Computational approaches and challenges in spatial transcriptomics
The development of spatial transcriptomics (ST) technologies has transformed genetic
research from a single-cell data level to a two-dimensional spatial coordinate system and …
research from a single-cell data level to a two-dimensional spatial coordinate system and …
[HTML][HTML] Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods
Abstract Analysis of differential gene expression from RNA-seq data has become a standard
for several research areas. The steps for the computational analysis include many data …
for several research areas. The steps for the computational analysis include many data …
Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans
A mysterious feature of Crohn's disease (CD) is the extra-intestinal manifestation of"
creeping fat"(CrF), defined as expansion of mesenteric adipose tissue around the inflamed …
creeping fat"(CrF), defined as expansion of mesenteric adipose tissue around the inflamed …
Single-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression
Glioblastoma (GBM) is an incurable primary malignant brain cancer hallmarked with a
substantial protumorigenic immune component. Knowledge of the GBM immune …
substantial protumorigenic immune component. Knowledge of the GBM immune …
Machine learning identifies candidates for drug repurposing in Alzheimer's disease
Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a large
amount of time and resources with largely negative results. Repurposing drugs already …
amount of time and resources with largely negative results. Repurposing drugs already …
Salmon provides fast and bias-aware quantification of transcript expression
We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA–
seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich …
seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich …
Scaling read aligners to hundreds of threads on general-purpose processors
B Langmead, C Wilks, V Antonescu, R Charles - Bioinformatics, 2019 - academic.oup.com
Motivation General-purpose processors can now contain many dozens of processor cores
and support hundreds of simultaneous threads of execution. To make best use of these …
and support hundreds of simultaneous threads of execution. To make best use of these …
Power analysis of single-cell RNA-sequencing experiments
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method
to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and …
to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and …
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis
Abstract RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies,
hundreds of analysis tools have been developed since it was debuted. Although recent …
hundreds of analysis tools have been developed since it was debuted. Although recent …
KEAP1/NFE2L2 Mutations Predict Lung Cancer Radiation Resistance That Can Be Targeted by Glutaminase Inhibition
Tumor genotyping is not routinely performed in localized non–small cell lung cancer
(NSCLC) due to lack of associations of mutations with outcome. Here, we analyze 232 …
(NSCLC) due to lack of associations of mutations with outcome. Here, we analyze 232 …