Literature DB >> 17681779

Biochemical and statistical network models for systems biology.

Nathan D Price1, Ilya Shmulevich.   

Abstract

The normal and abnormal behavior of a living cell is governed by complex networks of interacting biomolecules. Models of these networks allow us to make predictions about cellular behavior under a variety of environmental cues. In this review, we focus on two broad classes of such models: biochemical network models and statistical inference models. In particular, we discuss a number of modeling approaches in the context of the assumptions that they entail, the types of data required for their inference, and the range of their applicability.

Mesh:

Year:  2007        PMID: 17681779      PMCID: PMC2034526          DOI: 10.1016/j.copbio.2007.07.009

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  50 in total

Review 1.  Thirteen years of building constraint-based in silico models of Escherichia coli.

Authors:  Jennifer L Reed; Bernhard Ø Palsson
Journal:  J Bacteriol       Date:  2003-05       Impact factor: 3.490

2.  The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.

Authors:  Jason A Papin; Nathan D Price; Jeremy S Edwards; Bernhard Ø Palsson B
Journal:  J Theor Biol       Date:  2002-03-07       Impact factor: 2.691

3.  Integrating high-throughput and computational data elucidates bacterial networks.

Authors:  Markus W Covert; Eric M Knight; Jennifer L Reed; Markus J Herrgard; Bernhard O Palsson
Journal:  Nature       Date:  2004-05-06       Impact factor: 49.962

Review 4.  High-throughput phenomics: experimental methods for mapping fluxomes.

Authors:  Uwe Sauer
Journal:  Curr Opin Biotechnol       Date:  2004-02       Impact factor: 9.740

5.  Two-dimensional annotation of genomes.

Authors:  Bernhard Palsson
Journal:  Nat Biotechnol       Date:  2004-10       Impact factor: 54.908

6.  Stimulus specificity of gene expression programs determined by temporal control of IKK activity.

Authors:  Shannon L Werner; Derren Barken; Alexander Hoffmann
Journal:  Science       Date:  2005-09-16       Impact factor: 47.728

7.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Authors:  J S Edwards; R U Ibarra; B O Palsson
Journal:  Nat Biotechnol       Date:  2001-02       Impact factor: 54.908

8.  Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

Authors:  Ines Thiele; Nathan D Price; Thuy D Vo; Bernhard Ø Palsson
Journal:  J Biol Chem       Date:  2004-11-30       Impact factor: 5.157

9.  HER2-mediated effects on EGFR endosomal sorting: analysis of biophysical mechanisms.

Authors:  Bart S Hendriks; H Steven Wiley; Douglas Lauffenburger
Journal:  Biophys J       Date:  2003-10       Impact factor: 4.033

10.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).

Authors:  Jennifer L Reed; Thuy D Vo; Christophe H Schilling; Bernhard O Palsson
Journal:  Genome Biol       Date:  2003-08-28       Impact factor: 13.583

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  22 in total

Review 1.  Network biology methods integrating biological data for translational science.

Authors:  Gurkan Bebek; Mehmet Koyutürk; Nathan D Price; Mark R Chance
Journal:  Brief Bioinform       Date:  2012-03-05       Impact factor: 11.622

2.  Introduction to focus issue: genetic interactions.

Authors:  Daniel Segrè; Christopher J Marx
Journal:  Chaos       Date:  2010-06       Impact factor: 3.642

3.  Mapping high-growth phenotypes in the flux space of microbial metabolism.

Authors:  Oriol Güell; Francesco Alessandro Massucci; Francesc Font-Clos; Francesc Sagués; M Ángeles Serrano
Journal:  J R Soc Interface       Date:  2015-09-06       Impact factor: 4.118

Review 4.  Systems approaches to molecular cancer diagnostics.

Authors:  Shuyi Ma; Cory C Funk; Nathan D Price
Journal:  Discov Med       Date:  2010-12       Impact factor: 2.970

5.  Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

Authors:  Sriram Chandrasekaran; Nathan D Price
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

Review 6.  Systems approaches to identifying gene regulatory networks in plants.

Authors:  Terri A Long; Siobhan M Brady; Philip N Benfey
Journal:  Annu Rev Cell Dev Biol       Date:  2008       Impact factor: 13.827

7.  Systems biology update: cell type-specific transcriptional regulatory networks.

Authors:  Li Pu; Siobhan Brady
Journal:  Plant Physiol       Date:  2009-12-04       Impact factor: 8.340

Review 8.  In silico models of cancer.

Authors:  Lucas B Edelman; James A Eddy; Nathan D Price
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Jul-Aug

9.  Identification of neutral biochemical network models from time series data.

Authors:  Marco Vilela; Susana Vinga; Marco A Grivet Mattoso Maia; Eberhard O Voit; Jonas S Almeida
Journal:  BMC Syst Biol       Date:  2009-05-05

Review 10.  Bacteria as computers making computers.

Authors:  Antoine Danchin
Journal:  FEMS Microbiol Rev       Date:  2008-11-07       Impact factor: 16.408

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