bioRxiv

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LivecellX: Corrective Deep Learning for Object-Oriented Single-Cell Analysis in Live-Cell Imaging

bioRxiv Jan 1, 2025
Live-cell imaging uniquely captures single-cell dynamics in space and time, but robust analysis is limited by segmentation and tracking errors that accumulate across frames. We present LivecellX, a deep-learning–based pipeline that integrates instanc...
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How Much Does Protein Structure Really Help? A Case Study in Mutation-Induced Stability Prediction

bioRxiv Jan 1, 2025
Multimodal neural networks integrating protein language models (PLMs) with structure-derived features are increasingly common for predicting mutation effects, yet fundamental mechanisms remain poorly characterized. In this paper, we articulate and ad...
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Integrative multiomic analysis on single-nucleotide variants identifies candidate genes for human craniofacial malformation

bioRxiv Jan 1, 2025
Craniofacial malformation (CFM) is a congenital defect encompassing a wide range of phenotypic presentations and is largely driven by genetics. Despite the discovery of more than 300 causal genes, there are a myriad of CFM cases with unknown genetic ...
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Large-scale classification of metagenomic samples: a comparative analysis of classical machine learning techniques vs a novel brain-inspired hyperdimensional computing approach

bioRxiv Jan 1, 2025
Classical machine learning techniques have revolutionized bioinformatics, enabling researchers to extract knowledge from complex biological data. However, these techniques often struggle with high-dimensional data, where the increasing number of feat...
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You Are What You Sync: Neural Synchronization Predicts Religious Affiliation

bioRxiv Jan 1, 2025
Existing research has found that shared neural responses to naturalistic narratives are associated with shared understanding, especially among members of the same social group. In this fMRI study, we tested whether in-group neural synchronization sol...
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RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair

bioRxiv Jan 1, 2025
Aging and tissue repair involve multilayered and spatially heterogeneous remodeling across transcriptional, biochemical, and cellular dimensions, yet prevailing definitions rely on isolated molecular markers that obscure how biochemical and transcrip...
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Ensemble-DeepSets: an interpretable deep learning framework for single-cell resolution profiling of immunological aging

bioRxiv Jan 1, 2025
Immunological aging (immunosenescence) drives increased susceptibility to infections and reduced vaccine efficacy in elderly populations. Current bulk transcriptomic aging clocks mask critical cellular heterogeneity, limiting the mechanistic dissecti...
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Non-invasive vagus nerve stimulation modulates Pavlovian bias in a state-dependent manner

bioRxiv Jan 1, 2025
The vagus nerve transmits vital signals between organ systems of the body and the brain. Despite growing interest in non-invasive transcutaneous vagus nerve stimulation (tVNS) for treatments of various disorders, it is not known whether its modulator...
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Biophysically relevant network model of the piriform cortex predicts odor frequency encoding using network mechanisms

bioRxiv Jan 1, 2025
Olfactory-guided animals utilize fast concentration fluctuations in turbulent odor plumes to perceive olfactory landscapes. Recent studies demonstrate that the olfactory bulb (OB) encodes such temporal features present in natural odor stimuli. Howeve...
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The FERM Guild: A Differentially Correlated Microbial Module Drives Hypertension via Metabolic Flux Perturbations

bioRxiv Jan 1, 2025
Hypertension is a major risk factor for cardiovascular diseases, with changes in gut microbiota composition and function being closely associated with its onset and progression. However, the high inter-individual variability in gut microbiota complic...
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