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SARS-CoV-2

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A hybrid inception-dilated-ResNet architecture for deep learning-based prediction of COVID-19 severity.

Scientific reports
Chest computed tomography (CT) scans are essential for accurately assessing the severity of the novel Coronavirus (COVID-19), facilitating appropriate therapeutic interventions and monitoring disease progression. However, determining COVID-19 severit...

Disease diagnostics using machine learning of B cell and T cell receptor sequences.

Science (New York, N.Y.)
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system's own record of antigen exposures encoded by receptors on B cells and T ce...

RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing Epitopes.

Journal of chemical information and modeling
Interleukin-6 (IL-6) is a critical cytokine involved in immune regulation, inflammation, and the pathogenesis of various diseases, including autoimmune disorders, cancer, and the cytokine storm associated with severe COVID-19. Identifying IL-6 induci...

T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment.

Journal of chemical information and modeling
There is significant interest in targeting disease-causing proteins with small molecule inhibitors to restore healthy cellular states. The ability to accurately predict the binding affinity of small molecules to a protein target in silico enables the...

A web-based artificial intelligence system for label-free virus classification and detection of cytopathic effects.

Scientific reports
Identifying viral replication within cells demands labor-intensive isolation methods, requiring specialized personnel and additional confirmatory tests. To facilitate this process, we developed an AI-powered automated system called AI Recognition of ...

Identification of biomarkers in Alzheimer's disease and COVID-19 by bioinformatics combining single-cell data analysis and machine learning algorithms.

PloS one
BACKGROUND: Since its emergence in 2019, COVID-19 has become a global epidemic. Several studies have suggested a link between Alzheimer's disease (AD) and COVID-19. However, there is little research into the mechanisms underlying these phenomena. The...

Using Machine Learning and Optical Microscopy Image Analysis of Immunosensors Made on Plasmonic Substrates: Application to Detect the SARS-CoV-2 Virus.

ACS sensors
In this article, we introduce a diagnostic platform comprising an optical microscopy image analysis system coupled with machine learning. Its efficacy is demonstrated in detecting SARS-CoV-2 virus particles at concentrations as low as 1 PFU (plaque-f...

RNA-protein interaction prediction using network-guided deep learning.

Communications biology
Accurate computational determination of RNA-protein interactions remains challenging, particularly when encountering unknown RNAs and proteins. The limited number of RNAs and their flexibility constrained the effectiveness of the deep-learning models...

Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern.

PLoS computational biology
With the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its increasing adaptation to humans, several variants of concern (VOCs) and variants of interest (VOIs) have been identified since late 2020. These include...

Unraveling microglial spatial organization in the developing human brain with DeepCellMap, a deep learning approach coupled with spatial statistics.

Nature communications
Mapping cellular organization in the developing brain presents significant challenges due to the multidimensional nature of the data, characterized by complex spatial patterns that are difficult to interpret without high-throughput tools. Here, we pr...