AIMC Journal:
bioRxiv

Showing 2291 to 2300 of 4979 articles

CrossAffinity: A Sequence-Based Protein-Protein Binding Affinity Prediction Tool Using Cross-Attention Mechanism

bioRxiv Feb 23, 2026
Protein-protein binding affinity is important for understanding protein interactions within a protein complex and for identifying strong drug-peptide binders to a target protein. Many structure-based models were built previously with reasonable perfo...
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Bacterial protein function prediction via multimodal deep learning

bioRxiv Feb 22, 2026
Bacterial proteins are specialized with extensive functional diversity for survival in diverse and stressful environments. A significant portion of these proteins remains functionally uncharacterized, limiting our understanding of bacterial survival ...
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Leveraging Large Language Models to Extract Prognostic Pathology Features in Ewing Sarcoma

bioRxiv Feb 22, 2026
Background: Current risk stratification for Ewing sarcoma relies heavily on clinical factors such as metastatic status, failing to capture histologic heterogeneity as a potential prognostic indicator. Although pathology reports contain rich biologica...
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Reconstructing multi-scale tissue spatial architecture from single-cell RNA-seq with REMAP

bioRxiv Feb 22, 2026
Understanding spatial organization of cells is critical for deciphering tissue function and disease. Single-cell RNA-sequencing (scRNA-seq) profiles transcriptomes at scale but loses spatial context, while spatial transcriptomics (ST) preserves spati...
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Accelerated sampling of protein dynamics using BioEmu augmented molecular simulation

bioRxiv Feb 21, 2026
We introduce a workflow that integrates BioEmu-generated conformational ensemble with physics-based molecular simulations and Markov State Models to sample Boltzmann-weighted conformational populations across biomolecules. Molecular simulations initi...
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Genomic-island cassette architecture drives pathogenic Enterococcus cecorum lineages: Cassette2Vec-EC, a structural genomics and machine-learning framework

bioRxiv Feb 21, 2026
Mobile genetic elements and genomic islands (GIs) frequently encode antibiotic resistance and host-adaptation cargo, yet routine genome comparison pipelines often miss the higher-order organization of how genes co-occur as transferable, GI-anchored m...
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Development and Characterization of Self-Tracing Neural Progenitor Cells for Mapping Their Synaptic Integration into Endogenous Neural Networks

bioRxiv Feb 21, 2026
Neural progenitor cell (NPC) transplantation holds immense promise for neurodegenerative and traumatic central nervous system (CNS) pathologies. However, it is crucial to define which neural circuits and pathways are targeted with transplanted NPCs u...
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A lateral temporal network for transmodal combinatorial semantics: Convergent evidence from a multi-study investigation

bioRxiv Feb 20, 2026
This study integrates three literatures typically examined in isolation: single-concept semantics, combinatorial semantics, and theory of mind (ToM). We argue that these domains share overlapping computational principles and neuroanatomical networks....
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AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

bioRxiv Feb 20, 2026
Aptamers are single-stranded oligonucleotides that bind molecular targets with high affinity and specificity. However, their discovery remains time-consuming, expensive, and susceptible to experimental biases. Here we present AptaBLE, a deep learning...
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BEEP Learning: Multi-View Image Decomposition for Massively Multiplexed Biological Fluorescence Microscopy

bioRxiv Feb 20, 2026
Fluorescence imaging with spectrally variant fluorophores allows the spatial mapping of biological structures with exquisite cellular and molecular specificity. However, the ability to robustly discriminate multiple fluorophores in any single imaging...
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