A network-based cancer drug discovery: from integrated multi-omics approaches to precision medicine

B Turanli, K Karagoz, G Gulfidan… - Current …, 2018 - ingentaconnect.com
A complex framework of interacting partners including genetic, proteomic, and metabolic
networks that cooperate to mediate specific functional phenotypes drives human biological …

[HTML][HTML] Machine learning and bioinformatics models to identify gene expression patterns of ovarian cancer associated with disease progression and mortality

MA Hossain, SMS Islam, JMW Quinn, F Huq… - Journal of biomedical …, 2019 - Elsevier
Ovarian cancer (OC) is a common cause of cancer death among women worldwide, so there
is a pressing need to identify factors influencing OC mortality. Much OC patient clinical data …

Computational approaches leveraging integrated connections of multi-omic data toward clinical applications

HC Demirel, MK Arici, N Tuncbag - Molecular omics, 2022 - pubs.rsc.org
In line with the advances in high-throughput technologies, multiple omic datasets have
accumulated to study biological systems and diseases coherently. No single omics data type …

Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet

M Oubounyt, L Adlung, F Patroni, NK Wenke… - …, 2023 - academic.oup.com
Motivation The reconstruction of small key regulatory networks that explain the differences in
the development of cell (sub) types from single-cell RNA sequencing is a yet unresolved …

Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

P Schaepe, MJ Kwon, B Baumann… - Nucleic acids …, 2019 - academic.oup.com
A significant challenge in our understanding of biological systems is the high number of
genes with unknown function in many genomes. The fungal genus Aspergillus contains …

Pan-cancer mapping of differential protein-protein interactions

G Gulfidan, B Turanli, H Beklen, R Sinha, KY Arga - Scientific reports, 2020 - nature.com
Deciphering the variations in the protein interactome is required to reach a systems-level
understanding of tumorigenesis. To accomplish this task, we have considered the clinical …

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package

GG Lemoine, MP Scott-Boyer, B Ambroise, O Périn… - BMC …, 2021 - Springer
Background Network-based analysis of gene expression through co-expression networks
can be used to investigate modular relationships occurring between genes performing …

Identification of potential autophagy-related genes in steroid-induced osteonecrosis of the femoral head via bioinformatics analysis and experimental verification

XZ Liang, D Luo, YR Chen, JC Li, BZ Yan… - Journal of Orthopaedic …, 2022 - Springer
Purpose Steroid-induced osteonecrosis of the femoral head (SONFH) is a refractory
orthopaedic hip joint disease that occurs in young-and middle-aged people. Previous …

Multiomics analysis of tumor microenvironment reveals Gata2 and miRNA-124-3p as potential novel biomarkers in ovarian cancer

E Gov, M Kori, KY Arga - Omics: a journal of integrative biology, 2017 - liebertpub.com
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its
insidious onset and the current lack of robust early diagnostic tests. Tumors are complex …

Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response

M Lucchetta, I da Piedade, M Mounir, M Vabistsevits… - BMC cancer, 2019 - Springer
Background Genomic initiatives such as The Cancer Genome Atlas (TCGA) contain data
from-omics profiling of thousands of tumor samples, which may be used to decipher cancer …