Search
Search Results
-
Comparative Methods for Demystifying Spatial Transcriptomics
Spatial Transcriptomics (ST), coined as the term for parallel RNA-Seq on cell populations ordered spatially on a histological tissue section, has...
-
Transcriptomics Analysis in the Study of Mycorrhizal Symbiosis in Orchids
In past decades, high-throughput transcriptome sequencing has been widely applied to explore the transcript control of the gene expression during the...
-
Integrated metabolomics and transcriptomics analysis highlight key pathways involved in the somatic embryogenesis of Darjeeling tea
BackgroundDarjeeling tea is a globally renowned beverage, which faces numerous obstacles in sexual reproduction, such as self-incompatibility, poor...
-
Gene panel selection for targeted spatial transcriptomics
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of...
-
Bento: a toolkit for subcellular analysis of spatial transcriptomics data
The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture,...
-
ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction
Imaging-based spatial transcriptomics techniques provide valuable spatial and gene expression information at single-cell resolution. However, their...
-
Scalable transcriptomics analysis with Dask: applications in data science and machine learning
BackgroundGene expression studies are an important tool in biological and biomedical research. The signal carried in expression profiles helps derive...
-
Harmonizing heterogeneous transcriptomics datasets for machine learning-based analysis to identify spaceflown murine liver-specific changes
NASA has employed high-throughput molecular assays to identify sub-cellular changes impacting human physiology during spaceflight. Machine learning...
-
Transcriptomics in Health and Disease
The study of transcriptomics is key to understanding complex diseases. This new edition will build on the foundation of the first edition while...
-
Evaluating spatially variable gene detection methods for spatial transcriptomics data
BackgroundThe identification of genes that vary across spatial domains in tissues and cells is an essential step for spatial transcriptomics data...
-
A single workflow for multi-species blood transcriptomics
BackgroundBlood transcriptomic analysis is widely used to provide a detailed picture of a physiological state with potential outcomes for...
-
Statistical and machine learning methods for spatially resolved transcriptomics data analysis
The recent advancement in spatial transcriptomics technology has enabled multiplexed profiling of cellular transcriptomes and spatial locations. As...
-
Transcriptomics and Proteomics
DNA is transcribed into RNA—the ensemble of The proteome is the ensemble of expressed proteins in a cell (cf. Fig. 14.1), and proteomics is the study...
-
Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape
Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate...
-
Benchmarking spatial clustering methods with spatially resolved transcriptomics data
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the scope of tissue physiology studies from cell-centroid to...
-
Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis
The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange...
-
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the...
-
Profiling human brain vascular cells using single-cell transcriptomics and organoids
Angiogenesis and neurogenesis are functionally interconnected during brain development. However, the study of the vasculature has trailed other brain...
-
Comparative Analysis of Packages and Algorithms for the Analysis of Spatially Resolved Transcriptomics Data
The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological...
-
Detection of allele-specific expression in spatial transcriptomics with spASE
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the...
