Literature DB >> 20378394

Network thermodynamics in the post-genomic era.

Keng Cher Soh1, Vassily Hatzimanikatis.   

Abstract

Network models have been used to study the underlying processes and principles of biological systems for decades, providing many insights into the complexity of life. Biological systems require a constant flow of free energy to drive these processes that operate away from thermodynamic equilibrium. With the advent of high-throughput omics technologies, more and more thermodynamic knowledge about the biological components, processes and their interactions are surfacing that we can integrate using large-scale biological network models. This allows us to ask many fundamental questions about these networks, such as, how far away from equilibrium must the reactions in a network be displaced in order to allow growth, or what are the possible thermodynamic objectives of the cell. Copyright 2010 Elsevier Ltd. All rights reserved.

Mesh:

Year:  2010        PMID: 20378394     DOI: 10.1016/j.mib.2010.03.001

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  18 in total

1.  Energy-based analysis of biochemical cycles using bond graphs.

Authors:  Peter J Gawthrop; Edmund J Crampin
Journal:  Proc Math Phys Eng Sci       Date:  2014-11-08       Impact factor: 2.704

2.  Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN.

Authors:  Maria Masid; Meric Ataman; Vassily Hatzimanikatis
Journal:  Nat Commun       Date:  2020-06-04       Impact factor: 14.919

3.  Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Authors:  Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N Mendoza; Anne Richelle; Almut Heinken; Hulda S Haraldsdóttir; Jacek Wachowiak; Sarah M Keating; Vanja Vlasov; Stefania Magnusdóttir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu H J Chan; Maike K Aurich; Catherine M Clancy; Jennifer Modamio; John T Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C El Assal; Luis V Valcarcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M Le; Ding Ma; Yuekai Sun; Lin Wang; James T Yurkovich; Miguel A P Oliveira; Phan T Vuong; Lemmer P El Assal; Inna Kuperstein; Andrei Zinovyev; H Scott Hinton; William A Bryant; Francisco J Aragón Artacho; Francisco J Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A Saunders; Costas D Maranas; Nathan E Lewis; Thomas Sauter; Bernhard Ø Palsson; Ines Thiele; Ronan M T Fleming
Journal:  Nat Protoc       Date:  2019-03       Impact factor: 13.491

4.  Thermodynamics of random reaction networks.

Authors:  Jakob Fischer; Axel Kleidon; Peter Dittrich
Journal:  PLoS One       Date:  2015-02-27       Impact factor: 3.240

Review 5.  Thermodynamical journey in plant biology.

Authors:  Adelin Barbacci; Vincent Magnenet; Marc Lahaye
Journal:  Front Plant Sci       Date:  2015-06-30       Impact factor: 5.753

6.  Functional genomics of Plasmodium falciparum using metabolic modelling and analysis.

Authors:  Stepan Tymoshenko; Rebecca D Oppenheim; Dominique Soldati-Favre; Vassily Hatzimanikatis
Journal:  Brief Funct Genomics       Date:  2013-06-22       Impact factor: 4.241

7.  Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks.

Authors:  Daniele De Martino; Fabrizio Capuani; Matteo Mori; Andrea De Martino; Enzo Marinari
Journal:  Metabolites       Date:  2013-10-14

Review 8.  Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation.

Authors:  Tunahan Cakır; Mohammad Jafar Khatibipour
Journal:  Front Bioeng Biotechnol       Date:  2014-12-03

9.  Predicting internal cell fluxes at sub-optimal growth.

Authors:  André Schultz; Amina A Qutub
Journal:  BMC Syst Biol       Date:  2015-04-03

Review 10.  Quantification of Microbial Phenotypes.

Authors:  Verónica S Martínez; Jens O Krömer
Journal:  Metabolites       Date:  2016-12-09
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