Scaffolding and validation of bacterial genome assemblies using optical restriction maps. - Niranjan Nagarajan; Timothy D. Read; Mihai Pop (Bioinform., 2008)

DIYA: a bacterial annotation pipeline for any genomics lab. - Andrew C. Stewart; Brian Osborne; Timothy D. Read (Bioinform., 2009)

PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data. - Wenling E. Chang; Keri Sarver; Brandon W. Higgs; Timothy D. Read; Nichole M. E. Nolan; Carol E. Chapman; Kimberly A. Bishop-Lilly; Shanmuga Sozhamannan (BMC Bioinform., 2011)

Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes. - Rohan S. Mehta; Robert Petit; Timothy D. Read; Daniel B. Weissman (BMC Bioinform., 2023)