6,470 results found
    1. Computational and Systems Biology
    2. Genetics and Genomics

    A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution

    Xu Zhou et al.
    Computational analysis of MNase-seq data reveals that alternatively positioned nucleosomes are prevalent in both yeast and human cells and create significant heterogeneity within cell populations.
    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. Chromosomes and Gene Expression

    Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution

    Shanaya Shital Shah et al.
    D-loops are critical intermediates in homologous recombination, and the novel D-loop mapping assay defines position, length, and distribution of D-loops with near base-pair resolution.
    1. Physics of Living Systems

    Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

    Zhi Qi et al.
    The ability of an enzyme called XPD helicase to unwind the double helix is influenced by the DNA sequence and the availability of energy.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA

    Natasha M O'Brown et al.
    An identical DNA base pair change has occurred in divergent sticklebacks to alter the expression of a major developmental gene controlling armor plates, thus providing a molecular link between particular enhancer changes, cell signaling, and repeated skeletal evolution in natural populations.
    1. Evolutionary Biology
    2. Neuroscience

    Metazoan evolution of glutamate receptors reveals unreported phylogenetic groups and divergent lineage-specific events

    David Ramos-Vicente et al.
    The animal phylogeny of glutamate receptors indicates that vertebrate types do not account for all receptor classes originated during evolution, neither are they the pinnacle of a linear evolutive process.
    1. Cancer Biology
    2. Computational and Systems Biology

    5-hydroxymethylcytosine marks regions with reduced mutation frequency in human DNA

    Marketa Tomkova et al.
    Different types of epigenetic DNA modifications affect the likelihood of cytosine mutations in cancer.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Stochastic processes constrain the within and between host evolution of influenza virus

    John T McCrone et al.
    An analysis of influenza viruses from naturally infected people suggests a tight transmission bottleneck and little positive selection within hosts.
    1. Neuroscience

    Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning

    Shinji Urata et al.
    A method of generating comprehensive maps of cochlear cells was created and enabled researchers to study characteristics of cellular damage in aged and noise-exposed inner ear.
    1. Chromosomes and Gene Expression

    A simple method for generating high-resolution maps of genome-wide protein binding

    Peter J Skene, Steven Henikoff
    Building on previous work (Skene et al., 2014), we show that a new ChIP-seq protocol provides superior resolution and ease of use at low sequence depth of coverage for generating genome-wide maps of protein binding.

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