bioRxiv

Showing 4181 to 4190 of 5016 articles

Evaluation of computational tools for predicting CRISPR gRNA on-target efficiency in plants

bioRxiv Jan 1, 2025
CRISPR technologies has become an integral part of plant biotechnology, synthetic biology and basic plant research, routinely used by researchers for targeted genome modifications. CRISPR guide RNAs (gRNAs) undermines the highly programmable nature o...
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Benchmarking generative AI tools for literature retrieval and summarization in genomic variant interpretation

bioRxiv Jan 1, 2025
Generative AI is increasingly used to extract structured information across domains, but its reliability in academic and clinical research, where precision and accuracy are essential, remains largely unexplored. This study evaluates the ability of La...
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Temporal Expression Prediction by Integrating Genome Dynamics via Spatio-temporal GNNs

bioRxiv Jan 1, 2025
Temporal gene expression is being analyzed via high-throughput profiling of molecular data over time. The expression values of genes are impacted by their previous expression values as well as the expression of interacting genes over time. Hi-C provi...
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Multi-omics integration and batch correction using a modality-agnostic deep learning framework

bioRxiv Jan 1, 2025
State-of-the-art biotechnologies allow the detection of different molecular species on the same biological sample, generating complex highly-dimensional multi-modal datasets. Gaining a holistic understanding of biological phenomena, such as oncogenes...
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Hybrid Epidemic–Neuronal Dynamics: A SEIR–FitzHugh–Nagumo Model for Information Flow in Complex Neural Networks

bioRxiv Jan 1, 2025
Information transfer in neural systems is often modeled through diffusive or synaptic mechanisms that fail to capture the contagion-like propagation of activation across large-scale networks. In this study, we introduce a hybrid SEIR–FitzHugh– Nagumo...
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An Immuno-Linguistic Transformer for Multi-Scale Modeling of T-Cell Spatiotemporal Dynamics

bioRxiv Jan 1, 2025
Understanding the spatiotemporal dynamics of T-cell clones is a critical challenge in immunology and immunotherapy, with direct implications for cancer treatment and vaccine design. While Large Language Models (LLMs) have demonstrated immense power i...
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BiomarkerML: A cloud-based proteomics ML workflow for biomarker discovery

bioRxiv Jan 1, 2025
High-throughput affinity and mass-spectrometry-based proteomic studies of large clinical cohorts generate high-dimensional proteomic data useful for accelerated disease biomarker discovery. A powerful approach to realizing the potential of these big,...
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Deep Learning-Based Genetic Perturbation Models Do Outperform Uninformative Baselines on Well-Calibrated Metrics

bioRxiv Jan 1, 2025
Single cell genetic perturbation modeling involves predicting the effects of unobserved genetic manipulations, enabling scalable in silico screens for target discovery. Recent reports have claimed that deep learning-based perturbation models fail to ...
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Enhancing Medical Image Segmentation through Negative Sample Integration: A Study on Kvasir-SEG and Augmented Datasets

bioRxiv Jan 1, 2025
Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, with early and accurate detection being critical for improving patient outcomes. Automated image segmentation using deep learning has emerged as a transformative t...
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Mechanical stretch disrupts calcium dynamics and redistributes Piezo1 in human astrocytes

bioRxiv Jan 1, 2025
Astrocytes regulate the activity of nearby neurons so disruption of astrocyte calcium dynamics by traumatic brain injury (TBI) could have profound consequences for neural network activity in the brain. In this study, human induced pluripotent stem ce...
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