bioRxiv

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Decoding protein–membrane binding interfaces from surface-fingerprint-based geometric deep learning and molecular dynamics simulations

bioRxiv Jan 1, 2025
Predicting protein–membrane interactions is a formidable challenge due to the subtle physicochemical features that distinguish membrane-binding regions of a protein surface, as well as the scarcity of experimentally resolved membrane-bound protein co...
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Multi-omics Integration of Microbiota Transplant Therapy in Children with Autism Spectrum Disorders

bioRxiv Jan 1, 2025
Microbiota transplant therapy (MTT) is a promising avenue for the substantial improvement of gastrointestinal and behavioral symptoms in children with autism spectrum disorder (ASD). Previous work has demonstrated that microbiome and metabolite profi...
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Developmental Dysregulation of Synaptic and Myelin-Related Genes in Frontal Cortex and Serum Infrared Spectroscopy Signature in the Valproic Acid Model of Autism

bioRxiv Jan 1, 2025
Neural circuits emerge during development through dynamic interactions between genetic instructions and environmental cues that shape cell fate, connectivity, and the timing of myelination. In developmental disorders such as autism, abnormalities in ...
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Accuracy and Scalability of Machine Learning Methods for Genotype-Phenotype Association Data

bioRxiv Jan 1, 2025
Many machine learning methods can be applied to predicting phenotypes from genetic data. Which of these methods work best remains an open question, however. To answer this question, we propose to compare a variety of approaches’ ability to predict a ...
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Long-Read epigenetic clocks identify improved brain aging predictions

bioRxiv Jan 1, 2025
Epigenetic clocks are widely used to estimate biological aging, yet most are built from array-based data from peripheral tissues of predominantly European-ancestry individuals, limiting generalizability. Here, we present aging clocks trained using Ge...
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Label-free 3D subcellular phenotyping of mouse embryos by holotomography enables early prediction of blastocyst formation

bioRxiv Jan 1, 2025
Accurate embryo quality assessment is central to improving outcomes in in vitro fertilization (IVF), yet current practice relies mainly on subjective two-dimensional (2D) morphology. Here we present a label-free framework for quantitative three-dimen...
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Neural network-based cross-species chromatin annotation goes beyond sequence conservation

bioRxiv Jan 1, 2025
Analogous to the Encyclopedia of DNA Elements (ENCODE) project, the Functional Annotation of ANimal Genomes (FAANG) consortium has produced chromatin annotations for domesticated animals, albeit in smaller amounts. Classical methods based on sequence...
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Re-emergence of orientation coding in primate IT cortex and deep networks reveals functional hubs for visual processing

bioRxiv Jan 1, 2025
The primate visual system is a hierarchical network of brain areas that transform retinal inputs into rich percepts. According to efficient neural coding principles, basic visual features such as orientation, which are already represented in early vi...
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The functional landscape of the human ubiquitinome

bioRxiv Jan 1, 2025
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme activation. Mass spectrometry-based proteomics ha...
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pLM-SAV: A Δ-Embedding Approach for Predicting Pathogenic Single Amino Acid Variants

bioRxiv Jan 1, 2025
Predicting whether single amino acid variants (SAVs) in proteins lead to pathogenic outcomes is a critical challenge in molecular biology and precision medicine. Experimental determination of all possible mutation effects is infeasible, and while sta...
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