AIMC Journal:
bioRxiv

Showing 2241 to 2250 of 4979 articles

Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution

bioRxiv Feb 27, 2026
The spatial organization of microbial communities is a critical determinant of host-microbe interactions, yet species-level mapping remains challenging due to high 16S rRNA sequence homology and spectral crosstalk in multiplexed fluorescence in situ ...
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Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites

bioRxiv Feb 27, 2026
Transcription factors recognise and bind specific DNA sequence patterns in promoters and enhancers thereby regulating gene expression. Variations in the DNA sequence of transcription factor binding sites (TFBSs) can alter gene regulation and may disr...
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A Framework for Autonomous AI-Driven Drug Discovery

bioRxiv Feb 26, 2026
The exponential increase in biomedical data offers unprecedented opportunities for drug discovery, yet overwhelms traditional data analysis methods, limiting the pace of new drug development. Here we introduce a framework for autonomous artificial in...
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BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature

bioRxiv Feb 26, 2026
Protein-ligand bioactivity data published in literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated bioactivity extraction remains challenging because it requires not only in...
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AI predicted TCR-pMHC structures differentiate immune interactions

bioRxiv Feb 26, 2026
The T Cell Receptor (TCR) is a highly variable component of the T cell immune response that recognizes unique epitopes presented on MHC molecules (pMHC). Random genetic recombination limits the ability for sequence homology to predict epitope specifi...
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Deep learning enables feature extraction of 3D collagen architecture in cleared fibrotic tissues

bioRxiv Feb 26, 2026
Light-sheet fluorescence microscopy enables deep optical sectioning of large, cleared biological tissues. However, effective clearing of collagen-rich tissues remains a persistent technical challenge. Moreover, standardized workflows integrating thre...
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Permutation-calibrated stability discovery under ???? >> ????: A leak-controlled Machine Learning framework identifies candidate proteomics panels in antiseizure medication-related side effects

bioRxiv Feb 26, 2026
We investigated whether the plasma proteome distinguishes people with epilepsy who report central nervous system (CNS) side effects from antiseizure medications (ASMs) from those who do not. In 161 patients profiled using proximity extension assay-ba...
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Decoding the Allosteric Paradox: A Dual Framework Integrating AI Cofolding Models with Landscape-Guided Interpretable AI Framework of Ligand-Protein Binding

bioRxiv Feb 26, 2026
Artificial intelligence (AI) has transformed prediction of protein structure and biomolecular interactions, yet modeling of allosteric regulation remains a persistent and unresolved challenge. We develop a dual explainable AI framework that systemati...
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Transforming Histology into Virtual Multiplex Immunofluorescence to Decode Prognostic Spatial Immunity in Hepatocellular Carcinoma

bioRxiv Feb 26, 2026
The spatial organization of the tumor immune microenvironment (TIME) drives hepatocellular carcinoma (HCC) prognosis but remains unquantifiable on routine H&E slides. Here, we present HCCExplorer, a deep learning framework that translates H&E into vi...
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CellSwarm: LLM-Driven Cell Agents Recapitulate Tumor Microenvironment Dynamics and Sense Indirect Genetic Perturbations

bioRxiv Feb 26, 2026
Agent-based models of the tumor microenvironment (TME) traditionally rely on hand-coded rules that cannot generalize beyond their programmed logic. Here we present CellSwarm, a framework that replaces rule-based cell decision-making with large langua...
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