bioRxiv

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Accurate and scalable multi-disease classification from adaptive immune repertoires

bioRxiv Jan 1, 2025
Machine learning models trained on paratope-similarity networks have shown superior accuracy compared with clonotype-based models in binary disease classification. However, the computational demands of paratope networks hinder their use on large data...
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BIOTIA-DX RESISTANCE Achieved the Best Antimicrobial Resistance Phenotype Prediction Accuracy at CAMDA 2025

bioRxiv Jan 1, 2025
We have developed BIOTIA-DX RESISTANCE (BDXR), a bioinformatic tool for predicting antimicrobial resistance (AMR) from whole genome sequencing of microbial isolates. BDXR achieved the best accuracy of any submission to the CAMDA 2025 AMR Challenge. T...
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Neurotype matching in monogamous rodents is modulated by early-life sleep experience

bioRxiv Jan 1, 2025
Studies of human sociability indicate stronger social affinity in matched-neurotype dyads (e.g., two individuals with autism or two without) compared to mixed-neurotype dyads (e.g., one individual with autism paired with one without). Is this neuroty...
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Partial Inhibition of Viral Replication Machinery Enhances Recombination in Herpes Simplex Viruses

bioRxiv Jan 1, 2025
Herpes simplex viruses (HSV-1 and HSV-2) are widespread human pathogens, most commonly causing oral and genital lesions. These DNA viruses use recombination as a major driver of evolution. Intragenomic and intergenomic recombination events can be det...
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Gene-Family Encoding Boosts Domain-Adapted Single-Cell Language Models

bioRxiv Jan 1, 2025
Transformer-based single-cell foundation models often rely on ranked-gene (RG) sequences where genes, ranked by expression, are often not functionally related, weakening next-token learning and the structure of learned embeddings. Here, we introduce ...
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A comparative study of plant phenotyping workflows based on three-dimensional reconstruction from multi-view images

bioRxiv Jan 1, 2025
With the world facing escalating food demand, limited agricultural land, and environmental change, there is a growing need for data-driven sustainable agricultural management. Advances in sequencing and sensor networks have reduced costs of acquiring...
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Linking brain structure to stress reactivity: Cingulate surface area predicts acute cortisol responses

bioRxiv Jan 1, 2025
Altered stress responses are closely linked to mental disorders, but the role of brain structure in acute cortisol responses to psychosocial stress remains underexplored, particularly in healthy individuals. Previous studies, with predominantly small...
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Conformal Prediction of Molecule-induced Cancer Cell Growth Inhibition Challenged by Strong Distribution Shifts

bioRxiv Jan 1, 2025
The drug discovery process often employs phenotypic and target-based virtual screening to identify potential drug candidates. Despite the longstanding dominance of target-based approaches, phenotypic virtual screening is undergoing a resurgence due t...
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Retrospective image analysis for long-term demography using Google Earth imagery

bioRxiv Jan 1, 2025
Ecosystems are rapidly degrading. Widely used approaches to monitor ecosystems to manage them effectively are both expensive and time consuming. The recent proliferation of publicly available imagery from satellites, Google Earth, and citizen-science...
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FAST: Filamentous Actin Segmentation Tool for quantifying cytoskeletal organization

bioRxiv Jan 1, 2025
Studying how actin filaments are assembled into different subcellular structures can provide insights into both physiological processes and the mechanisms of disease. However, quantifying the size, abundance, and organization of different classes of ...
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