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- Andrew J. Sedgewick, Stephen C. Benz, Shahrooz Rabizadeh, Patrick Soon-Shiong, Charles J. Vaske
- Bioinformatics
- 2013

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High-dimensional '-omics' profiling provides a detailed molecular view of individual cancers; however, understanding the mechanisms by which tumors evade cellular defenses requires deep knowledge of the underlying cellular pathways within each cancer sample. We extended the PARADIGM algorithm (Vaske et al., 2010, Bioinformatics, 26, i237-i245), a… (More)

- Rory M Donovan, Andrew J Sedgewick, James R Faeder, Daniel M Zuckerman
- The Journal of chemical physics
- 2013

We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from a one-dimensional system to a system with 354 species and 3680 reactions. WE is relatively easy to implement, does not require extensive hand-tuning of… (More)

- Andrew J. Sedgewick, Ivy Shi, Rory M. Donovan, Panayiotis V. Benos
- BMC Bioinformatics
- 2016

Mixed graphical models (MGMs) are graphical models learned over a combination of continuous and discrete variables. Mixed variable types are common in biomedical datasets. MGMs consist of a parameterized joint probability density, which implies a network structure over these heterogeneous variables. The network structure reveals direct associations between… (More)

Graphical causal models are an important tool for knowledge discovery because they can represent both the causal relations between variables and the multivariate probability distributions over the data. Once learned, causal graphs can be used for classification, feature selection and hypothesis generation, while revealing the underlying causal network… (More)

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