bioRxiv

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WormSpot: a machine learning-powered viability scoring platform in C. elegans for Candida pathogenicity studies

bioRxiv Jan 1, 2025
Invasive Candida infections pose a critical health challenge, exacerbated by emerging antifungal resistance. Caenorhabditis elegans (C. elegans) offers a genetically tractable and scalable model for studying Candida pathogenicity, yet conventional vi...
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Physical Network Constraints Define the Multiplicative Architecture of the Brain’s Connectome

bioRxiv Jan 1, 2025
The brain has long been conceptualized as a network of neurons connected by synapses. However, attempts to describe the connectome using established network science models have yielded conflicting outcomes, leaving the architecture of neural networks...
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JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics

bioRxiv Jan 1, 2025
As spatially resolved transcriptomics (SRT) datasets increasingly span multiple adjacent or replicated slices, effective joint analysis across slices is needed to reconstruct tissue structures and identify consistent spatial gene expression patterns....
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Human gloss perception reproduced by tiny neural networks

bioRxiv Jan 1, 2025
A key goal of visual neuroscience is to explain how our brains infer object properties like colour, curvature, or gloss. Here, we used machine learning to identify computations underlying human gloss judgments from object images—traditionally conside...
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Systematic discovery of single-cell protein networks in cancer with Shusi

bioRxiv Jan 1, 2025
Context-specific protein-protein interaction (PPI) drive heterogeneity of primary tumor, forming a formidable challenge to effective cancer therapy. However, systematically mapping and modeling these interactions at single-cell resolution across dive...
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Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT

bioRxiv Jan 1, 2025
Spatial transcriptomics (ST) is a powerful tool for studying the molecular basis of brain diseases. However, most current analyses focus only on nuclear or somatic expression, overlooking distally localized mRNAs, known as the “dark transcriptome.” T...
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Micellangelo: a Generative Model of Cell-Topography Interactions

bioRxiv Jan 1, 2025
Understanding how materials influence cell behavior is central to biomaterial engineering, yet experimental approaches are limited by throughput and complexity. Here, we present Micellangelo, a generative AI model that simulates high-resolution fluor...
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AXIS: A Lab-in-the-Loop Machine Learning approach for generalized detection of macromolecular crystals

bioRxiv Jan 1, 2025
Macromolecular crystallography provides mechanistic understanding of biological processes and can be applied in drug design. Nowadays, the use of robotic systems for crystal growth and diffraction analysis is widespread and high throughput protein-to...
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Integrative epigenomic analysis uncovers asymmetry of enhancer activity in Brassica napus

bioRxiv Jan 1, 2025
Non-coding regulatory regions are essential to the determination of gene expression and plant phenotypes. In this work, we investigated the cis-regulatory landscape of a winter type rapeseed, Express617, across multiple sample types. Combining chroma...
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AI-Driven and 3D-Bioprinted New Approach Methodology (NAM) Identifies NEO100 as Potent Ultrasound-Activated Therapeutic for Primary and Metastatic Brain Tumors

bioRxiv Jan 1, 2025
Primary and metastatic brain tumors are among the deadliest and treatment-resistant cancers, mainly because of their inherent resistance to chemoradiation and limited drug delivery across the blood–brain barrier (BBB). Identifying molecules that can ...
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