Literature DB >> 22144167

Logical modelling of gene regulatory networks with GINsim.

Claudine Chaouiya1, Aurélien Naldi, Denis Thieffry.   

Abstract

Discrete mathematical formalisms are well adapted to model large biological networks, for which detailed kinetic data are scarce. This chapter introduces the reader to a well-established qualitative (logical) framework for the modelling of regulatory networks. Relying on GINsim, a software implementing this logical formalism, we guide the reader step by step towards the definition and the analysis of a simple model of the lysis-lysogeny decision in the bacteriophage λ.

Entities:  

Mesh：

Year:  2012        PMID： 22144167     DOI： 10.1007/978-1-61779-361-5_23

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


  41 in total

Review 1.  Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.

Authors:  Madalena Chaves; Hidde de Jong
Journal:  Methods Mol Biol       Date:  2021

2.  Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

Authors:  Samuel Collombet; Chris van Oevelen; Jose Luis Sardina Ortega; Wassim Abou-Jaoudé; Bruno Di Stefano; Morgane Thomas-Chollier; Thomas Graf; Denis Thieffry
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-06       Impact factor: 11.205

3.  Modeling genotypes in their microenvironment to predict single- and multi-cellular behavior.

Authors:  Dimitrios Voukantsis; Kenneth Kahn; Martin Hadley; Rowan Wilson; Francesca M Buffa
Journal:  Gigascience       Date:  2019-03-01       Impact factor: 6.524

4.  ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networks.

Authors:  Emna Ben Abdallah; Maxime Folschette; Olivier Roux; Morgan Magnin
Journal:  Algorithms Mol Biol       Date:  2017-08-15       Impact factor: 1.405

5.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Authors:  Anna Niarakis; Dagmar Waltemath; James Glazier; Falk Schreiber; Sarah M Keating; David Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomáš Helikar; Sylvain Soliman; Laurence Calzone
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

6.  Estimating Attractor Reachability in Asynchronous Logical Models.

Authors:  Nuno D Mendes; Rui Henriques; Elisabeth Remy; Jorge Carneiro; Pedro T Monteiro; Claudine Chaouiya
Journal:  Front Physiol       Date:  2018-09-07       Impact factor: 4.566

7.  Logical modeling of thymus and natural killer lymphocyte differentiation.

Authors:  Jianting Ye; Qingxi Chen; Ruiqi Wang
Journal:  J Biol Phys       Date:  2021-03-18       Impact factor: 1.365

8.  Dynamics of p53 and NF-κB regulation in response to DNA damage and identification of target proteins suitable for therapeutic intervention.

Authors:  Rainer Poltz; Michael Naumann
Journal:  BMC Syst Biol       Date:  2012-09-15

9.  Building Qualitative Models of Plant Regulatory Networks with SQUAD.

Authors:  Nathan Weinstein; Luis Mendoza
Journal:  Front Plant Sci       Date:  2012-04-19       Impact factor: 5.753

10.  Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

Authors:  Alexander Mitsos; Ioannis N Melas; Melody K Morris; Julio Saez-Rodriguez; Douglas A Lauffenburger; Leonidas G Alexopoulos
Journal:  PLoS One       Date:  2012-11-30       Impact factor: 3.240
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.