Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
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hdl:2117/334544
Tipus de documentArticle
Data publicació2020-11-18
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Reconeixement 4.0 Internacional
Abstract
Background:
The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software tools. However, the resulting integer linear program has a huge number of variables and constraints, rendering it of no practical use.
Results:
We present a compact integer linear programming reformulation of the protein-protein interaction network alignment problem, which can be solved using state-of-the-art mathematical modeling and integer linear programming software tools, along with empirical results showing that small biological networks, such as virus-host protein-protein interaction networks, can be aligned in a reasonable amount of time on a personal computer and the resulting alignments are structurally coherent and biologically meaningful.
Conclusions:
The implementation of the integer linear programming reformulation using current mathematical modeling and integer linear programming software tools provided biologically meaningful alignments of virus-host protein-protein interaction networks.
CitacióLlabrés, M. [et al.]. Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks. "BMC bioinformatics", 18 Novembre 2020, vol. 21, supplement 6, article 434, p. 1-14.
ISSN1471-2105
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s12859-020-03733-w.pdf | 1,571Mb | Visualitza/Obre |