Enumerating precursor sets of target metabolites in a metabolic network

L. Cottret; P. Vieira Milreu; V. Acuña; A. Marchetti Spaccamela; F. Viduani Martinez; M.F. Sagot; L. Stougie

doi:10.1007/978-3-540-87361-7_20

Enumerating precursor sets of target metabolites in a metabolic network

L. Cottret, P. Vieira Milreu, V. Acuña, A. Marchetti Spaccamela, F. Viduani Martinez, M.F. Sagot, L. Stougie

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

19 Citations (Scopus)

Abstract

We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications.

Original language	English
Title of host publication	Algorithms in Bioinformatics (Proceedings 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008)
Editors	K.A. Crandall, J. Lagergren
Place of Publication	Berlin
Publisher	Springer
Pages	233-244
ISBN (Print)	978-3-540-87360-0
DOIs	https://doi.org/10.1007/978-3-540-87361-7_20
Publication status	Published - 2008

Publication series

Name	Lecture Notes in Computer Science
Volume	5151
ISSN (Print)	0302-9743

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10.1007/978-3-540-87361-7_20

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Cottret, L., Vieira Milreu, P., Acuña, V., Marchetti Spaccamela, A., Viduani Martinez, F., Sagot, M. F., & Stougie, L. (2008). Enumerating precursor sets of target metabolites in a metabolic network. In K. A. Crandall, & J. Lagergren (Eds.), Algorithms in Bioinformatics (Proceedings 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008) (pp. 233-244). (Lecture Notes in Computer Science; Vol. 5151). Springer. https://doi.org/10.1007/978-3-540-87361-7_20

Cottret, L. ; Vieira Milreu, P. ; Acuña, V. ; Marchetti Spaccamela, A. ; Viduani Martinez, F. ; Sagot, M.F. ; Stougie, L. / Enumerating precursor sets of target metabolites in a metabolic network. Algorithms in Bioinformatics (Proceedings 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008). editor / K.A. Crandall ; J. Lagergren. Berlin : Springer, 2008. pp. 233-244 (Lecture Notes in Computer Science).

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title = "Enumerating precursor sets of target metabolites in a metabolic network",

abstract = "We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications.",

author = "L. Cottret and {Vieira Milreu}, P. and V. Acu{\~n}a and {Marchetti Spaccamela}, A. and {Viduani Martinez}, F. and M.F. Sagot and L. Stougie",

year = "2008",

doi = "10.1007/978-3-540-87361-7_20",

language = "English",

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Cottret, L, Vieira Milreu, P, Acuña, V, Marchetti Spaccamela, A, Viduani Martinez, F, Sagot, MF & Stougie, L 2008, Enumerating precursor sets of target metabolites in a metabolic network. in KA Crandall & J Lagergren (eds), Algorithms in Bioinformatics (Proceedings 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008). Lecture Notes in Computer Science, vol. 5151, Springer, Berlin, pp. 233-244. https://doi.org/10.1007/978-3-540-87361-7_20

Enumerating precursor sets of target metabolites in a metabolic network. / Cottret, L.; Vieira Milreu, P.; Acuña, V.; Marchetti Spaccamela, A.; Viduani Martinez, F.; Sagot, M.F.; Stougie, L.

Algorithms in Bioinformatics (Proceedings 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008). ed. / K.A. Crandall; J. Lagergren. Berlin : Springer, 2008. p. 233-244 (Lecture Notes in Computer Science; Vol. 5151).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

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T1 - Enumerating precursor sets of target metabolites in a metabolic network

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AU - Vieira Milreu, P.

AU - Acuña, V.

AU - Marchetti Spaccamela, A.

AU - Viduani Martinez, F.

AU - Sagot, M.F.

AU - Stougie, L.

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N2 - We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications.

AB - We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications.

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Cottret L, Vieira Milreu P, Acuña V, Marchetti Spaccamela A, Viduani Martinez F, Sagot MF et al. Enumerating precursor sets of target metabolites in a metabolic network. In Crandall KA, Lagergren J, editors, Algorithms in Bioinformatics (Proceedings 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008). Berlin: Springer. 2008. p. 233-244. (Lecture Notes in Computer Science). https://doi.org/10.1007/978-3-540-87361-7_20

Enumerating precursor sets of target metabolites in a metabolic network

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