bioRxiv

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Real-Time Segmentation and Classification of Birdsong Syllables for Learning Experiments

bioRxiv Jan 1, 2025
Songbirds are essential animal models for studying neuronal and behavioral mechanisms of learned vocalizations. Bengalese finch (Lonchura striata domestica) songs contain a limited number of acoustically distinct syllable types, which are combined in...
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Structure and evolution-guided design of minimal RNA-guided nucleases

bioRxiv Jan 1, 2025
The design of RNA-guided nucleases with properties not limited by evolution can expand programmable genome editing capabilities. However, generating diverse multi-domain proteins with robust enzymatic properties remains challenging. Here we use an ar...
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WSInsight as a cloud-native pipeline for single-cell pathology inference on whole-slide images

bioRxiv Jan 1, 2025
Digital pathology has increasingly embraced deep learning for large-scale tissue analysis, but most workflows remain limited by local execution and data accessibility.To address this challenge, we developed WSInsight, an open-source, cloud-native pip...
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Asymmetric Cross-Reactivity of Nuclear Receptors Reveals an Evolutionary Buffer Between Estrogen and Androgen Signaling

bioRxiv Jan 1, 2025
A comprehensive all-by-all receptor ligand affinity screen using Boltz-2, a deep learning framework for protein-ligand interaction prediction, reveals a previously unrecognized asymmetry in steroid hormone receptor binding. Using systematic in silico...
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Biologically Inspired Digital Histology for Deep Phenotyping of Placental Composition Changes Across Major Lesion Types

bioRxiv Jan 1, 2025
Placenta pathology provides diagnostic insights for understanding pregnancy complications and guides maternal and perinatal care. While placental abnormalities reflect both acute and chronic maternal-fetal health states, the organ’s spatial and tempo...
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Designing Convergent Overlapping Genes with Transformer Encoder Models and Lightweight Structural Proxies

bioRxiv Jan 1, 2025
Overlapping genes allow multiple proteins to be encoded from a single DNA sequence, including convergent (antisense; tail-to-tail) orientations across three reading frames (phases 0, 1, and 2), with phase 1 most frequently observed in nature. Designi...
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Benchmarking computational methods for multi-omics biomarker discovery in cancer

bioRxiv Jan 1, 2025
Multi-omics profiling characterizes cancer biology and supports biomarker discovery for prognosis and therapy selection. Although numerous computational methods have been proposed, their ability to identify clinically relevant biomarkers has not been...
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Analyzing associations and higher-order effects in multi-omics data with double machine learning

bioRxiv Jan 1, 2025
Integrative omics analyses enhance our understanding of disease mechanisms and biomarkers by investigating relationships among traits, omics measurements, genetic variants, and epidemiological factors. Statistically, these analyses are challenging an...
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Comprehensive Neural Representations of Naturalistic Stimuli through Multimodal Deep Learning

bioRxiv Jan 1, 2025
A central challenge in cognitive neuroscience is understanding how the brain represents and predicts complex, multimodal experiences in naturalistic settings. Traditional neural encoding models, often based on unimodal or static features, fall short ...
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Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry

bioRxiv Jan 1, 2025
Combined multi-omics analysis of proteomics, metabolomics, and lipidomics requires separate liquid chromatography–mass spectrometry (LC–MS), which limits throughput and increases costs, hindering the application of mass spectrometry-based multi-omics...
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