Literature DB >> 19879267

Systems analysis of cellular networks under uncertainty.

Hans-Michael Kaltenbach1, Sotiris Dimopoulos, Jörg Stelling.   

Abstract

Besides the often-quoted complexity of cellular networks, the prevalence of uncertainties about components, interactions, and their quantitative features provides a largely underestimated hallmark of current systems biology. This uncertainty impedes the development of mechanistic mathematical models to achieve a true systems-level understanding. However, there is increasing evidence that theoretical approaches from diverse scientific domains can extract relevant biological knowledge efficiently, even from poorly characterized biological systems. As a common denominator, the methods focus on structural, rather than more detailed, kinetic network properties. A deeper understanding, better scaling, and the ability to combine the approaches pose formidable challenges for future theory developments.

Mesh:

Year:  2009        PMID: 19879267     DOI: 10.1016/j.febslet.2009.10.074

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  11 in total

1.  Workflow for generating competing hypothesis from models with parameter uncertainty.

Authors:  David Gomez-Cabrero; Albert Compte; Jesper Tegner
Journal:  Interface Focus       Date:  2011-03-30       Impact factor: 3.906

2.  Computer-aided design of biological circuits using TinkerCell.

Authors:  Deepak Chandran; Frank T Bergmann; Herbert M Sauro
Journal:  Bioeng Bugs       Date:  2010 Jul-Aug

3.  Topological sensitivity analysis for systems biology.

Authors:  Ann C Babtie; Paul Kirk; Michael P H Stumpf
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

4.  Systems biology: new institute and applications.

Authors:  Jieming Chen
Journal:  Yale J Biol Med       Date:  2011-03

5.  Emergence of switch-like behavior in a large family of simple biochemical networks.

Authors:  Dan Siegal-Gaskins; Maria Katherine Mejia-Guerra; Gregory D Smith; Erich Grotewold
Journal:  PLoS Comput Biol       Date:  2011-05-12       Impact factor: 4.475

6.  Network-based scoring system for genome-scale metabolic reconstructions.

Authors:  M Ángeles Serrano; Francesc Sagués
Journal:  BMC Syst Biol       Date:  2011-05-19

7.  A Nonlinear Mixed Effects Approach for Modeling the Cell-To-Cell Variability of Mig1 Dynamics in Yeast.

Authors:  Joachim Almquist; Loubna Bendrioua; Caroline Beck Adiels; Mattias Goksör; Stefan Hohmann; Mats Jirstrand
Journal:  PLoS One       Date:  2015-04-20       Impact factor: 3.240

8.  Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.

Authors:  David R Penas; Patricia González; Jose A Egea; Ramón Doallo; Julio R Banga
Journal:  BMC Bioinformatics       Date:  2017-01-21       Impact factor: 3.169

9.  Wisdom of crowds for robust gene network inference.

Authors:  Daniel Marbach; James C Costello; Robert Küffner; Nicole M Vega; Robert J Prill; Diogo M Camacho; Kyle R Allison; Manolis Kellis; James J Collins; Gustavo Stolovitzky
Journal:  Nat Methods       Date:  2012-07-15       Impact factor: 28.547

Review 10.  Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

Authors:  Alejandro F Villaverde; Julio R Banga
Journal:  J R Soc Interface       Date:  2013-12-04       Impact factor: 4.118

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