Computational network biology: data, models, and applications

C Liu, Y Ma, J Zhao, R Nussinov, YC Zhang, F Cheng… - Physics Reports, 2020 - Elsevier
Biological entities are involved in intricate and complex interactions, in which uncovering the
biological information from the network concepts are of great significance. Benefiting from …

The BioGRID interaction database: 2019 update

R Oughtred, C Stark, BJ Breitkreutz, J Rust… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Biological General Repository for Interaction Datasets (BioGRID:
https://thebiogrid. org) is an open access database dedicated to the curation and archival …

Evaluation and comparison of multi-omics data integration methods for cancer subtyping

R Duan, L Gao, Y Gao, Y Hu, H Xu… - PLoS computational …, 2021 - journals.plos.org
Computational integrative analysis has become a significant approach in the data-driven
exploration of biological problems. Many integration methods for cancer subtyping have …

[HTML][HTML] Network diffusion promotes the integrative analysis of multiple omics

N Di Nanni, M Bersanelli, L Milanesi, E Mosca - Frontiers in genetics, 2020 - frontiersin.org
The development of integrative methods is one of the main challenges in bioinformatics.
Network-based methods for the analysis of multiple gene-centered datasets take into …

Cancer subtype classification and modeling by pathway attention and propagation

S Lee, S Lim, T Lee, I Sung, S Kim - Bioinformatics, 2020 - academic.oup.com
Motivation Biological pathway is an important curated knowledge of biological processes.
Thus, cancer subtype classification based on pathways will be very useful to understand …

[HTML][HTML] A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer

L Zhang, S Fan, J Vera, X Lai - Computational and structural biotechnology …, 2023 - Elsevier
Cancer is a heterogeneous disease mainly driven by abnormal gene perturbations in
regulatory networks. Therefore, it is appealing to identify the common and specific perturbed …

[HTML][HTML] Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression

F Morais-Rodrigues, R Silv́erio-Machado, RB Kato… - Gene, 2020 - Elsevier
Methods based around statistics and linear algebra have been increasingly used in attempts
to address emerging questions in microarray literature. Microarray technology is a long-used …

MONTI: a multi-omics non-negative tensor decomposition framework for gene-level integrative analysis

I Jung, M Kim, S Rhee, S Lim, S Kim - Frontiers in genetics, 2021 - frontiersin.org
Multi-omics data is frequently measured to enrich the comprehension of biological
mechanisms underlying certain phenotypes. However, due to the complex relations and …

[HTML][HTML] Classifying breast cancer molecular subtypes by using deep clustering approach

N Rohani, C Eslahchi - Frontiers in genetics, 2020 - frontiersin.org
Cancer is a complex disease with a high rate of mortality. The characteristics of tumor
masses are very heterogeneous; thus, the appropriate classification of tumors is a critical …

[PDF][PDF] Integrated analysis of ovarian cancer patients from prospective transcription factor activity reveals subtypes of prognostic significance

D Su, Y Xiong, H Wei, S Wang, J Ke, P Liang, H Zhang… - Heliyon, 2023 - cell.com
Transcription factors are protein molecules that act as regulators of gene expression.
Aberrant protein activity of transcription factors can have a significant impact on tumor …