Inference of dynamic biological networks based on responses to drug perturbations

Noah Berlow, Lara Davis, Charles Keller, Ranadip Pal

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1-16
Number of pages16
JournalTijdschrift voor Urologie
Volume2014
Issue number1
DOIs
StatePublished - Jan 17 2014

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Pharmaceutical Preparations
Markov Chains
Drug Design
Research
Neoplasms
Proteins
Therapeutics

Keywords

  • Drug perturbation experiments
  • Network inference
  • Pathway design

ASJC Scopus subject areas

  • Urology

Cite this

Inference of dynamic biological networks based on responses to drug perturbations. / Berlow, Noah; Davis, Lara; Keller, Charles; Pal, Ranadip.

In: Tijdschrift voor Urologie, Vol. 2014, No. 1, 17.01.2014, p. 1-16.

Research output: Contribution to journalArticle

Berlow, Noah ; Davis, Lara ; Keller, Charles ; Pal, Ranadip. / Inference of dynamic biological networks based on responses to drug perturbations. In: Tijdschrift voor Urologie. 2014 ; Vol. 2014, No. 1. pp. 1-16.
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