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    1. Computational and Systems Biology

    Permute-match tests: Detecting significant correlations between time series despite nonstationarity and limited replicates

    Alex E Yuan, Wenying Shou
    Not revised
    Reviewed Preprint v1
    • Important
    • Compelling
    1. Computational and Systems Biology

    AI-enabled alkaline-resistant evolution of protein to apply in mass production

    Liqi Kang, Banghao Wu ... Liang Hong
    The Pro-PRIME model demonstrates the ability to engineer VHH antibody with unprecedented alkali resistance and enhanced affinity, enabling industrial applications under extreme conditions previously unattainable with natural proteins.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Multiplexed assays of human disease-relevant mutations reveal UTR dinucleotide composition as a major determinant of RNA stability

    Jia-Ying Su, Yun-Lin Wang ... Chien-Ling Lin
    The UA-dinucleotide ratio in UTRs is negatively correlated with RNA stability both in the massively parallel reporter assay and in vivo, and is prevalent in fast-turnover genes.
    1. Neuroscience
    2. Computational and Systems Biology

    Computational modelling identifies key determinants of subregion-specific dopamine dynamics in the striatum

    Aske L Ejdrup, Jakob K Dreyer ... Ulrik Gether
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Compound Mutations in the Abl1 Kinase Cause Inhibitor Resistance by Shifting DFG Flip Mechanisms and Relative State Populations

    Gabriel Monteiro da Silva, Kyle Lam ... Brenda M Rubenstein
    Not revised
    Reviewed Preprint v1
    • Useful
    • Incomplete
    1. Computational and Systems Biology
    2. Medicine

    Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats

    Hong Yang, Cheng Zhang ... Adil Mardinoglu
    Inhibiting c-Jun N-terminal kinase exerts a cross-tissue therapeutic effect on metabolic dysfunction induced by sucrose overconsumption in rats.
    1. Computational and Systems Biology

    A model-based factorization method for scRNA data unveils bifurcating transcriptional modules underlying cell fate determination

    Jun Ren, Ying Zhou ... Qiyuan Li
    A novel method for factorizing complex cellular trajectories into interpretable bifurcation processes enhances the understanding of cell fate determination through the identification of key biological determinants in scRNA-seq data.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

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

    Ameya Harmalkar, Sergey Lyskov, Jeffrey J Gray
    Revised
    Reviewed Preprint v2
    Updated
    • Valuable
    • Convincing
    1. Computational and Systems Biology
    2. Cancer Biology

    Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures

    Daniel Osorio, Parastoo Shahrouzi ... Marieke L Kuijjer
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    1. Genetics and Genomics
    2. Computational and Systems Biology

    Methylation Clocks Do Not Predict Age or Alzheimer’s Disease Risk Across Genetically Admixed Individuals

    Sebastián Cruz-González, Esther Gu ... John A Capra
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Convincing
    • Incomplete
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