Optimizing a global alignment of protein interaction networks. - Leonid Chindelevitch; Cheng-Yu Ma; Chung-Shou Liao; Bonnie Berger (Bioinform., 2013)

Reconstruction of phyletic trees by global alignment of multiple metabolic networks. - Cheng-Yu Ma; Shu-Hsi Lin; Chi-Ching Lee; Chuan Yi Tang; Bonnie Berger; Chung-Shou Liao (BMC Bioinform., 2013)

Identification of protein complexes by integrating multiple alignment of protein interaction networks. - Cheng-Yu Ma; Yi-Ping Phoebe Chen; Bonnie Berger; Chung-Shou Liao (Bioinform., 2017)