A network-based perspective in Alzheimer's disease: current state and an integrative framework

A Dragomir, AG Vrahatis… - IEEE journal of …, 2018 - ieeexplore.ieee.org
A major rise in the prevalence and impact of Alzheimer's disease (AD) is projected in the
coming decades, resulting from increasing life expectancy, thus leading to substantially …

[HTML][HTML] Computational dynamic approaches for temporal omics data with applications to systems medicine

Y Liang, A Kelemen - BioData mining, 2017 - Springer
Modeling and predicting biological dynamic systems and simultaneously estimating the
kinetic structural and functional parameters are extremely important in systems and …

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 …

[HTML][HTML] Colorectal cancer characterization and therapeutic target prediction based on microRNA expression profile

P Xu, Y Zhu, B Sun, Z Xiao - Scientific reports, 2016 - nature.com
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and a major
cause of cancer death. However, the molecular mechanisms underlying CRC initiation …

Whole‐genome sequencing reveals forgotten lineages and recurrent hybridizations within the kelp genus Alaria (Phaeophyceae)

TT Bringloe, D Zaparenkov, S Starko… - Journal of …, 2021 - Wiley Online Library
The genomic era continues to revolutionize our understanding of the evolution of
biodiversity. In phycology, emphasis remains on assembling nuclear and organellar …

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments

AG Vrahatis, P Balomenos, AK Tsakalidis… - …, 2016 - academic.oup.com
DEsubs is a network-based systems biology R package that extracts disease-perturbed
subpathways within a pathway network as recorded by RNA-seq experiments. It contains an …

[HTML][HTML] 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 …

[HTML][HTML] Deblender: a semi−/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples

K Dimitrakopoulou, E Wik, LA Akslen, I Jonassen - BMC bioinformatics, 2018 - Springer
Background Towards discovering robust cancer biomarkers, it is imperative to unravel the
cellular heterogeneity of patient samples and comprehend the interactions between cancer …

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 …

[图书][B] Computational methods for processing and analysis of biological pathways

A Bezerianos, A Dragomir, P Balomenos - 2017 - books.google.com
This work offers a guided walkthrough of one of the most promising research areas in
modern life sciences, enabling a deeper understanding of involved concepts and …