Machine learning for microbiologists

F Asnicar, AM Thomas, A Passerini… - Nature Reviews …, 2024 - nature.com
Abstract Machine learning is increasingly important in microbiology where it is used for tasks
such as predicting antibiotic resistance and associating human microbiome features with …

Mass spectrometry‐based protein–protein interaction networks for the study of human diseases

AL Richards, M Eckhardt, NJ Krogan - Molecular systems biology, 2021 - embopress.org
A better understanding of the molecular mechanisms underlying disease is key for
expediting the development of novel therapeutic interventions. Disease mechanisms are …

Gene expression variability across cells and species shapes innate immunity

T Hagai, X Chen, RJ Miragaia, R Rostom, T Gomes… - Nature, 2018 - nature.com
As the first line of defence against pathogens, cells mount an innate immune response,
which varies widely from cell to cell. The response must be potent but carefully controlled to …

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

T Guirimand, S Delmotte, V Navratil - Nucleic acids research, 2015 - academic.oup.com
Abstract VirHostNet release 2.0 (http://virhostnet. prabi. fr) is a knowledgebase dedicated to
the network-based exploration of virus–host protein–protein interactions. Since the previous …

Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease

Y Zhang, JP Thomas, T Korcsmaros, L Gul - Cell Reports Medicine, 2024 - cell.com
The gut microbiome is crucial for nutrient metabolism, immune regulation, and intestinal
homeostasis with changes in its composition linked to complex diseases like inflammatory …

Viruses. STRING: a virus-host protein-protein interaction database

HV Cook, NT Doncheva, D Szklarczyk, C Von Mering… - Viruses, 2018 - mdpi.com
As viruses continue to pose risks to global health, having a better understanding of virus–
host protein–protein interactions aids in the development of treatments and vaccines. Here …

CovInter: interaction data between coronavirus RNAs and host proteins

K Amahong, W Zhang, Y Zhou, S Zhang… - Nucleic Acids …, 2023 - academic.oup.com
Coronavirus has brought about three massive outbreaks in the past two decades. Each step
of its life cycle invariably depends on the interactions among virus and host molecules. The …

Protein–protein interactions in virus–host systems

AF Brito, JW Pinney - Frontiers in microbiology, 2017 - frontiersin.org
To study virus–host protein interactions, knowledge about viral and host protein
architectures and repertoires, their particular evolutionary mechanisms, and information on …

Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms

S Li, S Wu, L Wang, F Li, H Jiang, F Bai - Current Opinion in Structural …, 2022 - Elsevier
Protein–protein interactions (PPIs) are essential in the regulation of biological functions and
cell events, therefore understanding PPIs have become a key issue to understanding the …

Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions

LV Nobre, K Nightingale, BJ Ravenhill, R Antrobus… - Elife, 2019 - elifesciences.org
Human cytomegalovirus (HCMV) extensively modulates host cells, downregulating> 900
human proteins during viral replication and degrading≥ 133 proteins shortly after infection …