Bipartite graphs in systems biology and medicine: a survey of methods and applications

GA Pavlopoulos, PI Kontou, A Pavlopoulou… - …, 2018 - academic.oup.com
The latest advances in high-throughput techniques during the past decade allowed the
systems biology field to expand significantly. Today, the focus of biologists has shifted from …

Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma

T Zengin, T Önal-Süzek - BMC bioinformatics, 2020 - Springer
Background Lung cancer is the leading cause of the largest number of deaths worldwide
and lung adenocarcinoma is the most common form of lung cancer. In order to understand …

Comprehensive profiling of genomic and transcriptomic differences between risk groups of lung adenocarcinoma and lung squamous cell carcinoma

T Zengin, T Önal-Süzek - Journal of personalized medicine, 2021 - mdpi.com
Lung cancer is the second most frequently diagnosed cancer type and responsible for the
highest number of cancer deaths worldwide. Lung adenocarcinoma (LUAD) and lung …

Pathway analysis using XGBoost classification in Biomedical Data

GN Dimitrakopoulos, AG Vrahatis… - Proceedings of the 10th …, 2018 - dl.acm.org
Given the fact that our biological existence is rooted in a complex system within our cells
with thousands of interactions among genes and metabolites, research community in …

psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression

J Han, X Han, Q Kong, L Cheng - Bioinformatics, 2020 - academic.oup.com
Subpathways, which are defined as local gene subregions within a biological pathway, have
been reported to be associated with the occurrence and development of cancer. The recent …

Recent advances in the systems biology of aging

MA McCormick, DEL Promislow - Antioxidants & Redox Signaling, 2018 - liebertpub.com
Significance: Reductionist studies have contributed greatly to our understanding of the basic
biology of aging in recent years but we still do not understand fundamental mechanisms for …

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

M Buti, M Moretto, E Barghini, F Mascagni, L Natali… - …, 2018 - academic.oup.com
Abstract Background The genus Potentilla is closely related to that of Fragaria, the
economically important strawberry genus. Potentilla micrantha is a species that does not …

Detecting disease specific pathway substructures through an integrated systems biology approach

S Alaimo, GP Marceca, A Ferro, A Pulvirenti - Non-coding RNA, 2017 - mdpi.com
In the era of network medicine, pathway analysis methods play a central role in the
prediction of phenotype from high throughput experiments. In this paper, we present a …

Gene set analysis methods for the functional interpretation of non-mRNA data—Genomic range and ncRNA data

A Mora - Briefings in bioinformatics, 2020 - academic.oup.com
Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current
omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA …

Topologically inferring active miRNA‐mediated subpathways toward precise cancer classification by directed random walk

Z Ning, C Feng, C Song, W Liu, D Shang… - Molecular …, 2019 - Wiley Online Library
Accurate predictions of classification biomarkers and disease status are indispensable for
clinical cancer diagnosis and research. However, the robustness of conventional gene …