bioRxiv

Showing 4841 to 4850 of 5021 articles

Multi-Dimensional Spatiotemporal Attention Neural Network for Next Generation Sequencing Basecalling

bioRxiv Jan 1, 2025
Next-generation sequencing (NGS) remains the most used sequencing technique in the field of genomics. Traditional basecall methods face significant challenges in decoding high density sequencing data due to inherent noise in biochemical reactions and...
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Control of gene output by intron RNA structure

bioRxiv Jan 1, 2025
Intron removal through pre-mRNA splicing is a central step in gene expression across Eukarya. The process initiates with the recognition of intronic sequence elements (splice sites) by highly conserved RNA-protein components of the spliceosome. 1,2 I...
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Prompt-to-Pill: Multi-Agent Drug Discovery and Clinical Simulation Pipeline

bioRxiv Jan 1, 2025
This study presents a comprehensive, modular framework for AI-driven drug discovery (DD) and clinical trial simulation, spanning from target identification to virtual patient recruitment. Synthesized from a systematic analysis of 51 LLM-based systems...
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Offline Reconstruction of Diffusion MRI Acquisitions for Comparison Between Complex PCA-based and AI-based Denoising

bioRxiv Jan 1, 2025
Optimal diffusion MRI (dMRI) data for image denoising is often unavailable from scanner reconstruction. In this work, we make available an offline reconstruction pipeline for GE dMRI acquisitions, giving access to complex dMRI data. Furthermore, we c...
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Simulation and empirical evaluation of biologically-informed neural network performance

bioRxiv Jan 1, 2025
Biologically-informed neural networks (BiNNs) offer interpretable deep learning models for biological data, but the dataset characteristics required for strong performance remain poorly understood. For instance, we previously developed P-NET, a BiNN ...
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Accelerating ligand discovery by combining Bayesian optimization with MMGBSA-based binding affinity calculations

bioRxiv Jan 1, 2025
Predicting protein–ligand binding affinity with high accuracy is critical in structure-based drug discovery. While docking methods offer computational efficiency, they often lack the precision required for reliable affinity ranking. In contrast, mole...
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A lettuce receptor-like kinase recognizes the highly conserved heptapeptide motif within microbial NEP1-like proteins

bioRxiv Jan 1, 2025
Plants rely on cell surface immune receptors to detect microbial patterns and initiate effective defense responses. Although the Asteraceae family is one of the largest and economically important plant groups, little information is available about it...
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Agent SPI-WSI: In context learning for computationally spatial pathway inferring on whole slide histopathology images conditioned on bulk RNA sequencing using pathologist in the loop

bioRxiv Jan 1, 2025
Bulk RNA sequencing, while cost-effective compared to high-resolution spatial transcriptomics, averages gene expression across heterogeneous cell populations and thus lacks spatial context. To address this limitation, we introduce a structured, human...
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Benchmarking Large Language Models for Pathogen–Disease Classification in Post-Acute Infection Syndromes

bioRxiv Jan 1, 2025
Post-Acute Infection Syndromes (PAIS) are medical conditions that persist following acute infections from pathogens such as SARS-CoV-2, Epstein-Barr virus, and Influenza virus. Despite growing global awareness of PAIS and the exponential increase in ...
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Deep Learning Bridges Histology and Transcriptomics to Predict Molecular Subtypes and Outcomes in Muscle-Invasive Bladder Cancer

bioRxiv Jan 1, 2025
Muscle-Invasive Bladder Cancer (MIBC) is a heterogeneous disease with distinct molecular subtypes influencing prognosis and therapeutic response. However, molecular profiling through RNA sequencing remains costly, time-consuming and complicated by in...
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