Single-cell RNA-seq methods to interrogate virus-host interactions
The twenty-first century has seen the emergence of many epidemic and pandemic viruses,
with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate …
with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate …
Accurate feature selection improves single-cell RNA-seq cell clustering
Cell clustering is one of the most important and commonly performed tasks in single-cell
RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select …
RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select …
The shaky foundations of simulating single-cell RNA sequencing data
HL Crowell, SX Morillo Leonardo, C Soneson… - Genome Biology, 2023 - Springer
Background With the emergence of hundreds of single-cell RNA-sequencing (scRNA-seq)
datasets, the number of computational tools to analyze aspects of the generated data has …
datasets, the number of computational tools to analyze aspects of the generated data has …
Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
Background Single-cell RNA-sequencing (scRNA-seq) technologies and associated
analysis methods have rapidly developed in recent years. This includes preprocessing …
analysis methods have rapidly developed in recent years. This includes preprocessing …
Benchmarking cell-type clustering methods for spatially resolved transcriptomics data
Spatially resolved transcriptomics technologies enable the measurement of transcriptome
information while retaining the spatial context at the regional, cellular or sub-cellular level …
information while retaining the spatial context at the regional, cellular or sub-cellular level …
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Abstract We present pipeComp (https://github. com/plger/pipeComp), a flexible R framework
for pipeline comparison handling interactions between analysis steps and relying on multi …
for pipeline comparison handling interactions between analysis steps and relying on multi …
Accurately clustering single-cell RNA-seq data by capturing structural relations between cells through graph convolutional network
Recent advances in single-cell RNA sequencing (scRNA-seq) technologies provide a great
opportunity to study gene expression at cellular resolution, and the scRNA-seq data has …
opportunity to study gene expression at cellular resolution, and the scRNA-seq data has …
Single‐cell sequencing methodologies: from transcriptome to multi‐dimensional measurement
Y Chen, J Song, Q Ruan, X Zeng, L Wu, L Cai… - Small …, 2021 - Wiley Online Library
Cells are the basic building blocks of biological systems, with inherent unique molecular
features and development trajectories. The study of single cells facilitates in‐depth …
features and development trajectories. The study of single cells facilitates in‐depth …
[HTML][HTML] Cross-comparison of human iPSC motor neuron models of familial and sporadic ALS reveals early and convergent transcriptomic disease signatures
Induced pluripotent stem cell (iPSC)-derived neural cultures from amyotrophic lateral
sclerosis (ALS) patients can model disease phenotypes. However, heterogeneity arising …
sclerosis (ALS) patients can model disease phenotypes. However, heterogeneity arising …
[HTML][HTML] Decoding the mosaic of inflammatory bowel disease: Illuminating insights with single-cell RNA technology
L Liu, B Davidorf, P Dong, A Peng, Q Song… - Computational and …, 2024 - Elsevier
Inflammatory bowel diseases (IBD), comprising ulcerative colitis (UC) and Crohn's disease
(CD), are complex chronic inflammatory intestinal conditions with a multifaceted pathology …
(CD), are complex chronic inflammatory intestinal conditions with a multifaceted pathology …