discuss the directions for further enhancement through integration with a cloud-based platform for research ...
Spatial Data Lab
core   +1 more source

Statistical methods for spatial transcriptomics data [PDF]

Treballs finals del Màster en Matemàtica Avançada, Facultat de Matemàtiques, Universitat de Barcelona: Any: 2025. Director: Alejandra CabañaSpatial transcriptomics is a set of techniques that enables the quantification of gene expression within intact ...
Moles Seró, Pere
core   +4 more sources

Spatially aware dimension reduction for spatial transcriptomics [PDF]

, 2022
Spatial transcriptomics are a collection of genomic technologies that have enabled transcriptomic profiling on tissues with spatial localization information. Analyzing spatial transcriptomic data is computationally challenging, as the data collected from
Shang, Lulu, Zhou, Xiang
core   +1 more source

WEST is an ensemble method for spatial transcriptomics analysis

Cell Reports: Methods
Summary: Spatial transcriptomics is a groundbreaking technology, enabling simultaneous profiling of gene expression and spatial orientation within biological tissues.
Jiazhang Cai, Huimin Cheng, Shushan Wu, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma   +5 more
doaj   +1 more source

MUSTANG: Multi-sample spatial transcriptomics data analysis with cross-sample transcriptional similarity guidance

Patterns
Summary: Spatially resolved transcriptomics has revolutionized genome-scale transcriptomic profiling by providing high-resolution characterization of transcriptional patterns.
Seyednami Niyakan, Jianting Sheng, Yuliang Cao, Xiang Zhang, Zhan Xu, Ling Wu, Stephen T.C. Wong, Xiaoning Qian   +7 more
doaj   +1 more source