Microbiome analyses of blood and tissues suggest cancer diagnostic approach | Nature
Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions, researchers re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer.
A benchmark of algorithms for the analysis of pooled CRISPR screens | Genome Biology
Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, the authors provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens.
Mass-spectrometry-based draft of the Arabidopsis proteome | Nature
Plants are essential for life and are extremely diverse organisms with unique molecular capabilities. Here researchers present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. The analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites).