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- Kean Ming Tan, Daniela M. Witten, Ali Shojaie
- Computational Statistics & Data Analysis
- 2015

The task of estimating a Gaussian graphical model in the high-dimensional setting is considered. The graphical lasso, which involves maximizing the Gaussian log likelihood subject to a lasso penalty, is a well-studied approach for this task. A surprising connection between the graphical lasso and hierarchical clustering is introduced: the graphical lasso in… (More)

- Ali Shojaie, George Michailidis
- Bioinformatics
- 2010

MOTIVATION
Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology.… (More)

- Ali Shojaie, George Michailidis
- Biometrika
- 2010

Directed acyclic graphs are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical and biological systems where directed edges between nodes represent the influence of components of the system on each other. Estimation of directed graphs from observational data… (More)

- Shizhe Chen, Daniela M Witten, Ali Shojaie
- Biometrika
- 2015

We consider the problem of estimating the parameters in a pairwise graphical model in which the distribution of each node, conditioned on the others, may have a different exponential family form. We identify restrictions on the parameter space required for the existence of a well-defined joint density, and establish the consistency of the neighbourhood… (More)

- Arend Voorman, Ali Shojaie, Daniela Witten
- Biometrika
- 2014

In recent years, there has been considerable interest in estimating conditional independence graphs in high dimensions. Most previous work has assumed that the variables are multivariate Gaussian, or that the conditional means of the variables are linear; in fact, these two assumptions are nearly equivalent. Unfortunately, if these assumptions are violated,… (More)

- Johanna W Lampe, Sandi L Navarro, Meredith A J Hullar, Ali Shojaie
- The Proceedings of the Nutrition Society
- 2013

Technologic advances now make it possible to collect large amounts of genetic, epigenetic, metabolomic and gut microbiome data. These data have the potential to transform approaches towards nutrition counselling by allowing us to recognise and embrace the metabolic, physiologic and genetic differences among individuals. The ultimate goal is to be able to… (More)

- Nagireddy Putluri, Ali Shojaie, +19 authors Arun Sreekumar
- Cancer research
- 2011

Although alterations in xenobiotic metabolism are considered causal in the development of bladder cancer, the precise mechanisms involved are poorly understood. In this study, we used high-throughput mass spectrometry to measure over 2,000 compounds in 58 clinical specimens, identifying 35 metabolites which exhibited significant changes in bladder cancer.… (More)

- Nagireddy Putluri, Ali Shojaie, +12 authors Arun Sreekumar
- PloS one
- 2011

Prostate cancer is the second leading cause of cancer related death in American men. Development and progression of clinically localized prostate cancer is highly dependent on androgen signaling. Metastatic tumors are initially responsive to anti-androgen therapy, however become resistant to this regimen upon progression. Genomic and proteomic studies have… (More)

- Ali Shojaie, George Michailidis
- Journal of Computational Biology
- 2009

Networks are often used to represent the interactions among genes and proteins. These interactions are known to play an important role in vital cell functions and should be included in the analysis of genes that are differentially expressed. Methods of gene set analysis take advantage of external biological information and analyze a priori defined sets of… (More)

- Ali Shojaie, George Michailidis
- Statistical applications in genetics and…
- 2010

Cellular functions of living organisms are carried out through complex systems of interacting components. Including such interactions in the analysis, and considering sub-systems defined by biological pathways instead of individual components (e.g. genes), can lead to new findings about complex biological mechanisms. Networks are often used to capture such… (More)