PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data. - David E. Frankhouser; Mark Murphy; James S. Blachly; Jincheol Park; Mike W. Zoller; Javkhlan-Ochir Ganbat; John Curfman; John C. Byrd; Shili Lin; Guido Marcucci; Pearlly Yan; Ralf Bundschuh (Bioinform., 2014)

MuCor: mutation aggregation and correlation. - Karl W. Kroll; Ann-Katherin Eisfeld; Gerard Lozanski; Clara D. Bloomfield; John C. Byrd; James S. Blachly (Bioinform., 2016)

Par-eXpress: A Tool for Analysis of Sequencing Experiments With Ambiguous Assignment of Fragments in Parallel. - Mücahid Kutlu; Gagan Agrawal; James S. Blachly (IPDPS Workshops, 2017)

On the analysis of the human immunome via an information theoretical approach. - Maciej Pietrzak; Gerard Lozanski; Michael Grever; Leslie Andritsos; James S. Blachly; Kerry Rogers; Michal Seweryn (Int. J. Comput. Biol. Drug Des., 2020)

Typesafe Coordinate Systems in High-Throughput Sequencing Applications. - Charles Thomas Gregory; James S. Blachly (CoRR, 2022)