Bioinformatics approaches for unveiling virus-host interactions

H Iuchi, J Kawasaki, K Kubo, T Fukunaga… - Computational and …, 2023 - Elsevier
Abstract The coronavirus disease-2019 (COVID-19) pandemic has elucidated major
limitations in the capacity of medical and research institutions to appropriately manage …

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

X Lian, X Yang, S Yang, Z Zhang - Briefings in Bioinformatics, 2021 - academic.oup.com
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 …

Kernel Bayesian nonlinear matrix factorization based on variational inference for human–virus protein–protein interaction prediction

Y Ma, Y Zhao, Y Ma - Scientific Reports, 2024 - nature.com
Identification of potential human–virus protein–protein interactions (PPIs) contributes to the
understanding of the mechanisms of viral infection and to the development of antiviral drugs …

A multitask transfer learning framework for the prediction of virus-human protein–protein interactions

TN Dong, G Brogden, G Gerold, M Khosla - BMC bioinformatics, 2021 - Springer
Background Viral infections are causing significant morbidity and mortality worldwide.
Understanding the interaction patterns between a particular virus and human proteins plays …

Machine-learning-based predictor of human–bacteria protein–protein interactions by incorporating comprehensive host-network properties

X Lian, S Yang, H Li, C Fu, Z Zhang - Journal of proteome …, 2019 - ACS Publications
The large-scale identification of protein–protein interactions (PPIs) between humans and
bacteria remains a crucial step in systematically understanding the underlying molecular …

Computational biology and machine learning approaches to understand mechanistic microbiome-host interactions

P Sudhakar, K Machiels, B Verstockt… - Frontiers in …, 2021 - frontiersin.org
The microbiome, by virtue of its interactions with the host, is implicated in various host
functions including its influence on nutrition and homeostasis. Many chronic diseases such …

[HTML][HTML] Host-pathogen protein-nucleic acid interactions: A comprehensive review

A Jain, S Mittal, LP Tripathi, R Nussinov… - Computational and …, 2022 - Elsevier
Recognition of pathogen-derived nucleic acids by host cells is an effective host strategy to
detect pathogenic invasion and trigger immune responses. In the context of pathogen …

Review of computational methods for virus–host protein interaction prediction: a case study on novel Ebola–human interactions

AK Halder, P Dutta, M Kundu, S Basu… - Briefings in functional …, 2018 - academic.oup.com
Identification of potential virus–host interactions is useful and vital to control the highly
infectious virus-caused diseases. This may contribute toward development of new drugs to …

Projection-based neighborhood non-negative matrix factorization for lncRNA-protein interaction prediction

Y Ma, T He, X Jiang - Frontiers in genetics, 2019 - frontiersin.org
Many long ncRNAs (lncRNA) make their effort by interacting with the corresponding RNA-
binding proteins, and identifying the interactions between lncRNAs and proteins is important …

Prediction and analysis of human‐herpes simplex virus type 1 protein‐protein interactions by integrating multiple methods

X Lian, X Yang, J Shao, F Hou, S Yang… - Quantitative …, 2020 - Wiley Online Library
Background Herpes simplex virus type 1 (HSV‐1) is a ubiquitous infectious pathogen that
widely affects human health. To decipher the complicated human‐HSV‐1 interactions, a …