This thesis is comprised of three parts. The first part describes a novel framework for computing importance measures on graph vertices. The concept of a D-spectrum is introduced, based on vertex ranks within certain chains of nested sub-graphs. We show that the D- spectrum integrates the degree distribution and coreness information of the graph as two particular such chains. We prove that these spectra are realized as fixed points of certain monotone and contractive SDSs we call t-systems. Finally, we give a vertex deletion algorithm that efficiently computes D-spectra, and we illustrate their correlation with stochastic SIR-processes on real world networks. The second part deals with the topology of the intersection nerve for a bi-secondary structure, and its singular homology. A bi-secondary structure R, is a combinatorial object that can be viewed as a collection of cycles (loops) of certain at most tetravalent planar graphs. Bi-secondary structures arise naturally in the study of RNA riboswitches - molecules that have an MFE binary structural degeneracy. We prove that this loop nerve complex has a euclidean 3-space embedding characterized solely by H2(R), its second homology group. We show that this group is the only non-trivial one in the sequence and furthermore it is free abelian. The third part further describes the features of the loop nerve. We identify certain disjoint objects in the structure of R which we call crossing components (CC). These are non-trivial connected components of a graph that captures a particular non-planar embedding of R. We show that each CC contributes a unique generator to H2(R) and thus the total number of these crossing components in fact equals the rank of the second homology group.