title: Heading in the right direction: thermodynamics-based network analysis and pathway engineering.
abstract: Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods.
authors.affiliation: Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
authors.forename: Meric
authors.initials: M
authors.lastname: Ataman
authors.affiliation: Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland. Electronic address: vassily.hatzimanikatis@epfl.ch.
authors.forename: Vassily
authors.initials: V
authors.lastname: Hatzimanikatis
mesh_terms: D000818:Animals; D006801:Humans; D007700:Kinetics; D060847:Metabolic Engineering; D008954:Models, Biological; D013816:Thermodynamics