AIMC Topic: Host-Pathogen Interactions

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A tuberculosis ontology for host systems biology.

Tuberculosis (Edinburgh, Scotland)
A major hurdle facing tuberculosis (TB) investigators who want to utilize a rapidly growing body of data from both systems biology approaches and omics technologies is the lack of a standard vocabulary for data annotation and reporting. Lacking a mea...

Predicting host-pathogen interactions with machine learning algorithms: A scoping review.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
BACKGROUND: Diseases caused by pathogenic microorganisms pose a persistent global health challenge. Pathogens exploit host mechanisms through intricate molecular interactions. Understanding these host-pathogen interactions (HPIs), particularly protei...

Predicting phage-host interactions via feature augmentation and regional graph convolution.

Briefings in bioinformatics
Identifying phage-host interactions (PHIs) is a crucial step in developing phage therapy, which is the promising solution to addressing the issue of antibiotic resistance in superbugs. However, the lifestyle of phages, which strongly depends on their...

deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions.

Briefings in bioinformatics
Host-pathogen protein interactions (HPPIs) play vital roles in many biological processes and are directly involved in infectious diseases. With the outbreak of more frequent pandemics in the last couple of decades, such as the recent outburst of Covi...

The reactome pathway knowledgebase 2022.

Nucleic acids research
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired dise...

Fighting COVID-19 with Artificial Intelligence.

Methods in molecular biology (Clifton, N.J.)
The development of vaccines for the treatment of COVID-19 is paving the way for new hope. Despite this, the risk of the virus mutating into a vaccine-resistant variant still persists. As a result, the demand of efficacious drugs to treat COVID-19 is ...

Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches.

Briefings in bioinformatics
During the course of a viral infection, virus-host protein-protein interactions (PPIs) play a critical role in allowing viruses to replicate and survive within the host. These interspecies molecular interactions can lead to viral-mediated perturbatio...

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2.

Proceedings of the National Academy of Sciences of the United States of America
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 ha...

Machine learning for phytopathology: from the molecular scale towards the network scale.

Briefings in bioinformatics
With the increasing volume of high-throughput sequencing data from a variety of omics techniques in the field of plant-pathogen interactions, sorting, retrieving, processing and visualizing biological information have become a great challenge. Within...

Current status and future perspectives of computational studies on human-virus protein-protein interactions.

Briefings in bioinformatics
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the ...