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bioRxiv

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DeltaNMF: A Two-Stage Neural NMF for Differential Gene Program Discovery

bioRxiv Jan 24, 2026
Non-negative matrix factorization (NMF) is a foundational dimensionality-reduction method in single-cell transcriptomics, valued for its interpretable gene programs. However, in case-control settings common in perturbation and disease research, stand...
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High-fidelity bioimage restoration via adversarial learning

bioRxiv Jan 24, 2026
Live-cell microscopy restoration is constrained by a trade-off between inference latency and texture preservation. While diffusion models provide high textural fidelity, the computational cost of iterative sampling currently limits their use in low-l...
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Explainable Artificial Intelligence Reveals Potential Candidate Mechanism of Strain-Specific Drug Depletion

bioRxiv Jan 24, 2026
Oral medications can be bioaccumulated or metabolised by gastrointestinal bacteria in a process collectively termed drug depletion. The precise biological mechanisms governing strain-specific depletion remain poorly understood, and systematic experim...
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ESMDisPred: A Structure-Aware CNN-Transformer Architecture for Intrinsically Disordered Protein Prediction

bioRxiv Jan 24, 2026
Intrinsically disordered proteins (IDPs) lack stable three-dimensional structures, yet play vital roles in key biological processes, including signaling, transcription regulation, and molecular scaffolding. Their structural flexibility presents signi...
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Reprogramming BCMA-Targeted CAR-T Cells through γ-Secretase Modulation Blocks Antigen Shedding and Extends CAR-T Longevity

bioRxiv Jan 23, 2026
B-cell maturation antigen (BCMA) shedding by {gamma}-secretase generates soluble BCMA (sBCMA) , which diminishes membrane antigen density, and limits the durability of BCMA-directed immunotherapies in multiple myeloma (MM). Here, using AI-driven diff...
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Quantifying the oxygen preferences of bacterial communities using a metagenome-based approach

bioRxiv Jan 23, 2026
Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ, one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate ae...
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Beta Diversity Meta-Analysis Shows Transformations Have Broadly Similar Performance in Machine Learning Applications Regardless of Compositional or Phylogenetic Awareness

bioRxiv Jan 23, 2026
Background Beta diversity quantifies pairwise differences between two or more communities through matrix transformations, which are either naive to phylogeny or phylogenetically aware. Methods have recently been introduced that also consider composit...
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AI-Powered Acoustic Surveillance for Early Detection of Calf Respiratory Disease

bioRxiv Jan 23, 2026
Effective management of Bovine Respiratory Disease Complex (BRDC) requires timely, non-invasive diagnostic tools to protect calf health and welfare. Among early clinical signs, coughing stands out as both frequent and informative. To explore its pote...
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Novel universal domain-centric method for protein classification

bioRxiv Jan 23, 2026
Human protein kinases constitute a large superfamily of about 500 genes, historically classified into subfamilies based on phylogenetic relationship. However, many kinases remain unclassified. Phylogeny is typically based on multiple sequence alignme...
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Clinical and Cross-Domain Validation of an LLM-Guided, Literature-Based Gene Prioritization Framework

bioRxiv Jan 23, 2026
Background: We previously published a literature based pipeline for sepsis gene prioritization (PS3 and candidate genes) using an LLM enabled retrieval and judging framework. Here, we extend that work to ask whether these prioritized genes show indep...
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