Browse our latest Computational and Systems Biology articles

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    1. Computational and Systems Biology

    Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription, and splicing from single-cell RNA sequencing data with TSvelo

    Jiachen Li, Zhe Wang ... Ye Yuan
    TSvelo provides a comprehensive RNA velocity mathematics framework that can model the cascade of gene regulation, transcription, and splicing.
    1. Immunology and Inflammation
    2. Computational and Systems Biology

    A predictive systems vaccinology framework enables rational optimization of MVA-based vaccines

    Vincent Deman, Philippe Castera ... Anne-Sophie Beignon
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    +Clonal stochasticity in early NK cell response to mouse cytomegalovirus is generated by mature subsets of varying proliferative ability

    Darren Wethington, Saeed Ahmad ... Jayajit Das
    Stochastic fluctuations play an important role in the MCMV-induced NK cell clonal expansion that ultimately gives rise to memory NK cells.
    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    Squidly harnesses enzyme functional hierarchy and contrastive learning to efficiently predict catalytic residues from sequence

    William JF Rieger, Mikael Bodén ... Ariane Mora
    Squidly enables efficient identification of enzyme catalytic residues by integrating functional hierarchies into a contrastive learning framework, requiring only protein sequences to produce scalable predictions across the known enzyme landscape.
    1. Computational and Systems Biology
    2. Neuroscience

    Individual differences drive social hierarchies in male mouse societies

    Jonathan Reinwald, Sarah Ghanayem ... Wolfgang Kelsch
    Automated, long-term tracking reveals that social rank in male mice is a stable individual trait that persists across group changes, with chasing serving to negotiate rank among dominant individuals.
    1. Genetics and Genomics
    2. Computational and Systems Biology

    Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

    Hanna Liao, Sanjay Kottapalli ... Sanjay Srivatsan
    Revised
    Reviewed Preprint v2
    Updated
    • Important
    • Convincing
    1. Cancer Biology
    2. Computational and Systems Biology

    Systematic analysis of network-driven adaptive resistance to CDK4/6 and oestrogen receptor inhibition using meta-dynamic network modelling

    Anthony Hart, Sung-Young Shin, Lan K Nguyen
    Meta Dynamic Network analysis can identify the capacity of a network to facilitate adaptive drug resistance and the respective underlying mechanistic causes.
    1. Computational and Systems Biology

    Protein generation with evolutionary diffusion: sequence is all you need

    Sarah Alamdari, Nitya Thakkar ... Kevin K Yang
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    1. Neuroscience
    2. Computational and Systems Biology

    Olfactory combinatorial coding supports risk-reward decision making in C. elegans

    Md Zubayer Hossain Saad, William G Ryan ... Bruce A Bamber
    Revised
    Reviewed Preprint v3
    Updated
    • Important
    • Convincing