Systems biology is a place of networks: gene regulatory networks, protein-protein interaction networks, food webs, social and contact networks.
Nodes of biological networks can be anything from microRNAs to genes to proteins, individuals to populations to species, and combinations thereof. The edges in the networks represent the different kinds of interactions these nodes can have with each other. These networks change over time, between species, and across ecosystems, but they often retain common features, the revelation of which can help us understand the most important aspects of the networks, and what changes may have taken place to transform one into another.
Biological networks have topological features that we can leverage to ease such comparisons; for example an abundance of certain motifs, the connectedness and degree distribution of nodes, and the overall diameter. We have developed methods (Node Fingerprinting  and Node Handprinting ) that leverage these features to create state of the art tools to align even large biological networks, with high accuracy and speed, and minimal memory. We have extended these alignment methods to estimate paths between networks, that describe plausible evolutionary routes through "network space" which can in turn provide estimates of evolutionary distance between networks – the Biological Network Edit Distance.
This poster describes our new methods, demonstrates their accuracy, and shows their potential for informing biologists interested in studying the relationships among biological networks.