bioRxiv

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A compressed code for memory discrimination

bioRxiv Jan 1, 2025
The ability to discriminate similar visual stimuli has been used as an important index of memory function. This ability is widely thought to be supported by expanding the dimensionality of relevant neural codes, such that neural representations for t...
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Supervised machine learning identifies impaired mitochondrial quality control in β cells with development of type 2 diabetes

bioRxiv Jan 1, 2025
In type 2 diabetes (T2D), molecular pathways driving β cell failure are difficult to resolve with standard single cell analysis. Here we developed an interpretable, supervised machine learning framework that couples sparse rule-based classification (...
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Citizen science gamers enable automated flow cytometry gating through machine learning

bioRxiv Jan 1, 2025
Manual flow cytometry gating requires up to one hour per sample with 32% inter-expert variability, creating critical bottlenecks in immunological research reproducibility. To address this, we developed flowMagic, a machine learning algorithm for auto...
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Generative modeling for RNA splicing prediction and design

bioRxiv Jan 1, 2025
Alternative splicing (AS) of pre-mRNA plays a crucial role in tissue-specific gene regulation, with disease implications due to splicing defects. Predicting and manipulating AS can therefore uncover new regulatory mechanisms and aid in therapeutics d...
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From model to field: predictive design of microbial communities for resilient crop performance

bioRxiv Jan 1, 2025
Synthetic microbial communities (SynComs) represent a promising approach to enhance crop growth and stress resilience through microbiome engineering. However, the systematic design and field validation of SynComs remain limited. Here, we present a pr...
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Cardiometabolic health and physical robustness map onto distinct patterns of brain structure and neurotransmitter systems

bioRxiv Jan 1, 2025
The link between brain health and risk/protective factors for non-communicable diseases (such as high blood pressure, high body mass index, diet, smoking, physical activity, etc.) is increasingly acknowledged. However, the specific effects that these...
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Designing a Model to Detect Beta Burst in EEG Using Nonlinear Dynamic Features Based on Machine Learning

bioRxiv Jan 1, 2025
Beta bursts are brief, transient increases in beta-band (13–30 Hz) EEG activity that play a key role in motor control, particularly in processes like movement initiation and inhibition. While most existing methods detect these bursts using simple amp...
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A deep learning approach for rational affinity maturation of anti-VEGF nanobodies

bioRxiv Jan 1, 2025
Nanobodies offer several advantages over conventional antibodies due to their lower immunogenicity, enhanced stability, and superior tissue penetration, making them promising candidates for cancer therapy. In this study, we employ deep learning algor...
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A Genomic Language Model for Zero-Shot Prediction of Promoter Variant Effects

bioRxiv Jan 1, 2025
Disease-associated genetic variants occur extensively in noncoding regions like promoters, but current methods focus primarily on single nucleotide variants (SNVs) that typically have small regulatory effect sizes. Expanding beyond single nucleotide ...
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Building an ‘epigenetic clock’: Utilizing whole genome DNA methylation patterns to predict age in haddock, Melanogrammus aeglefinus

bioRxiv Jan 1, 2025
Age-based population models are a gold standard approach to estimate stock size and sustainable catch recommendations for effective fisheries management. Traditional ageing by counting annuli on their ear stones (otoliths), is labor-intensive, lethal...
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