A Prototype for Multiple Whole Genome Alignment. - Jitender S. Deogun; Fangrui Ma; Jingyi Yang; Andrew Benson (HICSS, 2003)

RNA Secondary Structure Prediction with Simple Pseudoknots. - Jitender S. Deogun; Ruben Donts; Olga Komina; Fangrui Ma (APBC, 2004)

EMAGEN: An Efficient Approach to Multiple Whole Genome Alignment. - Jitender S. Deogun; Jingyi Yang; Fangrui Ma (APBC, 2004)

Applications of EMAGEN on Comparing Multiple Prokaryotic Genomes. - Jitender S. Deogun; Jingyi Yang; Fangrui Ma (METMBS, 2004)

The solution space of genome sequence alignment and LIS graph decomposition. - Fangrui Ma; Jitender S. Deogun (BCB, 2010)

Multiple genome alignment based on longest path in directed acyclic graphs. - Fangrui Ma; Jitender S. Deogun (Int. J. Bioinform. Res. Appl., 2010)