Browse our Research Advances

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    1. Chromosomes and Gene Expression

    DNA methylation-environment interactions in the human genome

    Rachel A Johnston, Katherine A Aracena ... Jenny Tung
    A massively parallel reporter assay, mSTARR-seq, reveals widespread DNA methylation-environment interactions across the genome, prioritizing CpG sites identified in epigenome-wide association studies that may be most relevant to biological embedding.
    1. Epidemiology and Global Health

    Region of Attainable Redaction, an extension of Ellipse of Insignificance analysis for gauging impacts of data redaction in dichotomous outcome trials

    David Robert Grimes
    Region of Attainable Redaction analysis allows scientists to estimate the potential impacts of redaction in biomedical science, helping to uncover potentially spurious or non-robust results.
    1. Neuroscience

    Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits

    Diek W Wheeler, Jeffrey D Kopsick ... Giorgio A Ascoli
    Hippocampome.org v1.0, a foundational classification system of hippocampal neuron types, has evolved into 2.0, which recenters the focus on new functionality to build real-scale, biologically detailed, data-driven computational simulations.
    1. Developmental Biology
    2. Physics of Living Systems

    Core PCP mutations affect short-time mechanical properties but not tissue morphogenesis in the Drosophila pupal wing

    Romina Piscitello-Gómez, Franz S Gruber ... Suzanne Eaton
    Quantitative analysis of cell dynamics over a range of timescales reveals that core PCP is not required to organize large-scale tissue flows but does affect short timescale mechanics.
    1. Neuroscience

    New genetic tools for mushroom body output neurons in Drosophila

    Gerald M Rubin, Yoshinori Aso
    Improved cell-type-specific genetic drivers for the study of learning and memory and other complex behaviors in Drosophila are provided and validated.
    1. Microbiology and Infectious Disease

    A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture

    Clare Andradi-Brown, Jan Stephan Wichers-Misterek ... Anna Bachmann
    An enhanced bioinformatic pipeline to quantify Plasmodium falciparum core gene and polymorphic var gene expression revealed changes occurring during early culture adaptation of parasites from naturally infected individuals.
    1. Cell Biology
    2. Computational and Systems Biology

    Reprogramming of cardiac phosphoproteome, proteome, and transcriptome confers resilience to chronic adenylyl cyclase-driven stress

    Jia-Hua Qu, Khalid Chakir ... Edward G Lakatta
    Numerous pathways/function predictions were identified via gene sets, phosphopeptides, and phosphoproteins, which may point to potential novel therapeutic targets to enhance heart adaptivity, maintaining heart performance while avoiding cardiac dysfunction.
    1. Ecology
    2. Physics of Living Systems

    Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth

    William R Shoemaker, Jacopo Grilli
    Microbial macroecological patterns under coarse-graining are captured by a null model of ecology, a result which was leveraged to successfully predict the relationship between fine and coarse-grained diversity.
    1. Neuroscience

    Silencing long-descending inter-enlargement propriospinal neurons improves hindlimb stepping after contusive spinal cord injuries

    Courtney T Shepard, Brandon L Brown ... David SK Magnuson
    Silencing long-descending propriospinal neurons that connect C6 to L2 disrupts right-left alternation of both the forelimbs and hindlimbs in the intact animal, but leads to improved stepping after a mild-moderate thoracic contusion spinal cord injury.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Mitochondrial electron transport chain, ceramide, and coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle

    Alexis Diaz-Vegas, Søren Madsen ... James G Burchfield
    In vitro and in vivo studies uncovered a molecular link between elevated mitochondrial ceramide levels, coenzyme Q depletion, and insulin resistance.