Systems bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches

A Oulas, G Minadakis, M Zachariou… - Briefings in …, 2019 - academic.oup.com
Abstract Systems Bioinformatics is a relatively new approach, which lies in the intersection of
systems biology and classical bioinformatics. It focuses on integrating information across …

An overview of graph databases and their applications in the biomedical domain

S Timón-Reina, M Rincón, R Martínez-Tomás - Database, 2021 - academic.oup.com
Over the past couple of decades, the explosion of densely interconnected data has
stimulated the research, development and adoption of graph database technologies. From …

Reactome graph database: Efficient access to complex pathway data

A Fabregat, F Korninger, G Viteri… - PLoS computational …, 2018 - journals.plos.org
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of
biomolecular pathways. One of its main priorities is to provide easy and efficient access to its …

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

V Robin, A Bodein, MP Scott-Boyer… - Frontiers in Molecular …, 2022 - frontiersin.org
At the heart of the cellular machinery through the regulation of cellular functions, protein–
protein interactions (PPIs) have a significant role. PPIs can be analyzed with network …

ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database

Z Mao, R Wang, H Li, Y Huang, Q Zhang… - Nucleic Acids …, 2022 - academic.oup.com
Cellular regulation is inherently complex, and one particular cellular function is often
controlled by a cascade of different types of regulatory interactions. For example, the activity …

A directed network analysis of the cardiome identifies molecular pathways contributing to the development of HFpEF

G Summer, AR Kuhn, C Munts, D Miranda-Silva… - Journal of Molecular and …, 2020 - Elsevier
Aims The metabolic syndrome and associated comorbidities, like diabetes, hypertension
and obesity, have been implicated in the development of heart failure with preserved …

Towards FAIRer biological knowledge networks using a hybrid linked data and graph database approach

M Brandizi, A Singh, C Rawlings… - Journal of integrative …, 2018 - degruyter.com
The speed and accuracy of new scientific discoveries–be it by humans or artificial
intelligence–depends on the quality of the underlying data and on the technology to …

Rationale of the FIBROTARGETS study designed to identify novel biomarkers of myocardial fibrosis

JP Ferreira, JL Machu, N Girerd, F Jaisser… - ESC heart …, 2018 - Wiley Online Library
Aims Myocardial fibrosis alters the cardiac architecture favouring the development of cardiac
dysfunction, including arrhythmias and heart failure. Reducing myocardial fibrosis may …

Fast and flexible analysis of linked microbiome data with mako

L Röttjers, K Faust - Nature methods, 2022 - nature.com
Mako is a software tool that converts microbiome data and networks into a graph database
and visualizes query results, thus allowing users without programming knowledge to carry …

NT-proBNP and stem cell factor plasma concentrations are independently associated with cardiovascular outcomes in end-stage renal disease hemodialysis patients

P Rossignol, K Duarte, E Bresso… - … heart journal open, 2022 - academic.oup.com
Aims End-stage renal disease (ESRD) treated by chronic hemodialysis (HD) is associated
with poor cardiovascular (CV) outcomes, with no available evidence-based therapeutics. A …