Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. - Timothy D. O'Connor; Nicholas I. Mundy (Bioinform., 2009)

AdmixKJump: identifying population structure in recently diverged groups. - Timothy D. O'Connor (Source Code Biol. Medicine, 2015)

Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data. - Suyash S. Shringarpure; Rasika A. Mathias; Ryan D. Hernandez; Timothy D. O'Connor; Zachary A. Szpiech (Bioinform., 2017)

STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. - Albert E. Zhou; Zalak V. Shah; Katie R. Bradwell; James B. Munro; Andrea A. Berry; David Serre; Shannon Takala-Harrison; Timothy D. O'Connor; Joana C. Silva; Mark A. Travassos (BMC Bioinform., 2022)