Top

Natural Computing

Published in:

01-09-2015

Combining flux balance analysis and model checking for metabolic network validation and analysis

Authors: Roberto Pagliarini, Mara Sangiovanni, Adriano Peron, Diego di Bernardo

Published in: Natural Computing | Issue 3/2015

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

Several human diseases are caused by metabolism defects. Discovering the mechanisms that govern the onset and progression of human metabolism-related diseases is not a straightforward process. Computational approaches, such as the flux balance analysis, have been successfully used to extract useful knowledge on the metabolic dysregulation processes from genome-scale network models. In this work, we propose a novel approach which integrates constraint-based techniques with model checking methods, with the aim to extract relevant qualitative information from a metabolic network model. As a case study, we applied our methodology to the simulation and analysis of the primary hyperoxaluria type I, an inherited disease in which the lack of a particular liver enzyme causes the kidney to accumulate excessive amounts of oxalate.

previous article Algorithms and models for complex natural systems

next article A hybrid method for inversion of 3D DC resistivity logging measurements

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science (New York, N.Y.) 322(5903):881–888CrossRef

Baier C, Katoen J (2008) Principles of Model Checking. The MIT Press, CambridgeMATH

Balsara Z, Roach S (2005) Prediction of inherited and genetic mutations using the software model checker SPIN. In: Haddad H, Liebrock LM, Omicini A, Wainwright RL (eds) SAC. ACM, New York, pp 208–209

Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I (2011) A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol 5(1):180+CrossRef

Brim L, Češka M, Šafránek D (2013) Model checking of biological systems. Formal methods for dynamical systems, Springer, pp 63–112

Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur Ö, Anwar N, Schultz N, Bader GD, Sander C (2011) Pathway commons, a web resource for biological pathway data. Nucleic Acids Res 39(Suppl 1):D685–D690CrossRef

Cimatti A, Clarke E, Giunchiglia E, Giunchiglia F, Pistore M, Roveri M, Sebastiani R, Tacchella A (2002) Nusmv 2: an opensource tool for symbolic model checking. In: Computer aided verification,Springer, pp 359–364

Clarke EM, Grumberg O, Peled DA (1999) Model checking. MIT Press, Cambridge

Cochat P, Rumsby G (2013) Primary hyperoxaluria. N Engl J Med 369(7):649–658CrossRef

Crawhall JC, Scowen EF, De Mowbray RR, Watts RWE (1959) Conversion of glycine to oxalate in normal subject. The Lancet, 274(7107):810 Originally published as Volume 2, Issue 7107CrossRef

Danpure CJ (2006) Primary hyperoxaluria type 1: Agt mistargeting highlights the fundamental differences between the peroxisomal and mitochondrial protein import pathways. Biochimica et Biophysica Acta (BBA) - Mol Cell Res 1763(12):1776–1784CrossRef

Danpure CJ, Jennings PR (1986) Peroxisomal alanine:glyoxylate aminotransferase deficiency in primary hyperoxaluria type i. FEBS Lett 201(1):20–34CrossRef

Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson B (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci 104(6):1777–1782CrossRef

Elder TD, Wyngaarden JB (1960) The biosynthesis and turnover of oxalate in normal and hyperoxaluric subjects *. J Clin Investig 39(8):1337–1344 8CrossRef

Emerson EA (2008) The beginning of model checking: a personal perspective. In: 25 Years of Model Checking, Springer, pp 27–45

Emerson EA, Clarke EM (1982) Using branching time temporal logic to synthesize synchronization skeletons. Sci Comput Progr, 2(3):241–266, 1982. cited By (since 1996)188.

Folger O, Jerby L, Frezza C, Gottlieb E, Ruppin E, Shlomi T (2011) Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol 7:501

Gille C, Bolling C, Hoppe A, Bulik S, Hoffmann S, Hubner K, Karlstadt A, Ganeshan R, Konig M, Rother K, Weidlich M, Behre J, Holzhutter H (2010) HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol 6(1)

Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298(5602):2345–2349CrossRef

Ross PH, Dean GA (1998) Glyoxylate synthesis, and its modulation and influence on oxalate synthesis. J Urol 160(5):1617–1624CrossRef

Holmes RP, Knight J, Assimos DG (2007) Origin of urinary oxalate. In: AIP Conference proceedings, vol 900(1)

Holzhütter HG (2004) The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur J Biochem 271(14):2905–2922CrossRef

Holzmann GJ (2003) The SPIN model checker: Primer and reference manual. Addison-Wesley Professional, 1 edn

Holzmann GJ, Joshi R, Groce A (2011) Swarm verification techniques. IEEE Trans Softw Eng 37(6):845–857CrossRef

Ideker T, Galitski T, Hood L (2001) A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2(1):343–372CrossRef

Jerby L, Shlomi T, Ruppin E (2010) Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 6(1)

Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30CrossRef

Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662–1664CrossRef

Lanpher B, Brunetti-Pierri N, Lee B (2006) Inborn errors of metabolism: the flux from mendelian to complex diseases. Nat Rev Genet 7(6):449–459CrossRef

Larsen KG, Pettersson P, Yi W (1997) Uppaal in a nutshell. Int J Softw Tools Technol Transf (STTT) 1(1):134–152CrossRefMATH

Lewis NE, Nagarajan H, Palsson BO (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Micro 10(4):291–305

Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I (2007). The edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol, 3(1)

Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D’Eustachio P (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37(Suppl 1):D619–D622CrossRef

Melham T (2012) Modelling, abstraction, and computation in systems biology: a view from computer science, Prog Biophys Mol Biol 111(2):129–136

Mysore V, Mishra B (2007) Algorithmic algebraic model checking iv: Characterization of metabolic networks. In Hirokazu Anai, Katsuhisa Horimoto, Temur Kutsia (eds) AB, volume 4545 of Lecture notes in computer science. Springer, New York, pp 170–184

Oberhardt MA, Palsson BO, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320

Orth JD, Thiele I, Palsson BO (2010) What is flux balance analysis? Nat Biotechnol 28(3):245–248CrossRef

Pagliarini R, di Bernardo D (2013) A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. J Comput Biol 20(5):383–397MathSciNetCrossRef

Pnueli A (1977) The temporal logic of programs. In Foundations of computer science, 1977, 18th Annual symposium on, pp 46–57

Shlomi T, Benyamini T, Gottlieb E, Sharan R, Ruppin E (2011) Genome-Scale metabolic modeling elucidates the role of proliferative adaptation in causing the warburg effect. PLoS Comput Biol 7(3):e1002018+

Shlomi T, Cabili MN, Ruppin E (2009) Predicting metabolic biomarkers of human inborn errors of metabolism. Mol Syst Biol 5(1)

Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Or Rolfsson, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JHGM, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol 31(5):419–425

Title: Combining flux balance analysis and model checking for metabolic network validation and analysis
Authors: Roberto Pagliarini
Mara Sangiovanni
Adriano Peron
Diego di Bernardo
Publication date: 01-09-2015
Publisher: Springer Netherlands
Published in: Natural Computing / Issue 3/2015
Print ISSN: 1567-7818
Electronic ISSN: 1572-9796
DOI: https://doi.org/10.1007/s11047-014-9419-8

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Other articles of this Issue 3/2015

To what extent is zero energy computing feasible?

Compressive scanning of an object signature

Computation with optical sensitive sheets

Holographic parallel processor for calculating Kronecker product

Optical SuperComputing: Preface to special issue

Algorithms and models for complex natural systems

Premium Partner