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    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. Neuroscience
    2. Computational and Systems Biology

    Deciphering the Genetic Code of Neuronal Type Connectivity: A Bilinear Modeling Approach

    Mu Qiao
    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
    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. Cancer Biology

    Optimal transport for automatic alignment of untargeted metabolomic data

    Marie Breeur, George Stepaniants ... Vivian Viallon
    1. Genetics and Genomics
    2. Computational and Systems Biology

    Spotless: a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics

    Chananchida Sang-aram, Robin Browaeys ... Yvan Saeys
    1. Immunology and Inflammation
    2. Computational and Systems Biology

    ImmCellTyper: an integrated computational pipeline for systematic mining of Mass Cytometry data to assist deep immune profiling

    Jing Sun, Desmond Choy ... Shahram Kordasti
    1. Neuroscience
    2. Computational and Systems Biology

    Dynamic organization of visual cortical networks revealed by machine learning applied to massive spiking datasets

    Colin Graber, Yurii Vlasov, Alexander Schwing
    1. Computational and Systems Biology
    2. Cancer Biology

    Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

    Aurélie AG Gabriel, Julien Racle ... David Gfeller
    1. Microbiology and Infectious Disease
    2. Computational and Systems Biology

    A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants

    Alon Avraham Ginatt, Maria Berihu ... Shiri Freilich
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