JavaShade: multiple sequence alignment box-and-shading on the World Wide Web. - Mark R. Southern; Alan P. Lewis (Bioinform., 1998)

The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data. - Bruce D. Pascal; Michael J. Chalmers; Scott A. Busby; C. C. Mader; Mark R. Southern; N. F. Tsinoremas; Patrick R. Griffin (BMC Bioinform., 2007)

A Java API for working with PubChem datasets. - Mark R. Southern; Patrick R. Griffin (Bioinform., 2011)

PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem. - Stephanie A. Canny; Yasel Cruz; Mark R. Southern; Patrick R. Griffin (Bioinform., 2012)

BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. - E. A. Howe; Andrea de Souza; David L. Lahr; S. Chatwin; Philip Montgomery; B. R. Alexander; Dac-Trung Nguyen; Yasel Cruz; D. A. Stonich; G. Walzer; J. T. Rose; Shaita C. Picard; et al. (Nucleic Acids Res., 2015)