Browse our latest Computational and Systems Biology articles

Page 3 of 121
    1. Medicine
    2. Computational and Systems Biology

    Calibration and validation strategy for electromechanical cardiac digital twins

    Zhinuo Jenny Wang, Maxx Holmes ... Blanca Rodriguez
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    • Incomplete
    1. Computational and Systems Biology

    Dynamical mechanisms of growth-feedback effects on adaptive gene circuits

    Ling-Wei Kong, Wenjia Shi ... Ying-Cheng Lai
    Systematic simulations reveal how growth feedback undermines the stability of adaptive gene circuits in a topology-dependent manner.
    1. Computational and Systems Biology
    2. Physics of Living Systems

    Overflow metabolism originates from growth optimization and cell heterogeneity

    Xin Wang
    The combination of growth optimization and cell heterogeneity enables a quantitative explanation of overflow metabolism in microbes and the classical Warburg effect in cancer cells, resolving this long-standing puzzle.
    1. Computational and Systems Biology

    Pathway activation model for personalized prediction of drug synergy

    Quang Thinh Trac, Yue Huang ... Trung Nghia Vu
    Drug synergy Interaction Prediction improves personalized drug synergy prediction by utilizing drug-specific pathway activation scores to predict personalized drug synergy and reveals mechanistic pathways underlying synergistic effects.
    1. Computational and Systems Biology

    Predicting the effect of CRISPR-Cas9-based epigenome editing

    Sanjit Singh Batra, Alan Cabrera ... Yun S Song
    Revised
    Reviewed Preprint v3
    Updated
    • Useful
    • Solid
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Reliable protein–protein docking with AlphaFold, Rosetta, and replica exchange

    Ameya Harmalkar, Sergey Lyskov, Jeffrey J Gray
    New protein-protein docking algorithm combining deep learning (AlphaFold2) and physics (Rosetta and enhanced sampling) achieves high success rates.
    1. Computational and Systems Biology

    Unsupervised reference-free inference reveals unrecognized regulated transcriptomic complexity in human single cells

    Roozbeh Dehghannasiri, George Henderson ... Julia Salzman
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Computational and Systems Biology

    Perturbation-response analysis of in silico metabolic dynamics revealed hard-coded responsiveness in the cofactors and network sparsity

    Yusuke Himeoka, Chikara Furusawa
    A computational study reveals that the kinetic models of Escherichia coli metabolism show strong responsiveness to perturbations and that it originates from cofactor dynamics and network sparsity.
    1. Computational and Systems Biology
    2. Neuroscience

    MorphoCellSorter is an Andrews plot-based sorting approach to rank microglia according to their morphological features

    Sarah Benkeder, Son-Michel Dinh ... Jean-Christophe Comte
    MorphoCellSorter is a versatile, user-friendly tool that automates microglial morphology ranking, enabling standardized, reproducible analysis across diverse models, imaging techniques, and conditions using principal component analysis and Andrews plots.
    1. Computational and Systems Biology
    2. Ecology

    Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

    Iva Veseli, Yiqun T Chen ... A Murat Eren
    Higher biosynthetic capacity of gut microbes in individuals diagnosed with noncommunicable diseases or taking antibiotics suggests that diversity loss and 'dysbiosis' result from microbiome restructuring in response to ecosystem disruption.