On the Realisability of Chemical Pathways

Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler

doi:10.1007/978-981-99-7074-2_32

On the Realisability of Chemical Pathways

Jakob L. Andersen
, Sissel Banke^*
, Rolf Fagerberg
, Christoph Flamm
, Daniel Merkle
, Peter F. Stadler

^*Corresponding author for this work

University of Vienna
Leipzig University
Max Planck Inst. Math. in the Sci.
Fraunhofer Institute for Cell Therapy and Immunology IZI
University of Copenhagen
Santa Fe Institute

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Abstract

The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Lastly, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways.

Original language	English
Title of host publication	Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings
Editors	Xuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky
Publisher	Springer Science+Business Media
Publication date	2023
Pages	409-419
ISBN (Print)	9789819970735
DOIs	https://doi.org/10.1007/978-981-99-7074-2_32
Publication status	Published - 2023
Event	19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023 - Wroclaw, Poland Duration: 9. Oct 2023 → 12. Oct 2023

Conference

Conference	19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023
Country/Territory	Poland
City	Wroclaw
Period	09/10/2023 → 12/10/2023

Series	Lecture Notes in Computer Science
Volume	14248
ISSN	0302-9743

Funding

This work is supported by the Novo Nordisk Foundation grant NNF19OC0057834 and by the Independent Research Fund Denmark, Natural Sciences, grant DFF-0135-00420B.

Documents & Links

10.1007/978-981-99-7074-2_32

https://arxiv.org/pdf/2309.10629

SDU Link

Check access to the material in SDU Library's search engine

Cite this

Andersen, J. L., Banke, S., Fagerberg, R., Flamm, C., Merkle, D., & Stadler, P. F. (2023). On the Realisability of Chemical Pathways. In X. Guo, S. Mangul, M. Patterson, & A. Zelikovsky (Eds.), Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings (pp. 409-419). Springer Science+Business Media. https://doi.org/10.1007/978-981-99-7074-2_32

Andersen, Jakob L. ; Banke, Sissel ; Fagerberg, Rolf et al. / On the Realisability of Chemical Pathways. Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings. editor / Xuan Guo ; Serghei Mangul ; Murray Patterson ; Alexander Zelikovsky. Springer Science+Business Media, 2023. pp. 409-419 (Lecture Notes in Computer Science, Vol. 14248).

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abstract = "The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Lastly, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways.",

author = "Andersen, \{Jakob L.\} and Sissel Banke and Rolf Fagerberg and Christoph Flamm and Daniel Merkle and Stadler, \{Peter F.\}",

note = "Funding Information: This work is supported by the Novo Nordisk Foundation grant NNF19OC0057834 and by the Independent Research Fund Denmark, Natural Sciences, grant DFF-0135-00420B.; 19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023 ; Conference date: 09-10-2023 Through 12-10-2023",

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Andersen, JL , Banke, S , Fagerberg, R, Flamm, C, Merkle, D & Stadler, PF 2023, On the Realisability of Chemical Pathways. in X Guo, S Mangul, M Patterson & A Zelikovsky (eds), Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings. Springer Science+Business Media, Lecture Notes in Computer Science, vol. 14248, pp. 409-419, 19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023, Wroclaw, Poland, 09/10/2023. https://doi.org/10.1007/978-981-99-7074-2_32

On the Realisability of Chemical Pathways. / Andersen, Jakob L.; Banke, Sissel ; Fagerberg, Rolf et al.
Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings. ed. / Xuan Guo; Serghei Mangul; Murray Patterson; Alexander Zelikovsky. Springer Science+Business Media, 2023. p. 409-419 (Lecture Notes in Computer Science, Vol. 14248).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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AU - Fagerberg, Rolf

AU - Flamm, Christoph

AU - Merkle, Daniel

AU - Stadler, Peter F.

N1 - Funding Information: This work is supported by the Novo Nordisk Foundation grant NNF19OC0057834 and by the Independent Research Fund Denmark, Natural Sciences, grant DFF-0135-00420B.

PY - 2023

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N2 - The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Lastly, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways.

AB - The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Lastly, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways.

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DO - 10.1007/978-981-99-7074-2_32

M3 - Article in proceedings

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SN - 9789819970735

T3 - Lecture Notes in Computer Science

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BT - Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings

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ER -

Andersen JL , Banke S , Fagerberg R, Flamm C, Merkle D, Stadler PF. On the Realisability of Chemical Pathways. In Guo X, Mangul S, Patterson M, Zelikovsky A, editors, Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings. Springer Science+Business Media. 2023. p. 409-419. (Lecture Notes in Computer Science, Vol. 14248). doi: 10.1007/978-981-99-7074-2_32