bioRxiv

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PubMind: Literature-Based Genetic Variant Extraction and Functional Annotation Using Large Language Models

bioRxiv Jan 1, 2025
The rapid growth of biomedical literature has produced extensive functional knowledge on genetic variants, much of which remains buried in unstructured texts. Current databases such as ClinVar and the Human Gene Mutation Database (HGMD) attempt to ca...
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Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4+ T Cells

bioRxiv Jan 1, 2025
In vivo genetic engineering of T cells could overcome the logistical, biological, and safety challenges of ex vivo modification, but effective and safe delivery systems remain limited by a lack of cellular specificity. Here, we developed aptamer-func...
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Engineering C3.5 Photosynthesis: Coupling Mitochondrial Bioenergetics to Rubisco Efficiency in Arabidopsis

bioRxiv Jan 1, 2025
Global food demand is projected to increase by more than 50 percent by 2050, yet most staple crops rely on inefficient C3 photosynthesis. A major limitation arises from Rubisco, the central carbon-fixing enzyme, which catalyzes oxygenation reactions ...
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Ontology pre-training improves machine learning-based predictions for metabolites

bioRxiv Jan 1, 2025
Recent advances in the field of machine learning have shown that integration of expert knowledge improves performances, in particular for complex domains such as biology. Bio-ontologies offer a rich source of curated biological knowledge that can be ...
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Independent genomic trajectories shape adaptation to life on land across animal lineages

bioRxiv Jan 1, 2025
How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared genomic mechanisms underlie these transitions. We com...
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Nematic cell alignment directs calcium waves

bioRxiv Jan 1, 2025
Tissues rely on supracellular signals to coordinate their cells over a long range. Two such tissue-scale cues are calcium waves and patterns of cell-cell alignment or nematic order. During wound healing, for example, calcium waves propagate across a ...
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Boosting Transcript Assembly via Delineating Transcript Start and End Sites

bioRxiv Jan 1, 2025
Transcript assembly remains a challenging task despite the development of numerous methods. A major contributor to low assembly accuracy is the difficulty in accurately determining transcript start sites (TSSs) and end sites (TESs), due to the weak a...
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DREAMER-S: Deep leaRning-Enabled Attention-based Multiple-instance approaches with Explainable Representations for Spatial biology

bioRxiv Jan 1, 2025
Identifying image features that associate strongly with diagnostic or prognostic classes in large-scale, multi-channel spatial imaging is challenging without pixel-level annotations. We present DREAMER-S, an attention-based multiple-instance learning...
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Maximizing Nature-based Solutions using Artificial Intelligence to align global biodiversity, climate, and water targets

bioRxiv Jan 1, 2025
Nature-based Solutions (NbS) encompass a spectrum of conservation and restoration actions aimed at improving biodiversity, climate, and/or water outcomes. Considerable research exists that focuses either on conservation or restoration, or on one part...
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Breast Cancer Subtyping with HyperCLSA: A Hypergraph Contrastive Learning Pipeline for Multi-Omics Data Integration

bioRxiv Jan 1, 2025
Accurate molecular subtyping of cancer is crucial for advancing personalized medicine. Although multiomics data contain valuable predictive information, effectively integrating them is challenging due to differences across modalities, high dimensiona...
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