[HTML][HTML] Mapping the transcriptome: Realizing the full potential of spatial data analysis

E Zormpas, R Queen, A Comber, SJ Cockell - Cell, 2023 - cell.com
RNA sequencing in situ allows for whole-transcriptome characterization at high resolution,
while retaining spatial information. These data present an analytical challenge for …

[HTML][HTML] Systems immunology spanning tumors, lymph nodes, and periphery

DN Sidiropoulos, WJ Ho, EM Jaffee, LT Kagohara… - Cell Reports …, 2023 - cell.com
The immune system defines a complex network of tissues and cell types that orchestrate
responses across the body in a dynamic manner. The local and systemic interactions …

[HTML][HTML] Spatial maps of hepatocellular carcinoma transcriptomes reveal spatial expression patterns in tumor immune microenvironment

Y Wang, S Yuan, H Jiang, Z Li, H Yin, J Tan, Z Dai… - Theranostics, 2022 - ncbi.nlm.nih.gov
Rationale: Hepatocellular carcinoma (HCC) is a highly heterogeneous and malignant
disease with the complex immune microenvironment, which ultimately influence clinic …

[HTML][HTML] CT-based radiomic nomogram for preoperative prediction of DNA mismatch repair deficiency in gastric cancer

Q Zeng, Y Zhu, L Li, Z Feng, X Shu, A Wu, L Luo… - Frontiers in …, 2022 - frontiersin.org
Background DNA mismatch repair (MMR) deficiency has attracted considerable attention as
a predictor of the immunotherapy efficacy of solid tumors, including gastric cancer. We …

[HTML][HTML] SRT-Server: powering the analysis of spatial transcriptomic data

S Yang, X Zhou - Genome Medicine, 2024 - Springer
Background Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set
of technologies that enable the measurement of gene expression in tissue while retaining …

[HTML][HTML] Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models

OE Ospina, AC Soupir, R Manjarres-Betancur… - Scientific Reports, 2024 - nature.com
Spatial transcriptomics (ST) assays represent a revolution in how the architecture of tissues
is studied by allowing for the exploration of cells in their spatial context. A common element …

[HTML][HTML] Spatial transcriptomics analysis identifies a tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease

H Alhaddad, OE Ospina, ML Khaled, Y Ren… - Cell Reports …, 2024 - cell.com
Leptomeningeal disease (LMD) remains a rapidly lethal complication for late-stage
melanoma patients. Here, we characterize the tumor microenvironment of LMD and patient …

A primer on preprocessing, visualization, clustering, and phenotyping of barcode-based spatial transcriptomics data

O Ospina, A Soupir, BL Fridley - Statistical Genomics, 2023 - Springer
Recent developments in spatially resolved transcriptomics (ST) have resulted in a large
number of studies characterizing the architecture of tissues, the spatial distribution of cell …

Spatial RNA sequencing methods show high resolution of single cell in cancer metastasis and the formation of tumor microenvironment

Y Zheng, X Yang - Bioscience Reports, 2023 - portlandpress.com
Cancer metastasis often leads to death and therapeutic resistance. This process involves
the participation of a variety of cell components, especially cellular and intercellular …

[HTML][HTML] Spatial transcriptomics analysis identifies a unique tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease

H Alhaddad, OE Ospina, ML Khaled, Y Ren, P Forsyth… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Leptomeningeal disease (LMD) remains a rapidly lethal complication for late-stage
melanoma patients. The inaccessible nature of the disease site and lack of understanding of …