Quantitative measures for the management and comparison of annotated genomes. - Karen Eilbeck; Barry Moore; Carson Holt; Mark Yandell (BMC Bioinform., 2009)

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. - Carson Holt; Mark Yandell (BMC Bioinform., 2011)

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing. - Carson Holt; Bojan Losic; Deepa Pai; Zhen Zhao; Quang Trinh; Sujata Syam; Niloofar Arshadi; Gun Ho Jang; Johar Ali; Tim Beck; John D. McPherson; Lakshmi B. Muthuswamy (Bioinform., 2014)

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. - William H. Majoros; Michael Campbell; Carson Holt; Erin K. DeNardo; Doreen Ware; Andrew S. Allen; Mark Yandell; Timothy E. Reddy (Bioinform., 2017)

Predicting gene structure changes resulting from genetic variants via exon definition features. - William H. Majoros; Carson Holt; Michael Campbell; Doreen Ware; Mark Yandell; Timothy E. Reddy (Bioinform., 2018)