bioRxiv

Showing 4731 to 4740 of 5021 articles

Classifying Calcium Imaging Dynamics with Deep Learning: Multi-Frequency Analysis through Quantile-Based Time-Series Network Representations

bioRxiv Jan 1, 2025
To address the limitations of calcium imaging data, we propose a segmentation-agnostic deep learning framework that integrates Quantile-Based Time-Series Network (QTN) representations with convolutional neural networks to classify neuronal dynamics a...
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LAMPP: A benchmark for continuous evaluation of host phenotype prediction from shotgun metagenomic data

bioRxiv Jan 1, 2025
Predicting host phenotypes from shotgun metagenomic data is essential for translating microbiome research into clinical practice. Despite the development of numerous computational tools for this task, researchers often default to traditional machine ...
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A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

bioRxiv Jan 1, 2025
Acute myeloid leukemia (AML) often enters remission after chemotherapy but frequently relapses due to chemotherapy-resistant leukemic stem cells (LSCs). Relapsed AML remains largely unresponsive to current therapies and carries a poor prognosis. We d...
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Pili are essential for conjugation also in many Gram-positive bacteria

bioRxiv Jan 1, 2025
Type IV secretion systems (T4SS) enable the spread of antibiotic resistance and other virulence factors. In Gram-positive bacteria, T4SSs have long been thought to lack VirB2-like proteins that form conjugative pili and instead rely on adhesins for c...
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scPRINT-2: Towards the next-generation of cell foundation models and benchmarks

bioRxiv Jan 1, 2025
Cell biology has been booming with foundation models trained on large single-cell RNA-seq databases, but benchmarks and capabilities remain unclear. We propose an additive benchmark across a gymnasium of tasks to discover which features improve perfo...
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MeLSI: Metric Learning for Statistical Inference in Microbiome Community Composition Analysis

bioRxiv Jan 1, 2025
Microbiome beta diversity analysis relies on distance-based methods including PERMANOVA combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly regardless of their biolo...
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Non-linear gene sets for digital biomarkers of amyotrophic lateral sclerosis

bioRxiv Jan 1, 2025
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by the loss of motor neurons. Accurate and accessible blood-based diagnosis of neurodegenerative diseases, including ALS, is becoming increasingly critical. It would be o...
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Memory network activity flow failures in temporal and frontal lobe epilepsy

bioRxiv Jan 1, 2025
Declarative memory deficits represent considerable challenges to adequate functioning and wellbeing in temporal lobe epilepsy (TLE) and frontal lobe epilepsy (FLE), two of the most common pharmaco-resistant epilepsies. TLE and FLE are impacted differ...
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Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens

bioRxiv Jan 1, 2025
Accurate prediction of ligand-bound protein complexes and ranking them by affinity are central problems in drug discovery. While deep learning co-folding methods can help address these challenges, their evaluation has been hampered by the difficultie...
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A Mechanism-Aware Dual Attention Deep Model for Molecular-Protein Binding Affinity Prediction with Enhanced Generalizability and Interpretability

bioRxiv Jan 1, 2025
Accurate prediction of molecular-protein binding affinity (MPBA) is paramount in drug discovery, yet current computational models often lack generalizability, interpretability, and explicit mechanistic understanding. To address these limitations, we ...
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