bioRxiv

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Understanding cortical computation through the lens of joint-embedding predictive architectures

bioRxiv Jan 1, 2025
Tracking prey or recognizing a lurking predator is as crucial for survival as anticipating their actions. To guide behavior, the brain must extract information about object identities and their dynamics from entangled sensory inputs. How it accomplis...
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Automated Annotation of Plant Gene Regions Using Supervised Machine Learning

bioRxiv Jan 1, 2025
Rapid sequencing now enables analysis across many species, including plants, but repeat-rich, redundant plant genomes still hinder precise annotation. Precise gene calls are vital for understanding biology, comparative genomics, and discovering trait...
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Sequence-aware Prediction of Point Mutation-induced Effects on Protein-Protein Binding Affinity using Deep Learning

bioRxiv Jan 1, 2025
Amino acid mutations may lead to significant changes in the binding affinity of protein complexes, thereby causing a series of cellular dysfunctions. Therefore, accurate prediction of protein-protein binding affinity changes (ΔΔG) induced by amino ac...
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A Minimal Plasma Proteome-Based Biomarker Panel for Accurate Prostate Cancer Diagnosis

bioRxiv Jan 1, 2025
Early and accurate diagnosis of prostate cancer (PRC) remains a major clinical challenge, particularly with existing biomarker panels relying on invasive sampling or large biomarker panels with limited interpretability. Here, we present a machine lea...
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Quantum and Classical Graph Convolutional Neural Networks for Protein Ligand Dissociation Constant Prediction

bioRxiv Jan 1, 2025
How long a drug stays bound to its target-the residence time - is now recognized as a stronger in vivo efficacy driver than binding affinity alone. Yet current machine learning (ML) models for dissociation kinetics (koff) ignore two critical sources ...
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IMMUNIA: A Multi-LLM Reasoning Agent for Immunoregulatory Surfaceome Discovery

bioRxiv Jan 1, 2025
Biomarker discovery for immunotherapy often requires reasoning across complex immune contexts. We present IMMUNIA, a multi-large-language-model (multi-LLM) reasoning agent designed to identify immunoregulatory surfaceome genes through interpretable, ...
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Integrative transcriptomic analysis identifies miR-642a-5p as a regulator of POFUT1 expression in colon cancer

bioRxiv Jan 1, 2025
Colorectal cancer (CRC) is one of the most common and deadly cancers worldwide, underscoring the urgent need for novel biomarkers and therapeutic targets. Protein O-fucosyltransferase 1 (POFUT1) is increasingly recognized as an oncogenic driver in CR...
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SOORENA: Self-lOOp containing or autoREgulatory Nodes in biological network Analysis

bioRxiv Jan 1, 2025
Autoregulatory mechanisms, in which proteins modify their own activity or expression, are fundamental components of biological regulatory systems but remain challenging to identify systematically within the scientific literature. Manual curation is o...
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LINKER-Pred: A Public Web Server for Accurate Prediction of Disordered Flexible Linkers in Proteins

bioRxiv Jan 1, 2025
Disordered Flexible Linkers (DFLs) are unstructured regions that play critical roles in inter-domain communication and multivalent protein interactions. Despite their biological significance, the accurate identification of DFLs remains challenging du...
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GlomExtractor: a versatile tool for extracting glomerular patches from whole slide kidney biopsy images

bioRxiv Jan 1, 2025
The extraction of glomerular image patches is a key step prior to the training and application of glomerular classification models. Numerous algorithms for detecting and segmenting glomeruli have already been described in the literature, but standard...
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