Qualimap: evaluating next-generation sequencing alignment data. - Fernando García-Alcalde; Konstantin Okonechnikov; José Carbonell; Luis M. Cruz; Stefan Götz 003; Sonia Tarazona; Joaquín Dopazo; Thomas F. Meyer; Ana Conesa (Bioinform., 2012)

Unipro UGENE: a unified bioinformatics toolkit. - Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov (Bioinform., 2012)

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. - Konstantin Okonechnikov; Ana Conesa; Fernando García-Alcalde (Bioinform., 2016)

High-throughput RNA sequencing: a step forward in transcriptome analysis. - Konstantin Okonechnikov (2016)

InTAD: chromosome conformation guided analysis of enhancer target genes. - Konstantin Okonechnikov; Serap Erkek; Jan O. Korbel; Stefan M. Pfister; Lukas Chavez (BMC Bioinform., 2019)