MULTAN: a program to align multiple DNA sequences. - William Bains (Nucleic Acids Res., 1986)

AXE: a program for isolating short segments of long DNA sequences. - William Bains (Comput. Appl. Biosci., 1988)

MULTAN (2), a multiple string alignment program for nucleic acids and proteins. - William Bains (Comput. Appl. Biosci., 1989)

A program to optimize DNA sequences for protein expression. - William Bains (Comput. Appl. Biosci., 1990)

Hexanucleotide frequency database. - William Bains (Comput. Appl. Biosci., 1997)

Low potency toxins reveal dense interaction networks in metabolism. - William Bains (BMC Syst. Biol., 2016)

A Data Resource for Sulfuric Acid Reactivity of Organic Chemicals. - William Bains; Janusz Jurand Petkowski; Sara Seager (Data, 2021)

A Data Resource for Prediction of Gas-Phase Thermodynamic Properties of Small Molecules. - William Bains; Janusz Jurand Petkowski; Zhuchang Zhan; Sara Seager (Data, 2022)

Linking Fungal Genomics to Thermal Growth Limits: A Dataset of 730 Sequenced Species. - William Bains (Data, 2025)