Probabilistic cell typing enables fine mapping of closely related cell types in situ
Understanding the function of a tissue requires knowing the spatial organization of its
constituent cell types. In the cerebral cortex, single-cell RNA sequencing (scRNA-seq) has …
constituent cell types. In the cerebral cortex, single-cell RNA sequencing (scRNA-seq) has …
Spatial omics: Navigating to the golden era of cancer research
Y Wu, Y Cheng, X Wang, J Fan… - Clinical and Translational …, 2022 - Wiley Online Library
The idea that tumour microenvironment (TME) is organised in a spatial manner will not
surprise many cancer biologists; however, systematically capturing spatial architecture of …
surprise many cancer biologists; however, systematically capturing spatial architecture of …
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
D Gyllborg, CM Langseth, X Qian, E Choi… - Nucleic acids …, 2020 - academic.oup.com
Visualization of the transcriptome in situ has proven to be a valuable tool in exploring single-
cell RNA-sequencing data, providing an additional spatial dimension to investigate …
cell RNA-sequencing data, providing an additional spatial dimension to investigate …
Classification of midbrain dopamine neurons using single-cell gene expression profiling approaches
JF Poulin, Z Gaertner, OA Moreno-Ramos… - Trends in …, 2020 - cell.com
Dysfunctional dopamine (DA) signaling has been associated with a broad spectrum of
neuropsychiatric disorders, prompting investigations into how midbrain DA neuron …
neuropsychiatric disorders, prompting investigations into how midbrain DA neuron …
A curated database reveals trends in single-cell transcriptomics
The more than 1000 single-cell transcriptomics studies that have been published to date
constitute a valuable and vast resource for biological discovery. While various 'atlas' projects …
constitute a valuable and vast resource for biological discovery. While various 'atlas' projects …
Spatial transcriptomics for profiling the tropism of viral vectors in tissues
A barrier to advancing engineered adeno-associated viral vectors (AAVs) for precision
access to cell subtypes is a lack of high-throughput, high-resolution assays to characterize in …
access to cell subtypes is a lack of high-throughput, high-resolution assays to characterize in …
UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization
AR Kriebel, JD Welch - Nature communications, 2022 - nature.com
Single-cell genomic technologies provide an unprecedented opportunity to define molecular
cell types in a data-driven fashion, but present unique data integration challenges. Many …
cell types in a data-driven fashion, but present unique data integration challenges. Many …
BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies
Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often
collected from multiple tissue sections. Here, we present a computational method, BASS …
collected from multiple tissue sections. Here, we present a computational method, BASS …
Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application
Alzheimer's disease (AD) is the most common form of dementia, characterized by
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …
SpaGE: spatial gene enhancement using scRNA-seq
Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of
biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome …
biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome …