Bipartite graphs in systems biology and medicine: a survey of methods and applications
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 …
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 …
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 …
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 …
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 …
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 …
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)
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 …
economically important strawberry genus. Potentilla micrantha is a species that does not …
Detecting disease specific pathway substructures through an integrated systems biology approach
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 …
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 …
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 …
clinical cancer diagnosis and research. However, the robustness of conventional gene …