The IRMA Community
Newsletters
Research IRM
Click a keyword to search titles using our InfoSci-OnDemand powered search:
|
Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets
Abstract
In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.
Related Content
Preethi, Sapna R., Mohammed Mujeer Ulla.
© 2023.
16 pages.
|
Srividya P..
© 2023.
12 pages.
|
Preeti Sahu.
© 2023.
15 pages.
|
Vandana Niranjan.
© 2023.
23 pages.
|
S. Darwin, E. Fantin Irudaya Raj, M. Appadurai, M. Chithambara Thanu.
© 2023.
33 pages.
|
Shankara Murthy H. M., Niranjana Rai, Ramakrishna N. Hegde.
© 2023.
23 pages.
|
Jothimani K., Bhagya Jyothi K. L..
© 2023.
19 pages.
|
|
|