bioRxiv

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AlphaRING-X: accurate interpretation of missense variant deleteriousness based on protein structural stability

bioRxiv Jan 1, 2025
Accurate interpretation of missense variants remains a significant challenge hindering genomic diagnosis. While state-of-the-art machine learning and deep learning predictors offer high accuracy, they often lack the transparency required for clinical...
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GPTAnno: Ontology-tree-guided hierarchical cell type annotation based on GPT models for single-cell data

bioRxiv Jan 1, 2025
Cell type annotation is critical for interpreting single-cell transcriptomic data but remains challenging due to uncertain cellular clustering granularity and inconsistent labeling across studies. Here we present GPTAnno, an automated, ontology-tree-...
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Environmental Conflict Modulates Pavlovian Bias

bioRxiv Jan 1, 2025
Pavlovian avoidance enables rapid defensive responding but can undermine goal-directed behaviour when it overrides instrumental control, a tendency amplified in anxiety. Whether such biases can be flexibly and rapidly modulated by environmental struc...
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Enigma: An Efficient Model for Deciphering Regulatory Genomics

bioRxiv Jan 1, 2025
Genomic sequence-to-function models have emerged as powerful tools for deciphering cis-regulatory grammar to advance our understanding of disease biology and guide therapeutic development. Recent advances have been driven by multi-task training of la...
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Prediction of biomolecule kinetics using physics-based Brownian dynamics to data-driven machine learning methods

bioRxiv Jan 1, 2025
We present a comprehensive review of biomolecular binding kinetics and their modeling via Brownian dynamics simulations, with particular emphasis on enzyme–substrate interactions in cellular environments. We outline the theoretical foundations of Bro...
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scMOBA: A conversational single-cell Multi-Omics Brain Agent across species

bioRxiv Jan 1, 2025
Single-cell and spatial multi-omics are revolutionizing our understanding of the complexity in the developmental, aging, and diseased brain, but integrating this knowledge across modalities and species remains challenging. To bridge this gap, we prop...
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B-PPI: A Cross-Attention Model for Large-Scale Bacterial Protein-Protein Interaction Prediction

bioRxiv Jan 1, 2025
Protein-protein interactions (PPIs) are essential for the study of cellular function, yet computational prediction of bacterial PPIs remains limited. Most existing methods are trained on human data, reducing their applicability to bacterial systems. ...
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The Dominance of Geometric Graph Models in Animal Social Networks

bioRxiv Jan 1, 2025
Detecting patterns in animal social behaviour and movement is complicated by the diversity of ecological, evolutionary, environmental, and biological drivers of these behaviours such as migration, foraging, assortative mixing, socio-ecological factor...
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A comprehensive bulk and single-cell transcriptional atlas of pediatric leukemias

bioRxiv Jan 1, 2025
Advancements in understanding the molecular factors driving pediatric leukemias have led to an ever-increasing volume and diversity of data being generated. Recent studies are moving beyond DNA-based profiling to incorporate transcriptional data, enh...
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Quantitative Logics for Directed Evolution of an Asexual Population

bioRxiv Jan 1, 2025
Directed evolution of asexual populations is expected to offer a wide range of benefits to humanity. Achieving efficient directed evolution (DE) requires a quantitative formulation of the experimental methodologies—or logics—that can address potentia...
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