miRNAkey: a software for microRNA deep sequencing analysis. - Roy Ronen; Ido Gan; Shira Modai; Alona Sukacheov; Gideon Dror; Eran Halperin; Noam Shomron (Bioinform., 2010)

SEQuel: improving the accuracy of genome assemblies. - Roy Ronen; Christina Boucher 001; Hamidreza Chitsaz; Pavel A. Pevzner (Bioinform., 2012)

Learning Natural Selection from the Site Frequency Spectrum. - Roy Ronen; Nitin Udpa; Eran Halperin; Vineet Bafna (RECOMB, 2013)

Identifying and Characterizing the Genomic Signatures of Natural Selection. - Roy Ronen (2014)

Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele. - Roy Ronen; Glenn Tesler; Ali Akbari; Shay Zakov; Noah A. Rosenberg; Vineet Bafna (RECOMB, 2015)

Misassembly detection using paired-end sequence reads and optical mapping data. - Martin D. Muggli; Simon J. Puglisi; Roy Ronen; Christina Boucher 001 (Bioinform., 2015)