Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …
does not capture their spatial distribution nor reveal local networks of intercellular …
[HTML][HTML] Tumor microenvironment: barrier or opportunity towards effective cancer therapy
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …
[HTML][HTML] IOBR: multi-omics immuno-oncology biological research to decode tumor microenvironment and signatures
Recent advances in next-generation sequencing (NGS) technologies have triggered the
rapid accumulation of publicly available multi-omics datasets. The application of integrated …
rapid accumulation of publicly available multi-omics datasets. The application of integrated …
[HTML][HTML] Benchmarking of cell type deconvolution pipelines for transcriptomics data
F Avila Cobos, J Alquicira-Hernandez… - Nature …, 2020 - nature.com
Many computational methods have been developed to infer cell type proportions from bulk
transcriptomics data. However, an evaluation of the impact of data transformation, pre …
transcriptomics data. However, an evaluation of the impact of data transformation, pre …
ImmuCellAI: a unique method for comprehensive T‐cell subsets abundance prediction and its application in cancer immunotherapy
The distribution and abundance of immune cells, particularly T‐cell subsets, play pivotal
roles in cancer immunology and therapy. T cells have many subsets with specific function …
roles in cancer immunology and therapy. T cells have many subsets with specific function …
Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons
Major depressive disorder (MDD) has an enormous impact on global disease burden,
affecting millions of people worldwide and ranking as a leading cause of disability for almost …
affecting millions of people worldwide and ranking as a leading cause of disability for almost …
Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins
by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific …
by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific …
[PDF][PDF] RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types
The molecular characterization of immune subsets is important for designing effective
strategies to understand and treat diseases. We characterized 29 immune cell types within …
strategies to understand and treat diseases. We characterized 29 immune cell types within …
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
Spatially resolved gene expression profiles are key to understand tissue organization and
function. However, spatial transcriptomics (ST) profiling techniques lack single-cell …
function. However, spatial transcriptomics (ST) profiling techniques lack single-cell …
[HTML][HTML] SpatialDWLS: accurate deconvolution of spatial transcriptomic data
Recent development of spatial transcriptomic technologies has made it possible to
characterize cellular heterogeneity with spatial information. However, the technology often …
characterize cellular heterogeneity with spatial information. However, the technology often …