Mapping human cell phenotypes to genotypes with single-cell genomics
JG Camp, R Platt, B Treutlein - Science, 2019 - science.org
The cumulative activity of all of the body's cells, with their myriad interactions, life histories,
and environmental experiences, gives rise to a condition that is distinctly human and specific …
and environmental experiences, gives rise to a condition that is distinctly human and specific …
[HTML][HTML] The covariance environment defines cellular niches for spatial inference
A key challenge of analyzing data from high-resolution spatial profiling technologies is to
suitably represent the features of cellular neighborhoods or niches. Here we introduce the …
suitably represent the features of cellular neighborhoods or niches. Here we introduce the …
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements
Spatial studies of transcriptome provide biologists with gene expression maps of
heterogeneous and complex tissues. However, most experimental protocols for spatial …
heterogeneous and complex tissues. However, most experimental protocols for spatial …
[HTML][HTML] SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and technologies
Properly integrating spatially resolved transcriptomics (SRT) generated from different
batches into a unified gene-spatial coordinate system could enable the construction of a …
batches into a unified gene-spatial coordinate system could enable the construction of a …
[HTML][HTML] Advances and challenges in spatial transcriptomics for developmental biology
K Choe, U Pak, Y Pang, W Hao, X Yang - Biomolecules, 2023 - mdpi.com
Development from single cells to multicellular tissues and organs involves more than just the
exact replication of cells, which is known as differentiation. The primary focus of research …
exact replication of cells, which is known as differentiation. The primary focus of research …
[HTML][HTML] Multiplex bioimaging of single-cell spatial profiles for precision cancer diagnostics and therapeutics
Cancers exhibit functional and structural diversity in distinct patients. In this mass, normal
and malignant cells create tumor microenvironment that is heterogeneous among patients. A …
and malignant cells create tumor microenvironment that is heterogeneous among patients. A …
Clustering spatial transcriptomics data
Motivation Recent advancements in fluorescence in situ hybridization (FISH) techniques
enable them to concurrently obtain information on the location and gene expression of …
enable them to concurrently obtain information on the location and gene expression of …
[HTML][HTML] Cerebral organoids as tools to identify the developmental roots of autism
Some autism spectrum disorders (ASD) likely arise as a result of abnormalities during early
embryonic development of the brain. Studying human embryonic brain development directly …
embryonic development of the brain. Studying human embryonic brain development directly …
[HTML][HTML] PROST: quantitative identification of spatially variable genes and domain detection in spatial transcriptomics
Y Liang, G Shi, R Cai, Y Yuan, Z Xie, L Yu… - Nature …, 2024 - nature.com
Computational methods have been proposed to leverage spatially resolved transcriptomic
data, pinpointing genes with spatial expression patterns and delineating tissue domains …
data, pinpointing genes with spatial expression patterns and delineating tissue domains …
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
SpatialExperiment is a new data infrastructure for storing and accessing spatially-resolved
transcriptomics data, implemented within the R/Bioconductor framework, which provides …
transcriptomics data, implemented within the R/Bioconductor framework, which provides …