Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques

Niranjan Nagarajan, Carl Kingsford
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by
more » ... trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human-and avianhosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced.
doi:10.1109/bibm.2008.78 dblp:conf/bibm/NagarajanK08 fatcat:5wivvyq4irfjppadt3phtmtz6q