bioRxiv

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Pocket Restraints Guided by B-Cell Epitope Prediction Improves Chai-1 Antibody-Antigen Structure Modeling

bioRxiv Jan 1, 2025
The accurate prediction of antibody-antigen (AbAg) complexes is a key challenge for computational immunology, with applications in therapeutic antibody design and diagnostics. Current deep learning methods, such as AlphaFold and Chai, have the potent...
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PolyGraph – Flexible, Biocompatible & Electrically Optimised Graphene-Polymer Composites for Next-Generation Neural Interfaces

bioRxiv Jan 1, 2025
Neural interfacing materials must deliver exceptional electrochemical performance, while integrating safely with the central nervous system. In this study we develop PolyGraph, a flexible, conductive, and biocompatible graphene-polycaprolactone (PCL)...
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Exploring Augmentation-Driven Invariances for Graph Self-supervised Learning in Spatial Omics

bioRxiv Jan 1, 2025
Spatial omics technologies provide rich insights into biological processes by jointly capturing molecular profiles and the spatial organization of cells. The resulting high-dimensional data can be naturally represented as graphs, where Graph Neural N...
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Asymmetric cortical projections to striatal direct and indirect pathways distinctly control actions

bioRxiv Jan 1, 2025
The striatal direct and indirect pathways constitute the core for basal ganglia function in action control. Although both striatal D1- and D2-spiny projection neurons (SPNs) receive excitatory inputs from the cerebral cortex, whether or not they shar...
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Predicting Clinical Outcomes in Helicobacter pylori-positive Patients using Supervised Learning through the Integration of Demographic and Genomic Features

bioRxiv Jan 1, 2025
Helicobacter pylori (H. pylori) infection is widespread globally and is linked to outcomes ranging from chronic gastritis to gastric cancer. However, only a minority of infected individuals progress to malignancy, influenced by a mix of bacterial, ho...
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Whole tissue spatial cellular analysis reveals increased macrophage infiltration in pancreata of autoantibody positive donors and patients with type 1 diabetes

bioRxiv Jan 1, 2025
While extensive efforts have characterized lymphoid populations that contribute to pancreatic ‘insulitis’ in type 1 diabetes, significant gaps remain regarding key properties of macrophages in this inflammatory lesion. Hence, we quantified the spatia...
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BioMedGraphica: An All-in-One Platform for Joint Textual Biomedical Prior Knowledge and Numeric Graph Generation

bioRxiv Jan 1, 2025
Multi-omic data analysis is essential for scientific discovery in precision medicine. However, translating statistical results of omic data analysis into novel scientific hypothesis remains a significant challenge. Human experts must manually review ...
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AMICI: Attention Mechanism Interpretation of Cell-cell Interactions

bioRxiv Jan 1, 2025
Spatial transcriptomic data enable study of cell–cell communication, yet current analysis tools often fail to provide dynamic, interpretable estimates of interactions and their spatial range across tissue. We present AMICI, an interpretable attention...
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Dual Inference Routes for Natural Language Hypothesis Generation in Multimodal Drug Discovery: An Early Experimentation Study

bioRxiv Jan 1, 2025
This study presents an early experimentation of a modular AI framework for multimodal drug discovery that integrates natural product based therapies with modern pharmaceuticals. The system combines structured biomedical data, knowledge graphs, and la...
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BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML

bioRxiv Jan 1, 2025
Large language model (LLM) agents hold promise for accelerating biomedical research and development (R&D). Several biomedical agents have recently been proposed, but their evaluation has largely been restricted to question answering (e.g., LAB-Bench)...
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