Using machine learning approaches for multi-omics data analysis: A review

PS Reel, S Reel, E Pearson, E Trucco… - Biotechnology advances, 2021 - Elsevier
With the development of modern high-throughput omic measurement platforms, it has
become essential for biomedical studies to undertake an integrative (combined) approach to …

Protein‐protein interaction detection: methods and analysis

VS Rao, K Srinivas, GN Su**i… - International journal of …, 2014 - Wiley Online Library
Protein‐protein interaction plays key role in predicting the protein function of target protein
and drug ability of molecules. The majority of genes and proteins realize resulting …

[HTML][HTML] Information fusion as an integrative cross-cutting enabler to achieve robust, explainable, and trustworthy medical artificial intelligence

A Holzinger, M Dehmer, F Emmert-Streib, R Cucchiara… - Information …, 2022 - Elsevier
Medical artificial intelligence (AI) systems have been remarkably successful, even
outperforming human performance at certain tasks. There is no doubt that AI is important to …

[HTML][HTML] A census of human soluble protein complexes

PC Havugimana, GT Hart, T Nepusz, H Yang… - Cell, 2012 - cell.com
Cellular processes often depend on stable physical associations between proteins. Despite
recent progress, knowledge of the composition of human protein complexes remains limited …

UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase–substrate interactions in eukaryotic species

X Wang, Y Li, M He, X Kong, P Jiang, X Liu… - Nucleic acids …, 2022 - academic.oup.com
As an important post-translational modification, ubiquitination mediates∼ 80% of protein
degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the …

IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species

M Kotlyar, C Pastrello, Z Malik… - Nucleic acids research, 2019 - academic.oup.com
Knowing the set of physical protein–protein interactions (PPIs) that occur in a particular
context—a tissue, disease, or other condition—can provide valuable insights into key …

Integration of biological networks and gene expression data using Cytoscape

MS Cline, M Smoot, E Cerami, A Kuchinsky… - Nature protocols, 2007 - nature.com
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and
genetic interaction networks. This protocol explains how to use Cytoscape to analyze the …

Fundamentals of protein interaction network map**

J Snider, M Kotlyar, P Saraon, Z Yao… - Molecular systems …, 2015 - embopress.org
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains
one of the major challenges in modern biomedicine. Such information is crucial to …

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

I Lee, UM Blom, PI Wang, JE Shim… - Genome …, 2011 - genome.cshlp.org
Network “guilt by association”(GBA) is a proven approach for identifying novel disease
genes based on the observation that similar mutational phenotypes arise from functionally …

Yeast two-hybrid, a powerful tool for systems biology

A Brückner, C Polge, N Lentze, D Auerbach… - International journal of …, 2009 - mdpi.com
A key property of complex biological systems is the presence of interaction networks formed
by its different components, primarily proteins. These are crucial for all levels of cellular …