LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. - Mitchell J. Machiela; Stephen J. Chanock (Bioinform., 2015)

LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation. - Mitchell J. Machiela; Stephen J. Chanock (Bioinform., 2018)

LDpop: an interactive online tool to calculate and visualize geographic LD patterns. - Theresa A. Alexander; Mitchell J. Machiela (BMC Bioinform., 2020)

PCAmatchR: a flexible R package for optimal case-control matching using weighted principal components. - Derek W. Brown; Timothy A. Myers; Mitchell J. Machiela (Bioinform., 2021)

LDexpress: an online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data. - Shu-Hong Lin; Rohit Thakur; Mitchell J. Machiela (BMC Bioinform., 2021)

PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project. - Eric Ruan; Erika Nemeth; Richard A. Moffitt; Lorena Sandoval; Mitchell J. Machiela; Neal D. Freedman; Wen-Yi Huang; Wendy Wong; Kai-Ling Chen; Brian Park; Kevin Jiang; Belynda Hicks; et al. (Bioinform., 2022)

Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region. - Weiyin Zhou; Wen-Yi Huang; Neal D. Freedman; Mitchell J. Machiela (BMC Bioinform., 2025)