Fully automated pipeline for detection of sex linked genes using RNA-Seq data. - Monika Michalovova; Zdenek Kubat; Roman Hobza; Boris Vyskot; Eduard Kejnovský (BMC Bioinform., 2015)

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. - Samarth Rangavittal; Robert S. Harris; Monika Cechova; Marta Tomaszkiewicz; Rayan Chikhi; Kateryna D. Makova; Paul Medvedev (Bioinform., 2018)

Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data. - Robert S. Harris; Monika Cechova; Kateryna D. Makova (Bioinform., 2019)

Ten simple rules for biologists initiating a collaboration with computer scientists. - Monika Cechova (PLoS Comput. Biol., 2020)

HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization. - Matej Lexa; Monika Cechova; Son Hoang Nguyen; Pavel Jedlicka; Viktor Tokan; Zdenek Kubat; Roman Hobza; Eduard Kejnovský (Bioinform., 2022)