1,938 results found
    1. Cancer Biology

    Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays

    Konrad H Stopsack, Svitlana Tyekucheva ... Lorelei A Mucci
    Tissue microarrays, a high-throughout approach to quantifying biomarkers used in hundreds of cancer studies every year, are susceptible to batch effects that can alter results but that are readily addressable.
    1. Ecology
    2. Physics of Living Systems

    Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

    Amir Erez, Jaime G Lopez ... Ned S Wingreen
    Whereas theories of ecological diversity mostly consider continuously supplied nutrients, a seasonal model uncovers a general mechanism that controls diversity and reconciles conflicting experimental findings.
    1. Computational and Systems Biology

    Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets

    Marie Trussart, Charis E Teh ... Terence P Speed
    CytofRUV is a computational algorithm that effectively enables batch effect reduction in multiple CyTOF batches with an adaptable normalisation method and an R-Shiny application with diagnostics plots.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

    Anthony S Findley, Alan Monziani ... Francesca Luca
    Investigation of dynamic gene regulation across cell types and environments reveals new GxE regulatory loci that are important for disease.
    1. Physics of Living Systems

    A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies

    Zoran S Marinkovic, Clément Vulin ... Pascal Hersen
    Metabolic gradients underlie gene expression patterns within spatially controlled expanding 2D microbial colonies.
    1. Stem Cells and Regenerative Medicine

    A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids

    Henrik Renner, Martha Grabos ... Jan M Bruder
    Automated liquid handling, whole mount staining, and clearing allow unbiased 3D quantitation of cell markers in human neural organoids with diameters of up to 1 mm at the single-cell level.
    1. Chromosomes and Gene Expression
    2. Medicine

    Cardiovascular disease risk factors induce mesenchymal features and senescence in mouse cardiac endothelial cells

    Karthik Amudhala Hemanthakumar, Shentong Fang ... Riikka Kivelä
    Endothelial dysfunction due to cardiovascular disease risk factors explained by cardiac endothelial cell transcriptome remodelling.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

    Dylan Kotliar, Adrian Veres ... Pardis C Sabeti
    A novel algorithm, consensus non-negative matrix factorization (cNMF), accurately identifies gene expression programs underlying cell-type identity and cellular activities from single-cell RNA-Seq data.
    1. Developmental Biology
    2. Genetics and Genomics

    Constraint and divergence of global gene expression in the mammalian embryo

    Noah Spies, Cheryl L Smith ... Arend Sidow
    Embryonic gene expression is strongly influenced by maternal genetic variation and by embryonic variation that acts in cis but not in trans.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Single-cell analysis of the aged ovarian immune system reveals a shift towards adaptive immunity and attenuated cell function

    Tal Ben Yaakov, Tanya Wasserman ... Yonatan Savir
    The ovarian immune system ages while coping with the two main challenges of the aging ovary before menopause, the inflammatory stimulations due to repeated cycles and the increasing need for clearance of accumulating atretic follicles.

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