Browse our latest Computational and Systems Biology articles

Page 12 of 128
    1. Immunology and Inflammation
    2. Computational and Systems Biology

    Restoring data balance via generative models of T cell receptors for antigen-binding prediction

    Emanuele Loffredo, Mauro Pastore ... Rémi Monasson
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    The flexible stalk domain of sTREM2 modulates its interactions with brain-based phospholipids

    David Saeb, Emma E Lietzke ... Kayla G Sprenger
    The flexible stalk region of sTREM2 binds the Ig-like domain, altering stability and ligand accessibility—a biochemically testable mechanism with broad implications for (s)TREM2 biology and rational Alzheimer's disease therapeutic design.
    1. Computational and Systems Biology
    2. Neuroscience

    Accept–reject decision-making revealed via a quantitative and ethological study of C. elegans foraging

    Jessica A Haley, Tianyi Chen ... Sreekanth H Chalasani
    C. elegans foraging decisions are guided by learned environmental features, integrating recent patch quality with internal satiety to balance exploration and exploitation.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    The lipocone superfamily, a unifying theme in metabolism of lipids, peptidoglycan and exopolysaccharides, inter-organismal conflicts and immunity

    A Maxwell Burroughs, Gianlucca G Nicastro, L Aravind
    A hitherto unrecognized superfamily of enzymes identified here provides unifying insights spanning lipid metabolism, anti-viral and anti-bacterial immunity, and the origin of developmental regulators like Wnt.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Atomistic simulation of voltage activation of a truncated BK channel

    Zhiguang Jia, Jianhan Chen
    Ten-microsecond atomistic simulations directly capture the voltage activation of the Core-MT big potassium channel, revealing novel voltage sensing and sensor-pore coupling mechanisms that have largely eluded the community.
    1. Computational and Systems Biology

    The Product neutrality function defining genetic interactions emerges from mechanistic models of cell growth

    Lucas Fuentes Valenzuela, Paul Francois, Jan M Skotheim
    Coarse-grained models of cellular growth and high-throughput empirical genetic data support the Product neutrality function in which a double-mutant fitness is the product of single-mutant fitnesses.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Thrifty wide-context models of B cell receptor somatic hypermutation

    Kevin Sung, Mackenzie M Johnson ... Frederick A Matsen
    Convolutional embedding models efficiently capture wide sequence context in antibody somatic hypermutation, avoiding exponential k-mer parameter scaling and eliminating the need for per-site modeling.
    1. Computational and Systems Biology

    Unsupervised pipeline for the identification of cortical excitatory and inhibitory neurons in high-density multielectrode arrays with ground-truth validation

    Eloise Giraud, Michael Lynn ... Jean-Philippe Thivierge
    A novel software tool and ground-truth optogenetic validation is provided to automatically detect putative excitatory and inhibitory cells in neuronal recordings performed with large-scale multielectrode arrays.
    1. Neuroscience
    2. Computational and Systems Biology

    An evolutionarily conserved scheme for reformatting odor concentration in early olfactory circuits

    Yang Shen, Arkarup Banerjee ... Saket Navlakha
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    • Incomplete
    1. Computational and Systems Biology
    2. Neuroscience

    A SMARTTR workflow for multi-ensemble atlas mapping and brain-wide network analysis

    Michelle Jin, Simon O Ogundare ... Christine Ann Denny
    A new scalable workflow for analyzing multiple ensemble datasets incorporates SMARTTR, an R package supporting network analysis, visualization, and the import of external datasets.