Publications by authors named "L Collado-Torres"
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigate splicing accuracy using RNA-sequencing data from >14k control samples and 40 human body sites, focusing on split reads partially mapping to known transcripts in annotation.
View Article and Find Full Text PDFArticle Synopsis
- - Maternal smoking during pregnancy has notable negative effects on the cognitive and behavioral development of offspring, with this study specifically comparing the impacts of nicotine and cigarette smoke on gene expression in developing brains.
- - Researchers found a significant number of differentially expressed genes (1,010 for nicotine and 4,165 for smoking) linked to prenatal exposure, indicating different neurodevelopmental pathways affected by each substance.
- - The findings suggest that while both prenatal nicotine exposure and maternal smoking have specific and overlapping effects on the developing brain, these effects are not replicated in the adult brain, highlighting developmental-stage sensitivity to smoke-related changes.
Article Synopsis
- Visium is a transcriptomics assay from 10x Genomics that struggles with overlapping tissue capture areas, needing better tools for combining data from multiple images effectively.
- A new R/Bioconductor package called visiumStitched has been developed to stitch these images together, allowing for more complex analysis while preserving data from overlapping areas.
- While visiumStitched simplifies the handling of multi-capture study designs, it does have some limitations regarding data accuracy when aligning with other reference atlases.
Article Synopsis
- The study investigates how neurodegenerative disorders, particularly Alzheimer's disease, affect brain microenvironments by analyzing brain tissue lesions associated with amyloid-β and hyperphosphorylated tau.
- Researchers used the advanced 10x Genomics Visium Spatial Proteogenomics platform to explore gene expression changes in post-mortem human brains, specifically in the inferior temporal cortex during late-stage Alzheimer's.
- The findings offer insights into molecular processes linked to brain pathology, provide a framework for analyzing spatial gene expression, and deliver accessible interactive resources for the scientific community to explore related datasets.
Article Synopsis
- Visium is a transcriptomics assay that allows researchers to analyze gene expression in tissue, but current software has limitations in merging more than two overlapping capture areas.* -
- A new R/Bioconductor package was developed to stitch images from overlapping capture areas and create visualizations, making it easier to analyze complex tissue structures without losing data.* -
- This solution enhances the flexibility of study designs involving multiple capture areas, paving the way for better spatial analysis while addressing issues with image alignment accuracy.*