AIMC Journal:
bioRxiv

Showing 2271 to 2280 of 4979 articles

EnhancerDetector: Enhancer Discovery from Human to Fly via Interpretable Deep Learning

bioRxiv Feb 24, 2026
Deciphering how enhancers encode regulatory information in DNA remains a central genomics challenge, as sequencing outpaces functional annotation. A key question is whether enhancers possess an intrinsic, sequence-based "enhancerness" distinguishing ...
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BOTANIC-0: a series of foundation models for plant genomic data

bioRxiv Feb 24, 2026
Genomic language models (gLMs) have emerged as a powerful paradigm for learning regulatory biology directly from DNA sequence. Here, we introduce Botanic0, a family of plant genomic foundation models spanning 100M to 1B parameters and pretrained on 4...
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OligoGraph: A novel geometric graph-based approach for siRNA efficacy prediction

bioRxiv Feb 24, 2026
RNA interference (RNAi) is a biological process in which a small interfering RNA (siRNA) prevents the translation of a messenger RNA (mRNA) into a protein by cleaving the mRNA before translation. We exploit this process to prevent the formation of ha...
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Thermal stress drives seagrass fragmentation in the Mediterranean Sea

bioRxiv Feb 24, 2026
Posidonia oceanica meadows, which underpin Mediterranean coastal ecosystems, are undergoing accelerated decline, partly driven by thermal stress. While previous quantitative studies have identified temperature thresholds beyond which seagrass mortali...
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RevelioPlots: An Interactive Web Application for Fast AI-Based Protein Models Quality Assessment

bioRxiv Feb 24, 2026
High-accuracy protein structure prediction by deep learning requires rigorous model quality assessment, a process currently hampered by fragmented, non-interactive tools designed for older experimental data formats. We present RevelioPlots, an open-s...
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SHAP-Guided CpG Selection with Ensemble Learning for Epigenetic Age Prediction

bioRxiv Feb 23, 2026
Abstract Epigenetic biomarkers offer critical insight into biological aging and disease risk, yet most deep learning models lack interpretability and generalization across tissues. We present a reproducible pipeline for interpretable age classificati...
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An snRNA-seq aging clock for the fruit fly head sheds light on sex-biased aging

bioRxiv Feb 23, 2026
Although multiple high-performing epigenetic aging clocks exist, few are based directly on gene expression. Such transcriptomic aging clocks allow us to identify potential age-associated genes directly. However, most existing transcriptomic clocks mo...
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Stabilization of recurrent neural networks through divisive normalization

bioRxiv Feb 23, 2026
Stability is a fundamental requirement for both biological and engineered neural circuits, yet it is surprisingly difficult to guarantee in the presence of recurrent interactions. Standard linear dynamical models of recurrent networks are sensitive t...
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Comprehensive top-down mass spectral repository enables pan-dataset analysis and top-down spectral prediction

bioRxiv Feb 23, 2026
Mass spectral libraries have become essential resources for training deep learning (DL) models for spectral prediction and de novo sequencing in bottom-up mass spectrometry (BU-MS). Compared with BU-MS, top-down MS (TD-MS) offers unique advantages fo...
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Inference of cancer driver mutations from tumor microenvironmentcomposition: a pan-cancer study with cross-platform external validation

bioRxiv Feb 23, 2026
Cancer driver mutations shape the tumor microenvironment (TME), yet whether TME composition alone can predict genotype has not been systematically evaluated across cancers with external validation. We trained machine learning models to predict driver...
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