Browse our latest Computational and Systems Biology articles

Page 21 of 121
    1. Immunology and Inflammation
    2. Computational and Systems Biology

    Context-Aware Amino Acid Embedding Advances Analysis of TCR-Epitope Interactions

    Pengfei Zhang, Seojin Bang ... Heewook Lee
    Revised
    Reviewed Preprint v2
    Updated
    • Important
    • Convincing
    1. Computational and Systems Biology
    2. Physics of Living Systems

    Development of equation of motion deciphering locomotion including omega turns of Caenorhabditis elegans

    Taegon Chung, Iksoo Chang, Sangyeol Kim
    ElegansBot, a two-dimensional rigid body chain model, simulates various locomotion of C. elegans, including omega and delta turns, using Newtonian equations of motion.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Imputation of 3D genome structure by genetic–epigenetic interaction modeling in mice

    Lauren Kuffler, Daniel A Skelly ... Gregory W Carter
    Genetic variants interact with open chromatin to alter gene expression within topologically associated domains of DNA in outbred mice.
    1. Computational and Systems Biology
    2. Developmental Biology

    A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

    Gang Xue, Xiaoyi Zhang ... Zhiyuan Li
    A top-down model-guided framework unveils the role of regulatory logics underlying gene regulatory networks in cell fate decisions.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Haplotype function score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

    Weichen Song, Yongyong Shi, Guan Ning Lin
    Using sequence-determined functional genomic features instead of original genotypes can partially overcome challenges in genetic association studies, such as rare variant exclusion and population structure.
    1. Computational and Systems Biology

    Genome-scale annotation of protein binding sites via language model and geometric deep learning

    Qianmu Yuan, Chong Tian, Yuedong Yang
    Integration of language model and geometric deep learning enables accurate and efficient genome-scale annotation of comprehensive protein-ligand binding sites.
    1. Computational and Systems Biology
    2. Physics of Living Systems

    The French flag problem revisited: Creating robust and tunable axial patterns without global signaling

    Stephan Kremser, Gabriel Vercelli, Ulrich Gerland
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    1. Cell Biology
    2. Computational and Systems Biology

    Neural network emulation of the human ventricular cardiomyocyte action potential for more efficient computations in pharmacological studies

    Thomas Grandits, Christoph M Augustin ... Alexander Jung
    Neural networks can emulate normal and abnormal human ventricular action potentials accurately and potentially much faster than regular simulations paving the way for more efficient quantitative systems pharmacology studies.
    1. Computational and Systems Biology
    2. Neuroscience

    Disrupting abnormal neuronal oscillations with adaptive delayed feedback control

    Domingos Leite de Castro, Miguel Aroso ... Paulo Aguiar
    Adaptive delayed feedback control is presented as a new real-time, closed-loop control algorithm for neurostimulation which can disrupt oscillations and reduce network synchrony in neuronal populations.
    1. Computational and Systems Biology

    Protein language model-embedded geometric graphs power inter-protein contact prediction

    Yunda Si, Chengfei Yan
    Integrating multiple protein language models using protein geometric graphs can dramatically improve the model performance for predicting the contacting residue pairs between interacting proteins.