title: The post-genomic era of biological network alignment.
abstract: Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches' biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556 USA ; Interdisciplinary Center for Network Science and Applications, University of Notre Dame, Notre Dame, IN, 46556 USA ; ECK Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556 USA.
authors.forename: Fazle E
authors.initials: FE
authors.lastname: Faisal
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556 USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Meng
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556 USA ; Interdisciplinary Center for Network Science and Applications, University of Notre Dame, Notre Dame, IN, 46556 USA ; ECK Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556 USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Crawford
authors.affiliation: Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556 USA ; Interdisciplinary Center for Network Science and Applications, University of Notre Dame, Notre Dame, IN, 46556 USA ; ECK Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556 USA.
authors.forename: Tijana
authors.initials: T
authors.lastname: Milenković
keywords: Across-species knowledge transfer; Aging; Biological network research; Functional orthology; Network alignment; Protein-protein interactions