Browse our latest Computational and Systems Biology articles

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    1. Computational and Systems Biology
    2. Neuroscience

    Evidence from pupillometry, fMRI, and RNN modelling shows that gain neuromodulation mediates task-relevant perceptual switches

    Gabriel Wainstein, Christopher J Whyte ... James M Shine
    Phasic neuromodulatory bursts actively drive adaptive perceptual updating by triggering large-scale brain network reconfigurations, as demonstrated through integrated pupillometry, fMRI, and computational modelling.
    1. Computational and Systems Biology
    2. Neuroscience

    A common alteration in effort-based decision-making in apathy, anhedonia, and late circadian rhythm

    Sara Z Mehrhof, Camilla L Nord
    Individuals with a late circadian rhythm show the same deficits in motivational decision-making as those with neuropsychiatric symptoms, but only when tested in the morning.
    1. Computational and Systems Biology

    Artificial intelligence driven tumor risk stratification from single-cell transcriptomics using phenotype algebra

    Namrata Bhattacharya, Anja Rockstroh ... Debarka Sengupta
    SCellBOW is a language model-based scRNA-seq analysis method that identifies malignant cell subpopulations and infers marker-free survival risks using transfer learning.
    1. Computational and Systems Biology

    A mathematical model that predicts human biological age from physiological traits identifies environmental and genetic factors that influence aging

    Sergiy Libert, Alex Chekholko, Cynthia Kenyon
    A model was developed to predict human biological age from physiological traits, enabling the prediction of future health and mortality and the identification of genetic loci that influence aging.
    1. Genetics and Genomics
    2. Computational and Systems Biology

    Systematic analysis of transcription factor combinatorial binding uncovers TEAD1 as an antagonist of tissue-specific transcription factors in human organogenesis

    Araceli Garcia-Mora, Joshua Mallen ... Nicoletta Bobola
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    • Convincing
    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
    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.
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