title: Inference of dynamic biological networks based on responses to drug perturbations.
abstract: Drugs that target specific proteins are a major paradigm in cancer research. In this article, we extend a modeling framework for drug sensitivity prediction and combination therapy design based on drug perturbation experiments. The recently proposed target inhibition map approach can infer stationary pathway models from drug perturbation experiments, but the method is limited to a steady-state snapshot of the underlying dynamical model. We consider the inverse problem of possible dynamic models that can generate the static target inhibition map model. From a deterministic viewpoint, we analyze the inference of Boolean networks that can generate the observed binarized sensitivities under different target inhibition scenarios. From a stochastic perspective, we investigate the generation of Markov chain models that satisfy the observed target inhibition sensitivities.
authors.affiliation: Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, 79409 TX USA.
authors.forename: Noah
authors.initials: N
authors.lastname: Berlow
authors.affiliation: Department of Pediatrics, Oregon Health & Science University, Portland, 97239 OR USA.
authors.forename: Lara
authors.initials: L
authors.lastname: Davis
authors.affiliation: Department of Pediatrics, Oregon Health & Science University, Portland, 97239 OR USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Keller
authors.affiliation: Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, 79409 TX USA.
authors.forename: Ranadip
authors.initials: R
authors.lastname: Pal
keywords: Drug perturbation experiments; Network inference; Pathway design