PUNCH: An Evolutionary Algorithm for Optimizing Bit Set Selection. - Adam J. Ruben; Stephen J. Freeland; Laura F. Landweber (DNA, 2001)

Genview and Gencode: a pair of programs to test theories of genetic code evolution. - T. Andrew Ronneberg; Stephen J. Freeland; Laura F. Landweber (Bioinform., 2001)

The Darwinian Genetic Code: An Adaptation for Adapting? - Stephen J. Freeland (Genet. Program. Evolvable Mach., 2002)

The Synthetic Gene Designer: a Flexible Web Platform to Explore Sequence Space of Synthetic Genes for Heterologous Expression. - Gang Wu 016; Nabila Bashir-Bello; Stephen J. Freeland (CSB Workshops, 2005)

An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices. - Blazej Bulka; Marie desJardins; Stephen J. Freeland (BMC Bioinform., 2006)

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. - Gang Wu 016; Yuanpu Zheng; Imran Qureshi; Htar Thant Zin; Tyler Beck; Blazej Bulka; Stephen J. Freeland (Nucleic Acids Res., 2007)

Beyond Terrestrial Biology: Charting the Chemical Universe of α-Amino Acid Structures. - Markus Meringer; H. James Cleaves II; Stephen J. Freeland (J. Chem. Inf. Model., 2013)