Pinpoint: Problem Determination in Large, Dynamic Internet Services. - Mike Y. Chen; Emre Kiciman; Eugene Fratkin; Armando Fox; Eric A. Brewer (DSN, 2002)

MotifCut: regulatory motifs finding with maximum density subgraphs. - Eugene Fratkin; Brian T. Naughton; Douglas L. Brutlag; Serafim Batzoglou (ISMB (Supplement of Bioinformatics), 2006)

Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. - Andreas Sundquist; Eugene Fratkin; Chuong B. Do; Serafim Batzoglou (RECOMB, 2008)

Application of non-parametric algorithms to computational biology. - Eugene Fratkin (2009)

The MADlib Analytics Library or MAD Skills, the SQL. - Joseph M. Hellerstein; Christopher Ré; Florian Schoppmann; Daisy Zhe Wang; Eugene Fratkin; Aleksander Gorajek; Kee Siong Ng; Caleb Welton; Xixuan Feng; Kun Li; Arun Kumar 001 (Proc. VLDB Endow., 2012)