Eleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
Orchestrating single-cell analysis with Bioconductor
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …
genome-wide features in individual cells. However, single-cell data present unique …
Mapping single-cell data to reference atlases by transfer learning
Large single-cell atlases are now routinely generated to serve as references for analysis of
smaller-scale studies. Yet learning from reference data is complicated by batch effects …
smaller-scale studies. Yet learning from reference data is complicated by batch effects …
Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin
Triple-negative breast cancer (TNBC) is an aggressive subtype associated with early
metastatic recurrence and worse patient outcomes. TNBC tumors express molecular …
metastatic recurrence and worse patient outcomes. TNBC tumors express molecular …
[HTML][HTML] Comprehensive integration of single-cell data
Single-cell transcriptomics has transformed our ability to characterize cell states, but deep
biological understanding requires more than a taxonomic listing of clusters. As new methods …
biological understanding requires more than a taxonomic listing of clusters. As new methods …
[HTML][HTML] Single-cell RNA-seq analysis of retinal development identifies NFI factors as regulating mitotic exit and late-born cell specification
Precise temporal control of gene expression in neuronal progenitors is necessary for correct
regulation of neurogenesis and cell fate specification. However, the cellular heterogeneity of …
regulation of neurogenesis and cell fate specification. However, the cellular heterogeneity of …
Single-cell transcriptomics in cancer: computational challenges and opportunities
Intratumor heterogeneity is a common characteristic across diverse cancer types and
presents challenges to current standards of treatment. Advancements in high-throughput …
presents challenges to current standards of treatment. Advancements in high-throughput …
Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development
The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution
analysis of cell-type diversity and transcriptional networks controlling cell-fate specification …
analysis of cell-type diversity and transcriptional networks controlling cell-fate specification …
SPACEL: deep learning-based characterization of spatial transcriptome architectures
H Xu, S Wang, M Fang, S Luo, C Chen, S Wan… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies detect mRNA expression in single cells/spots
while preserving their two-dimensional (2D) spatial coordinates, allowing researchers to …
while preserving their two-dimensional (2D) spatial coordinates, allowing researchers to …
Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing
K Morarach, A Mikhailova, V Knoflach, F Memic… - Nature …, 2021 - nature.com
Autonomous regulation of the intestine requires the combined activity of functionally distinct
neurons of the enteric nervous system (ENS). However, the variety of enteric neuron types …
neurons of the enteric nervous system (ENS). However, the variety of enteric neuron types …