Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies. - Nils Homer; Waibhav Tembe; Szabolcs Szelinger; Margot Redman; Dietrich A. Stephan; John V. Pearson; Stanley F. Nelson; David W. Craig (Bioinform., 2008)

Local alignment of two-base encoded DNA sequence. - Nils Homer; Barry Merriman; Stanley F. Nelson (BMC Bioinform., 2009)

Local alignment of generalized k-base encoded DNA sequence. - Nils Homer; Stanley F. Nelson; Barry Merriman (BMC Bioinform., 2010)

SeqWare Query Engine: storing and searching sequence data in the cloud. - Brian D. O'Connor; Barry Merriman; Stanley F. Nelson (BMC Bioinform., 2010)

High-throughput sequencing of the DBA/2J mouse genome. - Xusheng Wang; Richa Agarwala; John A. Capra; Zugen Chen; Deanna M. Church; Daniel C. Ciobanu; Zhengsheng Li; Lu Lu 004; Khyobeni Mozhui; Megan K. Mulligan; Stanley F. Nelson; Katherine S. Pollard; et al. (BMC Bioinform., 2010)

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. - Jarupon Fah Sathirapongsasuti; Hane Lee; Basil A. J. Horst; Georg Brunner; Alistair J. Cochran; Scott Binder; John Quackenbush; Stanley F. Nelson (Bioinform., 2011)

Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. - Michael Yourshaw; S. Paige Taylor; Aliz R. Rao; Martín G. Martín; Stanley F. Nelson (Briefings Bioinform., 2015)

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Lane Fitzsimmons; Maria T. Acosta; David R. Adams; Ben Afzali; Ali Al-Beshri; Eric Allenspach; Aimee Allworth; Raquel L. Alvarez; Justin Alvey; Ashley Andrews; Euan A. Ashley; Carlos A. Bacino; et al. (BioData Min., 2025)