PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. - Antonio Martínez-Alcántara; Efren Ballesteros; Chen Feng; Mark Rojas; H. Koshinsky; Viacheslav Fofanov; Paul Havlak; Yuriy Fofanov (Bioinform., 2009)

Co-Evolution of the Influenza Virus and Its Hosts. - Stephen Huff; Mark Rojas; Paul Havlak; Yuriy Fofanov (BIOCOMP, 2010)

Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation. - Georgiy Golovko; Kamil Khanipov; Mark Rojas; Antonio Martínez-Alcántara; Jesse J. Howard; Efren Ballesteros; Sharu Gupta; William Widger; Yuriy Fofanov (BMC Bioinform., 2012)

CoCo: An application to store High-Throughput Sequencing data in compact text and binary file formats. - Kamil Khanipov; Georgiy Golovko; Mark Rojas; Levent Albayrak; Otto Dobretsberger; Maria Pimenova; Nels Olson; Sergei Chumakov; Yuriy Fofanov (BIBM, 2015)

Exploration of Natural Alignment Scoring Rules and Clustering Thresholds for Bacterial Core/Pan Genome Analysis. - Levent L. Albayrak; Kamil Khanipov; Mark Rojas; George Golovko; Maria Pimenova; Michael Kosoy; Yuriy Fofanov (BIBE, 2017)