eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE). - Elliott H. Margulies; Jeffrey W. Innis (Bioinform., 2000)

Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. - Come Raczy; Roman Petrovski; Christopher T. Saunders; Ilya Chorny; Semyon Kruglyak; Elliott H. Margulies; Han-Yu Chuang; Morten Källberg; Swathi A. Kumar; Arnold Liao; Kristina M. Little; Michael P. Strömberg; et al. (Bioinform., 2013)

Nirvana: Clinical Grade Variant Annotator. - Michael Strömberg; Rajat Roy; Julien Lajugie; Yu Jiang; Haochen Li; Elliott H. Margulies (BCB, 2017)