Automated Design of Assemblable, Modular, Synthetic Chromosomes. - Sarah M. Richardson; Brian S. Olson; Jessica S. Dymond; Randal C. Burns; Srinivasan Chandrasegaran; Jef D. Boeke; Amarda Shehu; Joel S. Bader (PPAM (2), 2009)

BioPartsDB: a synthetic biology workflow web-application for education and research. - Giovanni Stracquadanio; Kun Yang 003; Jef D. Boeke; Joel S. Bader (Bioinform., 2016)

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. - Kun Yang 003; Giovanni Stracquadanio; Jingchuan Luo; Jef D. Boeke; Joel S. Bader (Bioinform., 2016)

Whole genome synthesis: from poliovirus to synthetic yeast. - Junbiao Dai; Yizhi Cai; Yinjing Yuan; Huanming Yang; Jef D. Boeke (Quant. Biol., 2017)