Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. - Cristian Coarfa; Fuli Yu; Christopher A. Miller 003; Zuozhou Chen; R. Alan Harris; Aleksandar Milosavljevic (BMC Bioinform., 2010)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

SVhound: detection of regions that harbor yet undetected structural variation. - Luis F. Paulin; Muthuswamy Raveendran; R. Alan Harris; Jeffrey Rogers; Arndt von Haeseler; Fritz J. Sedlazeck (BMC Bioinform., 2023)