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

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

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

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

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