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A critical examination of stoichiometric and path-finding approaches to metabolic pathways

F. J. Planes, J. E. Beasley
2008 Briefings in Bioinformatics  
In this article we give a critical overview of the theory, applications and key research challenges of stoichiometric and path-finding approaches to metabolic pathways.  ...  Singular attention has been devoted in the literature to stoichiometric approaches, and path-finding approaches, to metabolic pathways.  ...  CONCLUSIONS In this article stoichiometric and path-finding approaches to metabolic pathways have been considered.  ... 
doi:10.1093/bib/bbn018 pmid:18436574 fatcat:olgxica4m5ffplkeamvsdvr64i

Path finding methods accounting for stoichiometry in metabolic networks

Jon Pey, Joaquín Prada, John E Beasley, Francisco J Planes
2011 Genome Biology  
In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming.  ...  This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks.  ...  Acknowledgements The work of JPe was supported by the Basque Government. The authors would like to thank two anonymous referees for their valuable comments improving the manuscript.  ... 
doi:10.1186/gb-2011-12-5-r49 pmid:21619601 pmcid:PMC3219972 fatcat:2ijuevyckzbedgmab4kj4rj4ri

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways

Jon Pey, Kaspar Valgepea, Angel Rubio, John E Beasley, Francisco J Planes
2013 BMC Systems Biology  
This is illustrated in both a theoretical and real scenario. Finally, we apply this approach to find novel pathways relevant in the regulation of acetate overflow metabolism in Escherichia coli.  ...  We show that gene/protein expression data also influences the stoichiometric balancing of CFPs, which provides a more accurate picture of active metabolic pathways.  ...  Acknowledgements The work of Jon Pey was supported by the Basque Government.  ... 
doi:10.1186/1752-0509-7-134 pmid:24314206 pmcid:PMC3878952 fatcat:ob67zit4ancfngmtkptk4nmi4e

METABOLIC FLUX PROFILING OF REACTION MODULES IN LIVER DRUG TRANSFORMATION

JEONGAH YOON, KYONGBUM LEE
2006 Biocomputing 2007  
Results point to a welldefined TGZ transformation module that connects to other major pathways in the hepatocyte via amino acids and their derivatives.  ...  With appropriate models, the metabolic profile of a biological system may be interrogated to obtain both significant discriminatory markers as well as mechanistic insight into the observed phenotype.  ...  This work was in part funded by NIH grant 1-R21DK67228 to KL.  ... 
doi:10.1142/9789812772435_0019 fatcat:eyi6ukqxobd3tch2lgrh2w6mca

A review of parameters and heuristics for guiding metabolic pathfinding

Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett, Lydia E. Kavraki
2017 Journal of Cheminformatics  
Most biosynthesis pathways used in metabolic engineering applications have been discovered manually, requiring a tedious search of existing literature and metabolic databases.  ...  As assisted pathfinding approaches continue to become more sophisticated, the development of better methods for visualizing pathway results and integrating these results into existing metabolic engineering  ...  Acknowledgements We would like to acknowledge Allison Heath for introducing Sarah Kim to the topic of metabolic pathfinding.  ... 
doi:10.1186/s13321-017-0239-6 pmid:29086092 pmcid:PMC5602787 fatcat:xegamrehhnasbkj5r7p7xfdwv4

An Algorithm for Efficient Identification of Branched Metabolic Pathways

Allison P. Heath, George N. Bennett, Lydia E. Kavraki
2011 Journal of Computational Biology  
The ability to automatically identify branched pathways is important in applications that require a deeper understanding of metabolism, such as metabolic engineering and drug target identification.  ...  We provide results on several well characterized metabolic pathways that demonstrate that the new merging approach can efficiently find biologically relevant branched metabolic pathways.  ...  Additionally, a web server for some of our metabolic path finding methods is located at: http://metabolicpaths.kavrakilab.org.  ... 
doi:10.1089/cmb.2011.0165 pmid:21999288 fatcat:uq6oj7zfhvcedn62olous743vm

Organising metabolic networks: cycles in flux distributions

Maurício Kritz, Marcelo dos Santos, Sebastián Urrita, Jean-Marc Schwartz
2009 Nature Precedings  
Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment.  ...  The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms.  ...  Find the set N(ca) of elementary cycles in C that contain this critical arc ca . The set N(ca) is called the nexus of ca and is a subset of C . 1.  ... 
doi:10.1038/npre.2009.3932.1 fatcat:5watp6sfxjdznblw2ayykp7cka

Organising metabolic networks: Cycles in flux distributions

Maurício Vieira Kritz, Marcelo Trindade dos Santos, Sebastián Urrutia, Jean-Marc Schwartz
2010 Journal of Theoretical Biology  
Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment.  ...  The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms.  ...  Find the set N(ca) of elementary cycles in C that contain this critical arc ca . The set N(ca) is called the nexus of ca and is a subset of C . 1.  ... 
doi:10.1016/j.jtbi.2010.04.026 pmid:20435049 fatcat:qgnyjee5gfdxnmkkjorwt2eone

Identifying Antimalarial Drug Targets by Cellular Network Analysis [chapter]

Kitiporn Plaimas, Rainer König
2016 Current Topics in Malaria  
At equilibrium, production and consumption of internal metabolites need to be balanced leading to a large set of flux equations, and this can be used for metabolic flux simulations to identify drug targets  ...  To find drug targets, metabolic and signaling networks have been constructed. These networks have been investigated by graph theoretical methods.  ...  To find drug targets for the treatment of malaria, metabolic and signaling networks have been constructed and intensively investigated.  ... 
doi:10.5772/65432 fatcat:ykwxzydv4rfgdfvyuvz52zfc7i

Designing overall stoichiometric conversions and intervening metabolic reactions

Anupam Chowdhury, Costas D. Maranas
2015 Scientific Reports  
Linear Programming (LP) and Mixed Integer Linear Programming (MILP) approaches for pathway design, in general, extract a minimal stoichiometry-balanced sub-network that converts a source metabolite to  ...  Metabolic engineering harnesses this metabolic machinery for converting feedstock substrates to a growing range of products 1-3 .  ...  DE-SC0008091 and the NSF (http://www.nsf.gov/) award no. EEC-0813570. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1038/srep16009 pmid:26530953 pmcid:PMC4632160 fatcat:tj3dg2dqlnd6xok3fr54wnxdk4

Motion Planning In Metabolic Pathways Using Probabilistic Roadmap and A* Algorithms

Angela Makolo, Obotu Ojobo
2020 Zenodo  
A* search algorithm queries the roadmap to get the most relevant (cost effective) path using the thermodynamic feasibility of the reactions as the weighting scheme.  ...  This work applies motion planning algorithms to search for biochemically relevant pathways in metabolic pathways.  ...  [20] examined the effectiveness of using compound node connectivity in a path finding approach and also presented a path finding approach based upon integer programming.  ... 
doi:10.5281/zenodo.4431060 fatcat:fy55bffmnvddvhyyghkg3yh3qm

Can sugars be produced from fatty acids? A test case for pathway analysis tools

L. F. de Figueiredo, S. Schuster, C. Kaleta, D. A. Fell
2008 Bioinformatics  
This shows that, for metabolic pathway analysis, it is important to consider the topology (including bimolecular reactions) and stoichiometry of metabolic systems, as is done in EMA.  ...  Results: Elementary modes analysis (EMA) of a set of enzymes corresponding to the Krebs cycle, glycolysis and gluconeogenesis supports the scientific evidence showing that there is no pathway capable of  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btn621 pmid:19117076 fatcat:3gtrb2twbfbl3hbffc2n35ykxa

Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems

Mehmet A. Orman, Francois Berthiaume, Ioannis P. Androulakis, Marianthi G. Ierapetritou
2011 Critical reviews in biomedical engineering  
Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis.  ...  Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties.  ...  particular extreme pathway in the reconstruction to find a weight�spectrum (α�spectrum). 121 The α�spectrum showed which extreme pathways can and cannot be included in the reconstruction of a given steadystate  ... 
doi:10.1615/critrevbiomedeng.v39.i6.30 pmid:22196224 pmcid:PMC3634616 fatcat:4xjbcdsorve2zjiijwjapfzdlq

Design Automation for Synthetic Biological Systems

Douglas Densmore, Soha Hassoun
2012 IEEE Design & Test of Computers  
This article outlines bio-design automation using two complementary design approaches, bottom-up modular construction from biological primitives and pathway-based approaches.  ...  Editors' notes: Through principled engineering methods, synthetic biology aims to build specialized biological components that can be modularly composed to create complex systems.  ...  Acknowledgment The authors would like to thank Chris Voigt and Roza Ghamari for discussions on NOR-gate-based genetic regulatory networks.  ... 
doi:10.1109/mdt.2012.2193370 fatcat:zxaiso254bf63cxkskgdbatuti

Network models in the study of metabolism

Diogenes Infante, Arsenio Rodríguez
2009 Electronic Journal of Biotechnology  
A novel approach differs critically from metabolic flux analysis and previous genome-scale metabolic network reconstructions because it accommodates nonlinear terms that describe the dynamic behavior of  ...  In this approach, the intracellular fluxes are calculated using a stoichiometric model (metabolic pathway map) for the major intracellular reactions and applying mass balances around intracellular metabolites  ... 
doi:10.2225/vol12-issue4-fulltext-2 fatcat:cguod3s7kvfqno24tnju6nxpcq
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