Literature DB >> 35347689

Discrete Logic Modeling of Cell Signaling Pathways.

Nensi Ikonomi1, Silke D Werle1, Julian D Schwab1, Hans A Kestler2.   

Abstract

Cell signaling pathways often crosstalk generating complex biological behaviors observed in different cellular contexts. Frequently, laboratory experiments focus on a few putative regulators, alone unable to predict the molecular mechanisms behind the observed phenotypes. Here, systems biology complements these approaches by giving a holistic picture to complex signaling crosstalk. In particular, Boolean network models are a meaningful tool to study large network behaviors and can cope with incomplete kinetic information. By introducing a model describing pathways involved in hematopoietic stem cell maintenance, we present a general approach on how to model cell signaling pathways with Boolean network models.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Boolean networks; Discrete logics; Dynamic modeling; External stimulation; Hematopoietic stem cell; Long-term behavior; Niche induced homeostasis; Pathway prediction; Qualitative model; Signaling cascades

Mesh:

Year:  2022        PMID: 35347689     DOI: 10.1007/978-1-0716-2277-3_12

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  71 in total

Review 1.  Systems biology: a brief overview.

Authors:  Hiroaki Kitano
Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

Review 2.  Computational systems biology.

Authors:  Hiroaki Kitano
Journal:  Nature       Date:  2002-11-14       Impact factor: 49.962

Review 3.  From individual Wnt pathways towards a Wnt signalling network.

Authors:  Hans A Kestler; Michael Kühl
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2008-04-12       Impact factor: 6.237

Review 4.  Network modeling of signal transduction: establishing the global view.

Authors:  Hans A Kestler; Christian Wawra; Barbara Kracher; Michael Kühl
Journal:  Bioessays       Date:  2008-11       Impact factor: 4.345

5.  Metabolic stability and epigenesis in randomly constructed genetic nets.

Authors:  S A Kauffman
Journal:  J Theor Biol       Date:  1969-03       Impact factor: 2.691

6.  Switch-like behavior enables Wnt11 concentration specific response during dorso-ventral axis formation in Xenopus laevis.

Authors:  Jan Eric Sträng; Rainer Schuler; Michael Kühl; Hans A Kestler
Journal:  J Theor Biol       Date:  2017-06-23       Impact factor: 2.691

7.  Predicting Variabilities in Cardiac Gene Expression with a Boolean Network Incorporating Uncertainty.

Authors:  Melanie Grieb; Andre Burkovski; J Eric Sträng; Johann M Kraus; Alexander Groß; Günther Palm; Michael Kühl; Hans A Kestler
Journal:  PLoS One       Date:  2015-07-24       Impact factor: 3.240

Review 8.  Multiplicity of Mathematical Modeling Strategies to Search for Molecular and Cellular Insights into Bacteria Lung Infection.

Authors:  Martina Cantone; Guido Santos; Pia Wentker; Xin Lai; Julio Vera
Journal:  Front Physiol       Date:  2017-08-30       Impact factor: 4.566

Review 9.  Concepts in Boolean network modeling: What do they all mean?

Authors:  Julian D Schwab; Silke D Kühlwein; Nensi Ikonomi; Michael Kühl; Hans A Kestler
Journal:  Comput Struct Biotechnol J       Date:  2020-03-10       Impact factor: 7.271

10.  Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.

Authors:  Dominik M Wittmann; Jan Krumsiek; Julio Saez-Rodriguez; Douglas A Lauffenburger; Steffen Klamt; Fabian J Theis
Journal:  BMC Syst Biol       Date:  2009-09-28
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  1 in total

1.  Identification of dynamic driver sets controlling phenotypical landscapes.

Authors:  Silke D Werle; Nensi Ikonomi; Julian D Schwab; Johann M Kraus; Felix M Weidner; K Lenhard Rudolph; Astrid S Pfister; Rainer Schuler; Michael Kühl; Hans A Kestler
Journal:  Comput Struct Biotechnol J       Date:  2022-04-02       Impact factor: 6.155

  1 in total

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