Large Grain Size Stochastic Optimization Alignment. - Perry G. Ridge; Hyrum Carroll; Dan Sneddon; Mark J. Clement; Quinn Snell (BIBE, 2006)

Phylogenies scores for exhaustive searches and parsimony scores searches. - Hyrum Carroll; Perry G. Ridge; Mark J. Clement; Quinn Snell (Int. J. Bioinform. Res. Appl., 2007)

A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding. - David K. Crockett; Perry G. Ridge (BCB, 2010)

Feature selection for characterizing HLA class I peptide motif anchors. - Perry G. Ridge; David K. Crockett (BCB, 2010)

Cystic fibrosis testing in a referral laboratory: results and lessons from a six-year period. - Perry G. Ridge; Christine Miller; Pinar Bayrak-Toydemir; D. Hunter Best; Rong Mao; Jeffrey J. Swensen; Elaine Lyon; Karl V. Voelkerding (J. Clin. Bioinform., 2013)

Haplotype-centered mapping for improved alignments and genetic association studies. - Paul M. Bodily; Mark J. Clement; Quinn Snell; M. Stanley Fujimoto; Perry G. Ridge (BCB, 2014)

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files. - Mark T. W. Ebbert; Mark E. Wadsworth; Kevin L. Boehme; Kaitlyn L. Hoyt; Aaron R. Sharp; Brendan D. O'Fallon; John S. K. Kauwe; Perry G. Ridge (BMC Bioinform., 2014)

Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging. - Perry G. Ridge; Taylor J. Maxwell; Spencer J. Foutz; Matthew H. Bailey; Christopher D. Corcoran; JoAnn T. Tschanz; Maria C. Norton; Ronald G. Munger; Elizabeth O'Brien; Richard A. Kerber; Richard M. Cawthon; John S. K. Kauwe (BMC Bioinform., 2014)

Population substructure in Cache County, Utah: the Cache County study. - Aaron R. Sharp; Perry G. Ridge; Matthew H. Bailey; Kevin L. Boehme; Maria C. Norton; JoAnn T. Tschanz; Ronald G. Munger; Christopher D. Corcoran; John S. K. Kauwe (BMC Bioinform., 2014)

SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences. - Brandon D. Pickett; S. M. Karlinsey; C. E. Penrod; Michael J. Cormier; Mark T. W. Ebbert; Dennis K. Shiozawa; C. J. Whipple; Perry G. Ridge (Bioinform., 2016)

A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. - Paul M. Bodily; M. Stanley Fujimoto; Justin T. Page; Mark J. Clement; Mark T. W. Ebbert; Perry G. Ridge (BMC Bioinform., 2016)

Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. - Mark T. W. Ebbert; Mark E. Wadsworth; Lyndsay A. Staley; Kaitlyn L. Hoyt; Brandon D. Pickett; Justin Miller; John Duce; John S. K. Kauwe; Perry G. Ridge (BMC Bioinform., 2016)

Kmer-SSR: a fast and exhaustive SSR search algorithm. - Brandon D. Pickett; Justin Miller; Perry G. Ridge (Bioinform., 2017)

JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. - Justin Miller; Brandon D. Pickett; Perry G. Ridge (Bioinform., 2019)

Many bioinformatics programming tasks can be automated with ChatGPT. - Stephen R. Piccolo; Paul Denny 001; Andrew Luxton-Reilly; Samuel H. Payne; Perry G. Ridge (CoRR, 2023)

Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course. - Stephen R. Piccolo; Paul Denny 001; Andrew Luxton-Reilly; Samuel H. Payne; Perry G. Ridge (PLoS Comput. Biol., 2023)