bioRxiv

Showing 3261 to 3270 of 4993 articles

A Convex Point Process Model of Heartbeat Dynamics for Inference, Prediction, and Information Quantification

bioRxiv Jan 1, 2025
The dynamics of heartbeat intervals provide important insights into cardiovascular and autonomic nervous system function. Conventional analytical approaches often use fixed-window averaging, which can obscure rapid changes and reduce temporal resolut...
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PRESTIGE-ST: Patch Resolution and Encoder STrategies for Inference of Gene Expression from Spatial Transcriptomics

bioRxiv Jan 1, 2025
Spatial Transcriptomics (ST) integrates histology with spatially resolved gene expression, offering rich insights into tissue architecture and function. However, its clinical and large-scale deployment is hindered by high costs, technical complexity,...
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Differentiation hierarchy in adult B cell acute lymphoblastic leukemia at clonal resolution

bioRxiv Jan 1, 2025
While a differentiation hierarchy with leukemia-initiating stem cells (LICs) at the apex is well documented for acute myeloid leukemia, the existence of LICs and their trajectories in B cell acute lymphoblastic leukemia (B-ALL) are debated. B-ALL is ...
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PepCCD: A Contrastive Conditioned Diffusion Framework for Target-Specific Peptide Generation

bioRxiv Jan 1, 2025
Peptide-based drug design targeting “undruggable” proteins remains one of the most critical challenges in modern drug discovery. Conventional peptide-discovery pipelines rely on low-throughput experimental screening, which is both time-consuming and ...
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Axon termination of the SAB motor neurons in C. elegans depends on pre- and postsynaptic activity

bioRxiv Jan 1, 2025
Axon termination is a critical step in neural circuit formation, but the contribution of activity from postsynaptic targets to this process remains unclear. Using Caenorhabditis elegans SAB neurons as a model system, we showed that inhibition of musc...
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Integrative Microbiome Profiling of Colorectal Cancer Across South Asian and Western Cohorts Using Interpretable Machine Learning

bioRxiv Jan 1, 2025
The incidence of colorectal cancer (CRC) cases has been steadily rising in South Asian countries compared to western countries. Microbiome dysbiosis has been strongly associated with CRC development, with diet and demographic factors playing an impor...
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Movie-trained transformer reveals novel response properties to dynamic stimuli in mouse visual cortex

bioRxiv Jan 1, 2025
Understanding how the brain encodes complex, dynamic visual stimuli remains a fundamental challenge in neuroscience. Here, we introduce ViV1T, a transformer-based model trained on natural movies to predict neuronal responses in mouse primary visual c...
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DipGNNome: Diploid de novo genome assembly with geometric deep learning and beam-search

bioRxiv Jan 1, 2025
De novo genome assembly remains a central challenge in computational biology, particularly for diploid genomes where maternal and paternal haplotypes must be accurately resolved. Existing assemblers achieve impressive results through carefully design...
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α-SMA/VCAM-1 Dual-Targeted Nanoplatform Improves Drug Release and Therapeutic Efficacy in Liver Fibrosis

bioRxiv Jan 1, 2025
Liver fibrosis is a progressive pathological condition characterized by hepatic stellate cell (HSC) activation and vascular endothelial dysfunction, where single-target therapies often fail to disrupt the pathological feedback loop between inflammati...
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PhysiGym: bridging the gap between the Gymnasium reinforcement learning application interface and the PhysiCell agent-based model software

bioRxiv Jan 1, 2025
This paper presents PhysiGym, a framework that integrates agent-based biological simulation within standardized reinforcement learning environments. By integrating the agent-based modeling framework PhysiCell with the Gymnasium API, we provide a flex...
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