Simple and Fast Inverse Alignment. - John D. Kececioglu; Eagu Kim (RECOMB, 2006)

Inverse Sequence Alignment from Partial Examples. - Eagu Kim; John D. Kececioglu (WABI, 2007)

Learning Scoring Schemes for Sequence Alignment from Partial Examples. - Eagu Kim; John D. Kececioglu (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Inverse Parametric Alignment for Accurate Biological Sequence Comparison. - Eagu Kim (2008)

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure. - Eagu Kim; Travis J. Wheeler; John D. Kececioglu (RECOMB, 2009)

Aligning Protein Sequences with Predicted Secondary Structure. - John D. Kececioglu; Eagu Kim; Travis J. Wheeler (J. Comput. Biol., 2010)