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Description
  • In this paper, a novel approach to discrete modeling of gene regulatory networks is presented. The approach is based on timed automata and is new in: (i) reflecting discrete abstraction of gene expression with arbitrary granularity, (ii) combining boolean logic with approximation of Hill kinetics. This is achieved by introducing delays that change dynamically with respect to current activity levels of regulating genes. The approach is implemented in UPPAAL and evaluated on benchmark models and on a biological case study.
  • In this paper, a novel approach to discrete modeling of gene regulatory networks is presented. The approach is based on timed automata and is new in: (i) reflecting discrete abstraction of gene expression with arbitrary granularity, (ii) combining boolean logic with approximation of Hill kinetics. This is achieved by introducing delays that change dynamically with respect to current activity levels of regulating genes. The approach is implemented in UPPAAL and evaluated on benchmark models and on a biological case study. (en)
Title
  • Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization
  • Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization (en)
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  • Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization
  • Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization (en)
skos:notation
  • RIV/00216224:14330/13:00065956!RIV14-MSM-14330___
http://linked.open...avai/riv/aktivita
http://linked.open...avai/riv/aktivity
  • P(GAP202/11/0312), S
http://linked.open...vai/riv/dodaniDat
http://linked.open...aciTvurceVysledku
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http://linked.open...dnocenehoVysledku
  • 111108
http://linked.open...ai/riv/idVysledku
  • RIV/00216224:14330/13:00065956
http://linked.open...riv/jazykVysledku
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  • timed automata; gene regulatory networks; UPPAAL (en)
http://linked.open.../riv/klicoveSlovo
http://linked.open...ontrolniKodProRIV
  • [FD057ACD7258]
http://linked.open...v/mistoKonaniAkce
  • Florencie
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  • Neuveden
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  • Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)
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http://linked.open...vavai/riv/projekt
http://linked.open...UplatneniVysledku
http://linked.open...iv/tvurceVysledku
  • Brim, Luboš
  • Šafránek, David
  • Jacquet, Jean-Marie
  • Van Goethem, Simon
http://linked.open...vavai/riv/typAkce
http://linked.open.../riv/zahajeniAkce
issn
  • 1571-0661
number of pages
http://bibframe.org/vocab/doi
  • 10.1016/j.entcs.2013.02.019
http://purl.org/ne...btex#hasPublisher
  • Elsevier
http://localhost/t...ganizacniJednotka
  • 14330
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