Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. - Jonathan M. Mortensen; Natalie Telis; Jacob J. Hughey; Hua Fan-Minogue; Kimberly Van Auken; Michel Dumontier; Mark A. Musen (J. Biomed. Informatics, 2016)

Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease. - Lisa Bastarache; Jacob J. Hughey; Jeffery A. Goldstein; Julie A. Bastraache; Satya Das; Neil Charles Zaki; Chenjie Zeng; Leigh Anne Tang; Dan M. Roden; Joshua C. Denny (J. Am. Medical Informatics Assoc., 2019)

The risks of using the chi-square periodogram to estimate the period of biological rhythms. - Michael C. Tackenberg; Jacob J. Hughey (PLoS Comput. Biol., 2021)

Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS. - Rebecca Irlmeier; Jacob J. Hughey; Lisa Bastarache; Joshua C. Denny; Qingxia Chen (Bioinform., 2022)

The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants. - Layla Aref; Lisa Bastarache; Jacob J. Hughey (Bioinform., 2022)