bioRxiv

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Multi-agent AI enables evidence-based cell annotation in single-cell transcriptomics

bioRxiv Jan 1, 2025
Cell type annotation remains a critical bottleneck, with current methods often inaccurate and requiring extensive manual validation, particularly in disease contexts. While large language models (LLMs) show promise, they can be unreliable due to hall...
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cfOncoXpress: Tumor gene expression prediction from cell-free DNA whole-genome sequences

bioRxiv Jan 1, 2025
Cell-free DNA (cfDNA) fragments in the plasma capture cellular nucleosomal profiles since nucleosome-protected regions escape enzymatic degradation while nucleosome-depleted regions can not. We developed cfOncoXpress, a machine learning framework tha...
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Modelling cognitive outcomes in the UK Biobank: education, noradrenaline and frontoparietal networks

bioRxiv Jan 1, 2025
Education is often used as a surrogate measure of so called cognitive reserve (CR) benefiting cognitive functioning in later years. In line with Roberton’s theory we tested here a hypothesis that education acting on the noradrenergic system strengthe...
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Autonomous Liquid-handling Robotics Scripting for Accessible and Responsible Protein Engineering

bioRxiv Jan 1, 2025
Laboratory automation enhances experimental throughput and reproducibility, yet widespread adoption is constrained by the expertise required for robotic programming. Here, we introduce LabscriptAI, a multi-agent framework that enables large language ...
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Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy

bioRxiv Jan 1, 2025
Revealing how individual axons create a brain-wide connectome would be indispensable for understanding brain function and behavior, yet remains technically challenging. We introduce MAPL3, an end-to-end pipeline that integrates self-supervised learni...
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Targeting peptide–MHC complexes with designed T cell receptors and antibodies

bioRxiv Jan 1, 2025
Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise recognition of foreign or mutated peptide–MHC (pMHC) com...
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A memory-driven reinforcement learning model of phenotypic adaptation for anticipating therapeutic resistance in prostate cancer

bioRxiv Jan 1, 2025
While contemporary cancer treatment strategies have significantly prolonged the lives of patients, therapeutic resistance remains a predominant cause of disease progression and cancerrelated deaths. Cancer therapy often induces gene regulatory respon...
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AutoLead: An LLM-Guided Bayesian Optimization Framework for Multi-Objective Lead Optimization

bioRxiv Jan 1, 2025
The process of lead optimization in drug discovery is a complex, multi-objective challenge that remains a major bottleneck in the development of new therapeutics. Traditional approaches often struggle to efficiently explore the vast chemical space wh...
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Identity Domains Reveal How Life Experiences and the Microbiome Shape Individuality and Uncover the Presence of Social Memory in Drosophila

bioRxiv Jan 1, 2025
Personality is comprised of enduring traits that shape behavior across contexts and over time. Yet outside humans, research often equates individuality with personality, focusing on how one animal differs from another in each behavior. This overlooks...
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Low rank adaptation of chemical foundation models generates effective odorant representations

bioRxiv Jan 1, 2025
Featurizing odorants to enable robust prediction of their properties is difficult due to the complex activation patterns that odorants evoke in the olfactory system. Structurally similar odorants can elicit distinct activation patterns in both the se...
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