RNA sequencing: the teenage years
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …
transcriptome-wide analysis of differential gene expression and differential splicing of …
[HTML][HTML] A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
[HTML][HTML] Systems vaccinology of the BNT162b2 mRNA vaccine in humans
The emergency use authorization of two mRNA vaccines in less than a year from the
emergence of SARS-CoV-2 represents a landmark in vaccinology,. Yet, how mRNA …
emergence of SARS-CoV-2 represents a landmark in vaccinology,. Yet, how mRNA …
Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes
J Humphrey, S Venkatesh, R Hasan, JT Herb… - Nature …, 2023 - nature.com
Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease
affecting motor neurons in the brain and spinal cord. In this study, we investigated gene …
affecting motor neurons in the brain and spinal cord. In this study, we investigated gene …
[HTML][HTML] Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes
Triple-negative breast cancer (TNBC) is a collection of biologically diverse cancers
characterized by distinct transcriptional patterns, biology, and immune composition. TNBCs …
characterized by distinct transcriptional patterns, biology, and immune composition. TNBCs …
[HTML][HTML] Generation of a broadly useful model for COVID-19 pathogenesis, vaccination, and treatment
Summary COVID-19, caused by SARS-CoV-2, is a virulent pneumonia, with> 4,000,000
confirmed cases worldwide and> 290,000 deaths as of May 15, 2020. It is critical that …
confirmed cases worldwide and> 290,000 deaths as of May 15, 2020. It is critical that …
[HTML][HTML] 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 …
[HTML][HTML] Gene expression based inference of cancer drug sensitivity
S Chawla, A Rockstroh, M Lehman, E Ratther… - Nature …, 2022 - nature.com
Inter and intra-tumoral heterogeneity are major stumbling blocks in the treatment of cancer
and are responsible for imparting differential drug responses in cancer patients. Recently …
and are responsible for imparting differential drug responses in cancer patients. Recently …
[HTML][HTML] New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
The advent of Next-Generation Sequencing (NGS) technologies has opened new
perspectives in deciphering the genetic mechanisms underlying complex diseases …
perspectives in deciphering the genetic mechanisms underlying complex diseases …
[HTML][HTML] Aging is associated with a systemic length-associated transcriptome imbalance
Aging is among the most important risk factors for morbidity and mortality. To contribute
toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data …
toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data …