Special Issue "Metabolism and Systems Biology"

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

Deadline for manuscript submissions: 31 January 2015

Special Issue Editors

Guest Editor
Dr. Christoph Kaleta
Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Raum 15N10, Leutragraben 1, D-07743 Jena, Germany
Website: http://users.minet.uni-jena.de/~m3kach/
E-Mail: christoph.kaleta@uni-jena.de
Interests: analysis of metabolic and regulatory networks; system biology

Guest Editor
Dr. Ines Heiland
Arctic University of Norway, Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, Naturfagbygget, Dramsvegen 201, 9037 Tromsø, Norway
Website: http://en.uit.no/ansatte/organisasjon/ansatte/person?p_document_id=321907&p_dimension_id=88165
E-Mail: ines.heiland@uit.no
Interests: NAD-metabolism; tryptophan metabolism; circadian clocks; metabolic modelling; modelling of dynamic processes

Special Issue Information

Dear Colleagues,

Systems biological models of metabolism are widely used in biotechnology, pharmacy and medicine to optimise metabolite production, to predict drug targets or to understand metabolic discrepancies in diseases. Moreover, they have been shown to be key ingredients in the analysis of largescale data sets including transcriptomic, proteomic, fluxomic, metabolomic and genomic data sets. However, despite the success of these models, we are still very far from understanding the interaction between metabolism and signal transduction and models integrating both processes are still rare. This is in part due to the fact that different methods are used both in modelling as well as in experimental approaches targeting these pathways. We furthermore face the problem that data generation by far outpaces model construction efforts, which is especially true when it comes to kinetic models as the construction of these models is extremely time consuming. Thus, new approaches are required that combine the accuracy of kinetic models with semi automatic, less time consuming reconstruction methods as used for network based modeling approaches.

This special issue of Metabolites focuses on metabolic modelling approaches at the crossroad between kinetic and stiochiometric models as well as between signal transduction and metabolism. We furthermore welcome new approaches to improve the predictive capacity of genome scale metabolic models and approaches that integrate multiomics datasets.

Prof. Christoph Kaleta
Dr. Ines Heiland
Guest Editors

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • genome
  • scale metabolic models
  • reconstruction of metabolic networks
  • data integration into metabolic modeling
  • constraint
  • based modeling of metabolism
  • analysis of high
  • throughput datasets
  • transcriptomic data
  • proteomic data
  • fluxomic data
  • metabolomic data

Published Papers (14 papers)

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Displaying article 1-14
p. 673-700
by  and
Metabolites 2013, 3(3), 673-700; doi:10.3390/metabo3030673
Received: 31 May 2013; in revised form: 30 July 2013 / Accepted: 30 July 2013 / Published: 12 August 2013
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 1012-1030
by , , ,  and
Metabolites 2012, 2(4), 1012-1030; doi:10.3390/metabo2041012
Received: 14 August 2012; in revised form: 7 November 2012 / Accepted: 14 November 2012 / Published: 21 November 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 940-958
by , , , , , ,  and
Metabolites 2012, 2(4), 940-958; doi:10.3390/metabo2040940
Received: 20 October 2012; in revised form: 10 November 2012 / Accepted: 12 November 2012 / Published: 16 November 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 844-871
by , , , , , , , ,  and
Metabolites 2012, 2(4), 844-871; doi:10.3390/metabo2040844
Received: 17 October 2012; Accepted: 29 October 2012 / Published: 12 November 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 872-890
by , ,  and
Metabolites 2012, 2(4), 872-890; doi:10.3390/metabo2040872
Received: 4 September 2012; in revised form: 29 October 2012 / Accepted: 1 November 2012 / Published: 12 November 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
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p. 818-843
by ,  and
Metabolites 2012, 2(4), 818-843; doi:10.3390/metabo2040818
Received: 20 August 2012; in revised form: 12 October 2012 / Accepted: 29 October 2012 / Published: 6 November 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
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p. 733-755
by , , , , ,  and
Metabolites 2012, 2(4), 733-755; doi:10.3390/metabo2040733
Received: 8 August 2012; in revised form: 24 September 2012 / Accepted: 25 September 2012 / Published: 16 October 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 756-774
by  and
Metabolites 2012, 2(4), 756-774; doi:10.3390/metabo2040756
Received: 1 August 2012; in revised form: 29 August 2012 / Accepted: 10 October 2012 / Published: 16 October 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 701-716
by , , , ,  and
Metabolites 2012, 2(4), 701-716; doi:10.3390/metabo2040701
Received: 1 August 2012; in revised form: 12 September 2012 / Accepted: 25 September 2012 / Published: 10 October 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 614-631
by
Metabolites 2012, 2(3), 614-631; doi:10.3390/metabo2030614
Received: 1 August 2012; in revised form: 24 August 2012 / Accepted: 4 September 2012 / Published: 12 September 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 567-595
by  and
Metabolites 2012, 2(3), 567-595; doi:10.3390/metabo2030567
Received: 12 July 2012; in revised form: 25 August 2012 / Accepted: 29 August 2012 / Published: 11 September 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
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p. 553-566
by  and
Metabolites 2012, 2(3), 553-566; doi:10.3390/metabo2030553
Received: 7 July 2012; in revised form: 22 August 2012 / Accepted: 28 August 2012 / Published: 6 September 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 529-552
by ,  and
Metabolites 2012, 2(3), 529-552; doi:10.3390/metabo2030529
Received: 20 July 2012; in revised form: 15 August 2012 / Accepted: 17 August 2012 / Published: 29 August 2012
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(This article belongs to the Special Issue Metabolism and Systems Biology)
p. 382-397
by  and
Metabolites 2012, 2(3), 382-397; doi:10.3390/metabo2030382
Received: 29 March 2012; in revised form: 7 June 2012 / Accepted: 25 June 2012 / Published: 3 July 2012
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Last update: 21 October 2014

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