bioRxiv

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Center-surround inhibition by expectation: a neuro-computational account

bioRxiv Jan 1, 2025
Expectation is beneficial for adaptive behavior through quickly deducing plausible interpretations of information. The profile and underlying neural computations of this process, however, remain unclear. When participants expected a grating with a sp...
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Tissue Reassembly with Generative AI

bioRxiv Jan 1, 2025
The spatial arrangement of cells is fundamental to their function, but single-cell RNA sequencing loses spatial context by dissociating cells from tissues. We present LUNA, a generative AI model that reassembles dissociated cells into tissue structur...
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Recurrent dynamics underlying transient neural representations

bioRxiv Jan 1, 2025
Brain networks are high-dimensional and interacting complex systems that exhibit substantial structural heterogeneity as well as temporal variability. Yet, when exposed to a stimulus, their recurrent circuits perform reliable computations. The mechan...
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Coding for Circuit Integration in the Injured Brain by Transplanted Human Neurons

bioRxiv Jan 1, 2025
Neural transplantation holds the potential to repair damaged neural circuits in neurological diseases. However, it remains unknown how the grafted neurons project axons to and make functional connections with the appropriate targets to repair the dam...
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A natural history of AMR in Klebsiella pneumoniae: Global diversity, predictors, and predictions of evolutionary pathways

bioRxiv Jan 1, 2025
Antimicrobial resistance (AMR) is a substantial and growing global health burden. Understanding, and predicting, its evolution in specific pathogens will help responses across scales from individual patient cases to large-scale policy. Data-driven ap...
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Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies

bioRxiv Jan 1, 2025
Transcriptional regulation involves complex interactions with chromatin-associated proteins, but disentangling these mechanistically remains challenging. Here, we generate deep learning models to predict RNA Pol-II occupancy from chromatin-associated...
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Robust Prediction of Enzyme Variant Kinetics with RealKcat

bioRxiv Jan 1, 2025
Predicting enzyme kinetics directly from sequence remains a central challenge in computational biology, particularly in resolving the effects of mutations at catalytically essential residues. Existing models frequently overlook the functional consequ...
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DNAi: an open-source AI tool for unbiased DNA fiber analysis

bioRxiv Jan 1, 2025
DNA fiber assays are powerful tools for investigating replication dynamics at the single-molecule level. However, their application and widespread adoption has been hampered by the labor-intensive and tedious nature of manual analysis of large number...
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Best practices and challenges for urban tree detection, classification, and geolocation with street-level images across North American cities

bioRxiv Jan 1, 2025
Accurate and up-to-date catalogs of urban tree populations are crucial for quantifying ecosystem services and enhancing the quality of life in cities. However, identifying and mapping tree species cost-effectively remains a significant challenge. Rem...
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AlphaMissense pathogenicity scores predict response to immunotherapy and enhances the predictive capability of tumor mutation burden

bioRxiv Jan 1, 2025
Tumor Mutational Burden (TMB) is a widely used biomarker for selecting cancer patients for immune checkpoint inhibitor (ICI) therapy. However, TMB alone has limited predictive power, as it fails to account for the functional impact of mutations. We i...
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