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iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.
PLoS Comput Biol
October 2024
Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America.
Public gene expression databases are a rapidly expanding resource of organism responses to diverse perturbations, presenting both an opportunity and a challenge for bioinformatics workflows to extract actionable knowledge of transcription regulatory network function. Here, we introduce a five-step computational pipeline, called iModulonMiner, to compile, process, curate, analyze, and characterize the totality of RNA-seq data for a given organism or cell type. This workflow is centered around the data-driven computation of co-regulated gene sets using Independent Component Analysis, called iModulons, which have been shown to have broad applications.
View Article and Find Full Text PDFOn the informative value of community-based indoor radon values in relation to lung cancer.
Cancer Med
August 2024
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, University of Toronto, Toronto, Ontario, Canada.
Article Synopsis
- Radon is a radioactive gas that can increase the risk of lung cancer, and researchers studied this relationship using data from a large group of people from Europe, North America, and Israel.
- They found that lower levels of radon exposure (under 200 Bq/m) had a complex effect on lung cancer risk, with the lowest risk at an exposure of 58 Bq/m.
- The study showed that men and younger people (under 69) were more affected by radon exposure, and the results suggest that measuring radon exposure might not always follow the usual rules we think it does.
Publisher Correction: Understanding the genetic complexity of puberty timing across the allele frequency spectrum.
Nat Genet
August 2024
MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.
Understanding the genetic complexity of puberty timing across the allele frequency spectrum.
Nat Genet
July 2024
MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK.
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- Scientists looked at the timing of when girls start their periods (called menarche) and how it can affect their health later in life.
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Methylation patterns associated with C-reactive protein in racially and ethnically diverse populations.
Epigenetics
December 2024
Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Systemic low-grade inflammation is a feature of chronic disease. C-reactive protein (CRP) is a common biomarker of inflammation and used as an indicator of disease risk; however, the role of inflammation in disease is not completely understood. Methylation is an epigenetic modification in the DNA which plays a pivotal role in gene expression.
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