The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. - Can Alkan; Evan E. Eichler; Jeffrey A. Bailey; Süleyman Cenk Sahinalp; Eray Tüzün (J. Comput. Biol., 2004)

Manipulating multiple sequence alignments via MaM and WebMaM. - Can Alkan; Eray Tüzün; Jerome Buard; Franck Lethiec; Evan E. Eichler; Jeffrey A. Bailey; Süleyman Cenk Sahinalp (Nucleic Acids Res., 2005)

coiaf: Directly estimating complexity of infection with allele frequencies. - Aris Paschalidis; Oliver J. Watson; Ozkan Aydemir; Robert Verity; Jeffrey A. Bailey (PLoS Comput. Biol., 2023)