bioRxiv

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A Multi-Agent Approach to Generating Context-Rich Gene Sets

bioRxiv Jan 1, 2025
Gene sets are collections of genes that share a common biological function, process, or component that can be used to get insight into the biological relevance of genomic data. Databases containing these gene sets aids in a wide array of analytical m...
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What kind of birds are more susceptible to avian malaria? A global analysis based on interpretable machine learning approach

bioRxiv Jan 1, 2025
Avian malaria (genus Plasmodium) is a mosquito-transmitted parasitic disease of birds. It has a wide distribution across the world, infecting more than 2,400 bird species, posing a great threat to bird health. However, over half of bird species have ...
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Synergistic short-term synaptic plasticity mechanisms for working memory

bioRxiv Jan 1, 2025
Working memory (WM) is essential for almost every cognitive task. The neural and synaptic mechanisms supporting the rapid encoding and maintenance of memories in diverse tasks are the subject of an ongoing debate. The traditional view of WM as statio...
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Harnessing artificial intelligence to automate environmental predictions

bioRxiv Jan 1, 2025
Predicting heterogeneous and non-linear processes remains a fundamental challenge in Earth sciences. Here, we present an artificial intelligence (AI)-guided framework that iteratively combines predictive modeling with targeted field sampling to rapid...
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YOLito: A generalizable model for automated mosquito detection

bioRxiv Jan 1, 2025
Understanding mosquito behavior is key to advancing research in ecology, evolution, and disease control, yet most behavioral assays rely on human-dependent methods, such as real-time observation or manual frame-by-frame annotation, limiting throughpu...
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Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research

bioRxiv Jan 1, 2025
High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in on-cology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read Archive-SRA. However, fragmented, ambiguous or missing metada...
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Mapping high resolution, multidimensional phase diagrams of physiological protein condensates

bioRxiv Jan 1, 2025
Biomolecular condensates are membraneless compartments, crucial for organising and regulating diverse cellular processes. Current approaches to study condensate biology either use simplified recombinant protein systems with limited physiological rele...
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CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants

bioRxiv Jan 1, 2025
Genomic selection (GS), which integrates genomic markers with phenotypic data, has emerged as a powerful breeding strategy for predicting phenotypes and estimating breeding values in candidate populations. The success of GS fundamentally depends on t...
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Nucleotide context models outperform protein language models for predicting antibody affinity maturation

bioRxiv Jan 1, 2025
Antibodies play a crucial role in adaptive immunity. They develop as B cell receptors (BCRs): membrane-bound forms of antibodies that are expressed on the surfaces of B cells. BCRs are refined through affinity maturation, a process of somatic hypermu...
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Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish

bioRxiv Jan 1, 2025
Gene expression changes across embryonic development reflect both differentiation and genes whose expression varies strictly with developmental time, independent of cell type. Multiple embryonic timing systems set the onset and pace of developmental ...
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