With an ever-increasing wealth of information made available to researchers from expanding genomic sequence and protein structure databases, traditional experimentation and research are being drastically revisited. The unidirectional study of single molecules and pathways is being replaced by a combinatorial and cross-disciplinary platform that investigates interactive biological systems and dynamic networks. The complement system constitutes an ideal paradigm of how this concept is being applied in the field of contemporary immunology. Our laboratory has adopted such a cross-disciplinary approach in elucidating key aspects of complement functions and determining the role of several complement proteins in both inflammatory and developmental processes. Here we discuss recent findings pertaining to the rational development of complement inhibitors, our studies on protein-protein interactions and our progress in the study of viral immune evasion and complement evolution. Furthermore, we present recent studies implicating complement components in complex developmental processes, such as organ regeneration, hematopoietic development, and stem cell engraftment.