CLARK, accurate and efficient classification of DNA sequences. - Rachid Ounit; Timothy J. Close; Steve Wanamaker; Stefano Lonardi (BCB, 2014)

Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers. - Rachid Ounit; Stefano Lonardi (WABI, 2015)

BRAT-nova: fast and accurate mapping of bisulfite-treated reads. - Elena Yavorska Harris; Rachid Ounit; Stefano Lonardi (Bioinform., 2016)

Higher classification sensitivity of short metagenomic reads with CLARK-S. - Rachid Ounit; Stefano Lonardi (Bioinform., 2016)

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison. - Lars Hahn; Chris-André Leimeister; Rachid Ounit; Stefano Lonardi; Burkhard Morgenstern (PLoS Comput. Biol., 2016)

Computing the Microbiome: Faster, More Accurate and More Efficient Methods for the Analysis of Metagenomes. - Rachid Ounit (2017)