Browse our latest Computational and Systems Biology articles

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    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. Neuroscience
    2. Computational and Systems Biology

    Morphogenesis and morphometry of brain folding patterns across species

    Sifan Yin, Chunzi Liu ... L Mahadevan
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    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. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling

    Caleb Hallinan, Hyun Joo Ji ... Jean Fan
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Convincing
    1. Computational and Systems Biology

    Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage

    Zhiwei Huang, Songhao Luo ... Jiajun Zhang
    Revised
    Reviewed Preprint v2
    Updated
    • Valuable
    • Solid
    1. Computational and Systems Biology
    2. Physics of Living Systems

    Exploiting fluctuations in gene expression to detect causal interactions between genes

    Euan Joly-Smith, Mir Mikdad Talpur ... Andreas Hilfinger
    Revised
    Reviewed Preprint v3
    Updated
    • Important
    • Solid
    1. Computational and Systems Biology

    Targeted Computational Design of an Interleukin-7 Superkine with Enhanced Folding Efficiency and Immunotherapeutic Efficacy

    See-Khai Lim, Wen-Ching Lin ... Kurt Yun Mou
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    1. Computational and Systems Biology

    Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates

    Irene Lamberti, Jeffrey A Chao ... Felix Naef
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    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
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