6,658 results found
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    An open-source computational and data resource to analyze digital maps of immunopeptidomes

    Etienne Caron et al.
    A community-based international effort generates standardized HLA allele-specific peptide assay libraries and enables the analysis of the human immunopeptidome by SWATH mass spectrometry.
    1. Computational and Systems Biology

    Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells

    Dana M King et al.
    The independent effects of transcription factor binding sites are large regardless of sequence context, but the interactions between sites are context dependent.
    1. Physics of Living Systems

    Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

    William T Ireland et al.
    A combination of massively parallel reporter assays and mass spectrometry uncovers the regulation of previously unexplored promoters across the Escherichia coli genome.
    1. Cancer Biology
    2. Genetics and Genomics

    Endogenous p53 expression in human and mouse is not regulated by its 3′UTR

    Sibylle Mitschka, Christine Mayr
    The endogenous 3′UTR does not regulate TP53 mRNA or protein level and the 3′UTR is repressive when used alone in reporters, but addition of the coding region has a dominant repressive effect.
    1. Physics of Living Systems

    Measuring cis-regulatory energetics in living cells using allelic manifolds

    Talitha L Forcier et al.
    A novel strategy is presented for quantitatively measuring protein-DNA and protein-protein interactions that regulate transcription in living cells.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Information content differentiates enhancers from silencers in mouse photoreceptors

    Ryan Z Friedman et al.
    Silencers and enhancers targeted by a common transcription factor in photoreceptors are distinguished by the number and diversity of binding transcription factor binding sites they contain.
    1. Developmental Biology

    Developmentally regulated Tcf7l2 splice variants mediate transcriptional repressor functions during eye formation

    Rodrigo M Young et al.
    The inclusion of a new alternatively spliced exon in Tcf7l2 can switch its function to repress transcription of Wnt target genes.
    1. Evolutionary Biology
    2. Genetics and Genomics

    A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae

    Pengyao Jiang et al.
    Certain mutational signatures vary in their contribution to genetic variation across the yeast phylogeny due to genetically encoded natural mutator phenotypes whose activity can be directly measured in the lab.
    1. Genetics and Genomics

    Genome-wide quantification of the effects of DNA methylation on human gene regulation

    Amanda J Lea et al.
    mSTARR-seq identifies regions of the genome where DNA methylation causally impacts gene expression, providing a map of which epigenetic marks may influence trait variation.
    1. Biochemistry and Chemical Biology

    Structural and functional characterization of G protein–coupled receptors with deep mutational scanning

    Eric M Jones et al.
    Linking deep mutational scanning with engineered transcriptional reporters in human cell lines establishes a generalizable method for exploring pharmacogenomics, structure, and function across broad classes of drug receptors.

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