Constructing Aligned Sequence Blocks. - Webb Miller; Mark Boguski; Balaji Raghavachari; Zheng Zhang 004; Ross C. Hardison (J. Comput. Biol., 1994)

Chaining Multiple-Alignment Blocks. - Zheng Zhang 004; Balaji Raghavachari; Ross C. Hardison; Webb Miller (J. Comput. Biol., 1994)

Progressive Multiple Alignment with Constraints. - Gene Myers; Sanford Selznick; Zheng Zhang 004; Webb Miller (J. Comput. Biol., 1996)

Aligning a DNA Sequence with a Protein Sequence. - Zheng Zhang 004; William R. Pearson; Webb Miller (J. Comput. Biol., 1997)

Alignments without Low-Scoring Regions. - Zheng Zhang 004; Piotr Berman; Webb Miller (J. Comput. Biol., 1998)

Post-processing long pairwise alignments. - Zheng Zhang 004; Piotr Berman; Thomas Wiehe; Webb Miller (Bioinform., 1999)

Winnowing Sequences from a Database Search. - Piotr Berman; Zheng Zhang 004; Yuri I. Wolf; Eugene V. Koonin; Webb Miller (J. Comput. Biol., 2000)

A Greedy Algorithm for Aligning DNA Sequences. - Zheng Zhang 004; Scott Schwartz; Lukas Wagner 002; Webb Miller (J. Comput. Biol., 2000)