MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data. - William J. Salerno; Samuel M. Seaver; Brian R. Armstrong; Ishwar Radhakrishnan (Nucleic Acids Res., 2004)

PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping. - Adam C. English; William J. Salerno; Jeffrey G. Reid (BMC Bioinform., 2014)

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. - Jeffrey G. Reid; Andrew Carroll; Narayanan Veeraraghavan; Mahmoud Dahdouli; Andreas Sundquist; Adam C. English; Matthew N. Bainbridge; Simon White; William J. Salerno; Christian Buhay; Fuli Yu; Donna M. Muzny; et al. (BMC Bioinform., 2014)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. - Yuk Yee Leung; Otto Valladares; Yi-Fan Chou; Han-Jen Lin; Amanda Kuzma; Laura Cantwell; Liming Qu; Prabhakaran Gangadharan; William J. Salerno; Gerard D. Schellenberg; Li-San Wang (Bioinform., 2019)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. - Yuk Yee Leung; Otto Valladares; Yi-Fan Chou; Han-Jen Lin; Amanda Kuzma; Laura Cantwell; Liming Qu; William J. Salerno; Gerard D. Schellenberg; Li-San Wang (Bioinform., 2019)

Sparse Project VCF: efficient encoding of population genotype matrices. - Michael F. Lin; Xiaodong Bai; William J. Salerno; Jeffrey G. Reid (Bioinform., 2021)