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oai:repisalud.isciii.es:20.500.12105/228672024-11-28T19:58:52Zcom_20.500.12105_15322com_20.500.12105_2051col_20.500.12105_16967
Repisalud author Llabres, Merce author Riera, Gabriel author Rossello, Francesc author Valiente, Gabriel 2024-09-13T09:11:45Z 2024-09-13T09:11:45Z 2020-11-18 Llabres M, Riera G, Rossello F, Valiente G. Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks. BMC Bioinformatics. 2020 Nov 18;21 Suppl 6:434. 10.1186/s12859-020-03733-w 1471-2105 BMC Bioinformatics https://hdl.handle.net/20.500.13003/19432 33203352 L633455102 2-s2.0-85096119380 https://hdl.handle.net/20.500.12105/22867 594994500011 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. eng Systems biology Virus-host protein-protein interaction Integer linear programming Network alignment Graph matching Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks research article