[HTML][HTML] Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies
Background Integrating the rich information from multi-omics data has been a popular
approach to survival prediction and bio-marker identification for several cancer studies. To …
approach to survival prediction and bio-marker identification for several cancer studies. To …
[HTML][HTML] Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors
Background Phenotypic classification is problematic because small samples are ubiquitous;
and, for these, use of prior knowledge is critical. If knowledge concerning the feature-label …
and, for these, use of prior knowledge is critical. If knowledge concerning the feature-label …
[HTML][HTML] Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer
Background Integrative analysis on multi-omics data has gained much attention recently. To
investigate the interactive effect of gene expression and DNA methylation on cancer, we …
investigate the interactive effect of gene expression and DNA methylation on cancer, we …
Incorporation of biological pathway knowledge in the construction of priors for optimal Bayesian classification
MS Esfahani, ER Dougherty - IEEE/ACM Transactions on …, 2013 - ieeexplore.ieee.org
Small samples are commonplace in genomic/proteomic classification, the result being
inadequate classifier design and poor error estimation. The problem has recently been …
inadequate classifier design and poor error estimation. The problem has recently been …
[HTML][HTML] Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network
N Khunlertgit, BJ Yoon - BMC bioinformatics, 2016 - Springer
Background Discovering robust markers for cancer prognosis based on gene expression
data is an important yet challenging problem in translational bioinformatics. By integrating …
data is an important yet challenging problem in translational bioinformatics. By integrating …
Deep graph representations embed network information for robust disease marker identification
Motivation Accurate disease diagnosis and prognosis based on omics data rely on the
effective identification of robust prognostic and diagnostic markers that reflect the states of …
effective identification of robust prognostic and diagnostic markers that reflect the states of …
A PSO-based approach for pathway marker identification from gene expression data
M Mandal, J Mondal… - IEEE Transactions on …, 2015 - ieeexplore.ieee.org
In this article, a new and robust pathway activity inference scheme is proposed from gene
expression data using Particle Swarm Optimization (PSO). From microarray gene …
expression data using Particle Swarm Optimization (PSO). From microarray gene …
An optimization-based framework for the transformation of incomplete biological knowledge into a probabilistic structure and its application to the utilization of gene …
MS Esfahani, ER Dougherty - IEEE/ACM Transactions on …, 2015 - ieeexplore.ieee.org
Phenotype classification via genomic data is hampered by small sample sizes that
negatively impact classifier design. Utilization of prior biological knowledge in conjunction …
negatively impact classifier design. Utilization of prior biological knowledge in conjunction …
Computational prediction of pathogenic network modules in Fusarium verticillioides
Fusarium verticillioides is a fungal pathogen that triggers stalk rots and ear rots in maize. In
this study, we performed a comparative analysis of wild type and loss-of-virulence mutant F …
this study, we performed a comparative analysis of wild type and loss-of-virulence mutant F …
[HTML][HTML] Personalized prediction of acquired resistance to EGFR-targeted inhibitors using a pathway-based machine learning approach
Epidermal growth factor receptor (EGFR) inhibitors have benefitted cancer patients
worldwide, but resistance inevitably develops over time, resulting in treatment failures. An …
worldwide, but resistance inevitably develops over time, resulting in treatment failures. An …