Special Issue "Metabolic Network Models"

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A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: closed (31 August 2012)

Special Issue Editor

Guest Editor
Dr. Kyongbum Lee
Department of Chemical and Biological Engineering, Tufts University, Room 142, 4 Colby Street, Medford, MA 02155, USA
Website: http://engineering.tufts.edu/chbe/tme/default.asp
E-Mail: kyongbum.lee@tufts.edu
Interests: adipose tissue metabolism; liver drug transformation; dynamic models of metabolic networks; targeted metabolomics

Special Issue Information

Dear Colleagues,

Network models have been instrumental in advancing quantitative knowledge of cellular metabolism by characterizing the systems-level features and properties that arise from the biochemical interactions between metabolites, enzymes and regulatory molecules. Network models are now widely used in both basic and applied studies, ranging from investigations on the evolutionary origins of hierarchical modularity in metabolism to design of synthetic pathways for the overproduction of commercially useful molecules. By exploiting parallel advances in genomics, proteomics and bioinformatics, significant progress has been achieved in modeling metabolic networks, especially in the reconstruction and characterization of whole cell metabolic networks.

Many challenges remain, however, in developing dynamic models capable of predicting the response of cellular metabolism to environmental perturbations or genetic modifications. Given the size and complexity of metabolic networks, new modeling approaches are needed to incorporate existing and new knowledge on regulation, account for uncertainty, and systematically construct an identifiable model whose parameters can be robustly estimated from data. Therefore, this special issue of Metabolites will be dedicated for publishing current advances on dynamic metabolic network models, multi-scale and multi-resolution models, transcriptional and allosteric regulation, integration with signaling and other biochemical networks, parameter estimation from metabolomics data, and modeling of noise and uncertainty.

Prof. Kyongbum Lee
Guest Editor

Keywords

  • metabolic network
  • dynamic model
  • multi-scale
  • multi-resolution
  • model reduction
  • transcriptional regulation
  • allosteric regulation
  • metabolomics data
  • parameter estimation
  • network flexibility
  • robust design

Published Papers (10 papers)

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Displaying article 1-10
p. 1-23
by , , ,  and
Metabolites 2013, 3(1), 1-23; doi:10.3390/metabo3010001
Received: 8 October 2012; in revised form: 18 December 2012 / Accepted: 31 December 2012 / Published: 8 January 2013
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(This article belongs to the Special Issue Metabolic Network Models)
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p. 983-1003
by , ,  and
Metabolites 2012, 2(4), 983-1003; doi:10.3390/metabo2040983
Received: 29 August 2012; in revised form: 18 October 2012 / Accepted: 7 November 2012 / Published: 21 November 2012
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(This article belongs to the Special Issue Metabolic Network Models)
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p. 1031-1059
by , , , , , , , , , ,  and
Metabolites 2012, 2(4), 1031-1059; doi:10.3390/metabo2041031
Received: 18 September 2012; in revised form: 30 October 2012 / Accepted: 31 October 2012 / Published: 21 November 2012
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(This article belongs to the Special Issue Metabolic Network Models)
p. 891-912
by ,  and
Metabolites 2012, 2(4), 891-912; doi:10.3390/metabo2040891
Received: 14 September 2012; in revised form: 2 November 2012 / Accepted: 5 November 2012 / Published: 12 November 2012
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(This article belongs to the Special Issue Metabolic Network Models)
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p. 667-700
by
Metabolites 2012, 2(4), 667-700; doi:10.3390/metabo2040667
Received: 20 July 2012; in revised form: 7 September 2012 / Accepted: 24 September 2012 / Published: 8 October 2012
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(This article belongs to the Special Issue Metabolic Network Models)
p. 632-647
by ,  and
Metabolites 2012, 2(3), 632-647; doi:10.3390/metabo2030632
Received: 1 August 2012; in revised form: 28 August 2012 / Accepted: 12 September 2012 / Published: 24 September 2012
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(This article belongs to the Special Issue Metabolic Network Models)
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p. 429-457
by
Metabolites 2012, 2(3), 429-457; doi:10.3390/metabo2030429
Received: 24 May 2012; in revised form: 26 June 2012 / Accepted: 9 July 2012 / Published: 12 July 2012
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(This article belongs to the Special Issue Metabolic Network Models)
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p. 268-291
by , , ,  and
Metabolites 2012, 2(1), 268-291; doi:10.3390/metabo2010268
Received: 15 February 2012; in revised form: 5 March 2012 / Accepted: 6 March 2012 / Published: 14 March 2012
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(This article belongs to the Special Issue Metabolic Network Models)
p. 242-253
by  and
Metabolites 2012, 2(1), 242-253; doi:10.3390/metabo2010242
Received: 30 January 2012; in revised form: 18 February 2012 / Accepted: 27 February 2012 / Published: 2 March 2012
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(This article belongs to the Special Issue Metabolic Network Models)
p. 221-241
by ,  and
Metabolites 2012, 2(1), 221-241; doi:10.3390/metabo2010221
Received: 30 December 2011; in revised form: 8 February 2012 / Accepted: 10 February 2012 / Published: 27 February 2012
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Last update: 27 February 2014

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