bioRxiv

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The brain’s lipid landscapes uncovered by mass spectrometry imaging and explainable machine learning

bioRxiv Jan 1, 2025
Recent computational advances in mass-spectrometry imaging (MSI) now enable unprecedented insight into organ-wide molecular composition and functional architecture. We present the first high-resolution, molecular-computational atlas of the brain lipi...
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Unfolding the Black Box of Recurrent Neural Networks for Path Integration

bioRxiv Jan 1, 2025
Path integration is essential for spatial navigation. Experimental studies have identified neural correlates for path integration, but exactly how the neural system accomplishes this computation remains unresolved. Here, we adopt recurrent neural net...
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Global Analysis of Aggregation Determinants in Small Protein Domains

bioRxiv Jan 1, 2025
Protein aggregation is an obstacle for engineering effective recombinant proteins for biotechnology and therapeutic applications. Predicting protein aggregation propensity remains challenging due to the complex interplay of sequence, structure, envir...
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Overlooked features lead to divergent neurobiological interpretations of brain-based machine learning biomarkers

bioRxiv Jan 1, 2025
A central objective in human neuroimaging is to understand the neurobiology underlying cognition and mental health. Machine learning models trained on brain connectivity data are increasingly used as tools for predicting behavioral phenotypes 1,2, en...
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Molecular Evolution under Macro-Perturbation Barrier and the Fixation Process of Polyploidization

bioRxiv Jan 1, 2025
The Neutral Theory in molecular evolution mainly addresses the allele frequency change of individual loci, postulating that the fixation process of a mutant is independent of other loci. For instance, the basic formula of molecular evolution claims t...
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CCK * (Convex Closure K *): A Suite of Algorithms for the De Novo Design of L- and D-peptide Binders

bioRxiv Jan 1, 2025
The computational design of L-peptides and their mirror-image counterparts, D-peptides, is a valuable area in drug design. L- and D-peptides offer exceptional structural diversity and high binding specificity, while D-peptides additionally confer cri...
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Accessible AI Enhances Monitoring of Coral Seeding Devices in Reef Restoration

bioRxiv Jan 1, 2025
1. Coral seeding devices (CSDs) – tools designed to deliver sexually propagated corals to target locations – offer a promising means to increase coral abundance on degraded reefs. However, evaluating CSD effectiveness for coral reef restoration acros...
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Examining Selection Dynamics and Limitations in Multi-round Protein Selection of High Diversity Libraries

bioRxiv Jan 1, 2025
Proteins and peptides underpin essential biological functions and technological applications, from targeting disease-relevant interactions to providing broad enzymatic activities. However, engineering molecules with desired properties remains difficu...
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Preference-Based Fine-Tuning of Genomic Sequence Models for Personal Expression Prediction with Data Augmentation

bioRxiv Jan 1, 2025
Despite substantial progress in genomic foundation models, accurately predicting inter-individual variation in gene expression from DNA sequence alone remains a major challenge. Current sequence-based models, such as Enformer and Borzoi, trained excl...
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Computational design of cysteine proteases

bioRxiv Jan 1, 2025
Despite advances in de novo enzyme design, success has been largely limited to low energy barrier model reactions. Amide bonds such as those linking amino acids along the peptide backbone are stable for hundreds of years in neutral aqueous solution b...
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