Personalized (patient-specific) approaches have recently emerged with a precision medicine paradigm that acknowledges the fact that molecular pathway structures and activity might be considerably different within and across tumors. The functional …
Identifying patient-specific prognostic biomarkers is of critical importance in developing personalized treatment for clinically and molecularly heterogeneous diseases such as cancer. In this article, we propose a novel regression framework, Bayesian …
We consider the problem of modeling conditional independence structures in heterogenous data in the presence of additional subject-level covariates—termed graphical regression. We propose a novel specification of a conditional (in)dependence function …
Multi-dimensional data constituted by measurements along multiple axes have emerged across many scientific areas such as genomics and cancer surveillance. A common objective is to investigate the conditional dependencies among the variables along …
Cancer progression and development are initiated by aberrations in various molecular networks through coordinated changes across multiple genes and pathways. It is important to understand how these networks change under different stress conditions …
Gene regulatory networks represent the regulatory relationships between genes and their products and are important for exploring and defining the underlying biological processes of cellular systems. We develop a novel framework to recover the …
Reverse-phase protein array (RPPA) analysis is a powerful, relatively new platform that allows for high-throughput, quantitative analysis of protein networks. One of the challenges that currently limit the potential of this technology is the lack of …
Identification of molecular-based signatures is one of the critical steps toward finding therapeutic targets in cancer. In this paper, we propose methods to discover prognostic gene signatures under a causal structure learning framework across the …
It is well-established that the development of a disease, especially cancer, is a complex process that results from the joint effects of multiple genes involved in various molecular signaling pathways. In this article, we propose methods to discover …
Rapid development of genome-wide profiling technologies has made it possible to conduct integrative analysis on genomic data from multiple platforms. In this study, we develop a novel integrative Bayesian network approach to investigate the …