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    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. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver

    Bryan J Matthews, David J Waxman
    Certain types of 3D chromatin loops are easy to predict from existing or easily obtainable 2D information, which benefits gene expression studies in tissues/cells/organisms without extensive pre-existing 3D information.
    1. Neuroscience

    Real-time classification of experience-related ensemble spiking patterns for closed-loop applications

    Davide Ciliberti et al.
    A brain–computer interface for real-time identification of transient neural activity patterns enables causal inference of the role of these patterns in cognition through closed-loop manipulation.
    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

    Augusto Berrocal et al.
    Live quantitative monitoring of transcriptional bursting reveals that enhancers responding to different regulators use the same kinetic strategy to produce a complex composite pattern of developmental expression.
    1. Cell Biology
    2. Computational and Systems Biology

    Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics

    Saskia MA de Man et al.
    Genome editing, advanced live-cell microscopy, and computational modeling were combined to measure WNT/CTNNB1 signaling parameters at the single molecule level, revealing critical regulatory nodes in this important signal transduction pathway.
    1. Computational and Systems Biology
    2. Neuroscience

    Uncovering the computational mechanisms underlying many-alternative choice

    Armin W Thomas et al.
    A comparison of different computational models reveals that looking behavior, during value-based choices from 9, 16, 25, or 36 snack foods, actively influences the subjective values of the available alternatives.
    1. Neuroscience

    Using the past to estimate sensory uncertainty

    Ulrik Beierholm et al.
    For perceptual inference, human observers do not estimate sensory uncertainty instantaneously from the current sensory signals alone, but by combining past and current sensory inputs consistent with a Bayesian learner.
    1. Developmental Biology

    Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

    Yifu Ding et al.
    X-ray histotomography produces the first 3-dimensional images with the combined submicron resolution, centimeter fields-of-view, soft-tissue contrast, and potential throughput to enable quantitative, histopathological and centimeter-scale phenotyping for whole-organism phenomics.
    1. Biochemistry and Chemical Biology

    Identification of an allosteric binding site on the human glycine transporter, GlyT2, for bioactive lipid analgesics

    Shannon N Mostyn et al.
    Identification of how bioactive lipids bind and inhibit glycine transporters has the potential to be exploited in the development of a new class of analgesics for chronic pain.
    1. Neuroscience

    Temporally delayed linear modelling (TDLM) measures replay in both animals and humans

    Yunzhe Liu et al.
    Temporally delayed linear modelling provides a domain-general linear framework for sequence detection and statistical testing, and is able to detect replays in both human neuroimaging and animal electrophysiology.