title: Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.
abstract: Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology.
authors.affiliation: Department of Surgical and Medical Sciences, University Magna Graecia, Catanzaro, 88100 Italy.
authors.forename: Pietro Hiram
authors.initials: PH
authors.lastname: Guzzi
authors.affiliation: Department of Computer Science and Engineering, Interdisciplinary Center for Network Science and Applications (iCeNSA), ECK Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: Tijana
authors.initials: T
authors.lastname: Milenkovic
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins