Topology-based cancer classification and related pathway mining using microarray data

CC Liu, WSE Chen, CC Lin, HC Liu… - Nucleic acids …, 2006 - academic.oup.com
Cancer classification is the critical basis for patient-tailored therapy, while pathway analysis
is a promising method to discover the underlying molecular mechanisms related to cancer …

Topologically inferring risk-active pathways toward precise cancer classification by directed random walk

W Liu, C Li, Y Xu, H Yang, Q Yao, J Han… - …, 2013 - academic.oup.com
Motivation: The accurate prediction of disease status is a central challenge in clinical cancer
research. Microarray-based gene biomarkers have been identified to predict outcome and …

Pathway network analysis of complex diseases based on multiple biological networks

F Zheng, L Wei, L Zhao, FC Ni - BioMed Research International, 2018 - Wiley Online Library
Biological pathways play important roles in the development of complex diseases, such as
cancers, which are multifactorial complex diseases that are usually caused by multiple …

Classification of cancers based on a comprehensive pathway activity inferred by genes and their interactions

P Xu, G Zhao, Z Kou, G Fang, W Liu - IEEE Access, 2020 - ieeexplore.ieee.org
Cancers, a group of multifactorial complex diseases, are generally caused by mutation of
multiple genes or dysregulation of gene interactions. Applying machine learning methods to …

Identifying dysregulated pathways in cancers from pathway interaction networks

KQ Liu, ZP Liu, JK Hao, L Chen, XM Zhao - BMC bioinformatics, 2012 - Springer
Background Cancers, a group of multifactorial complex diseases, are generally caused by
mutation of multiple genes or dysregulation of pathways. Identifying biomarkers that can …

Joint network and node selection for pathway-based genomic data analysis

S Zhe, SAZ Naqvi, Y Yang, Y Qi - Bioinformatics, 2013 - academic.oup.com
Motivation: By capturing various biochemical interactions, biological pathways provide
insight into underlying biological processes. Given high-dimensional microarray or RNA …

Identification of Robust Pathway Markers for Cancer through Rank‐Based Pathway Activity Inference

N Khunlertgit, BJ Yoon - Advances in bioinformatics, 2013 - Wiley Online Library
One important problem in translational genomics is the identification of reliable and
reproducible markers that can be used to discriminate between different classes of a …

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 …

Pathway-based personalized analysis of Pan-Cancer transcriptomic data

C Pian, M He, Y Chen - Biomedicines, 2021 - mdpi.com
The occurrence of cancer is closely related to the deregulation of certain pathways. Based
on pathway deregulation scores (PDS) inferred by the Pathifier algorithm, we analyzed …

Multiclass cancer classification based on gene expression comparison

S Yang, DQ Naiman - … applications in genetics and molecular biology, 2014 - degruyter.com
As the complexity and heterogeneity of cancer is being increasingly appreciated through
genomic analyses, microarray-based cancer classification comprising multiple …