bioRxiv

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Evolutionary Tree in Chemical Space of Natural Products

bioRxiv Jan 1, 2025
Natural products (NPs) are key to biological function and adaptation, with their distribution shaped by complex evolutionary and ecological forces. While it may seem reasonable to assume that closely related species produce chemically similar NPs, th...
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DeviceAgent: An autonomous multimodal AI agent for flexible bioelectronics

bioRxiv Jan 1, 2025
The development of flexible bioelectronics remains a complex, multidisciplinary process that demands specialized expertise and labor-intensive efforts, limiting scalability, adaptability and accessibility. Here, we introduce DeviceAgent, an autonomou...
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Cell-type-specific encoding of prediction and reward in cortical microcircuits during novelty detection

bioRxiv Jan 1, 2025
Cortical circuits comprise diverse neuron types whose distinct activity patterns suggest specialized computational roles. Recent large-scale recordings reveal striking, cell-type-specific responses to novelty in cortex: excitatory neurons respond str...
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Linking protein residues in literature and structure

bioRxiv Jan 1, 2025
Protein structures are crucial in understanding function, mechanism and disease-causing variants of proteins within any living cell. A number of experimental techniques are employed by researchers to determine said structure. Through structure inspec...
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Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer

bioRxiv Jan 1, 2025
The study of cell-free circulating DNA (cirDNA) fragments (fragmentomics) from liquid biopsies has received increasing attention. By constructing an atlas of these well-positioned nucleosomes, which we called WPNA, we found that their occupancy was a...
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Consensus Pituitary Atlas, a scalable resource for annotation, novel marker discovery and analyses in pituitary gland research

bioRxiv Jan 1, 2025
Previous single-cell profiling studies of the pituitary gland have yielded minimally reproducible insights largely due to their low statistical power and methodological inconsistencies. To address this problem, we generated a uniformly pre-processed ...
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Diverse Perceptual Representations Across Visual Pathways Emerge from A Single Objective

bioRxiv Jan 1, 2025
How the human brain supports diverse behaviours has been debated for decades. The canonical account posits distinct pathways in perceptual processing, such as the “what” and “where/how” visual streams, though their developmental origins and interdepe...
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It’s Not Always Crystal Clear: In-Pocket Analysis for Understanding Binding Site Microenvironment Properties

bioRxiv Jan 1, 2025
Structural biology enabled key advances in biochemistry, drug discovery, and AI-driven three-dimensional structure modelling. Despite its centrality, no general and reliable computational tools exist to chemically validate structural models, especial...
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Deep learning for mass extinction detection on fossilized phylogenies: power, limitations, and lessons for simulation-based phylodynamic inference

bioRxiv Jan 1, 2025
Detecting mass extinction events from phylogenies is a fundamental yet challenging task. While traditional likelihood-based methods are available, deep learning offers a powerful, simulation-based alternative. Here, we evaluate a deep learning approa...
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Usefulness of scRNA-seq data in predicting plant metabolic pathway genes

bioRxiv Jan 1, 2025
It is an ever challenging task to make genome-wide predictions for plant metabolic pathway genes (MPGs) encoding enzymes that catalyze the biosynthesis of plant natural products. Here, starting from 1,129 benchmark MPGs that have experimental evidenc...
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