Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks
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RESEARCH
Open Access
Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks Mercè Llabrés1,2 , Gabriel Riera1,2 , Francesc Rosselló1,2 and Gabriel Valiente3* From 15th International Symposium on Bioinformatics Research and Applications (ISBRA’19) Barcelona, Spain. 3-6 June 2019 *Correspondence: [email protected] 3 Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034 Barcelona, Spain Full list of author information is available at the end of the article
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. Keywords: Systems biology, Virus-host protein-protein interaction, Integer linear programming, Network alignment, Graph matching
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Llabré et al. BMC Bioinformatics 2020, 21(Suppl 6):434
Background Many meaningful questions in molecular biology have be
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