LOCP - locating pilus operons in Gram-positive bacteria. - Ilya Plyusnin; Liisa Holm; Matti Kankainen (Bioinform., 2009)

Comprehensive comparison of graph based multiple protein sequence alignment strategies. - Ilya Plyusnin; Liisa Holm (BMC Bioinform., 2012)

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. - Ilya Plyusnin; Liisa Holm; Petri Törönen (PLoS Comput. Biol., 2019)

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. - Phuoc Thien Truong Nguyen; Ilya Plyusnin; Tarja Sironen; Olli Vapalahti; Ravi Kant 005; Teemu Smura (BMC Bioinform., 2021)

ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. - Ilya Plyusnin; Phuoc Thien Truong Nguyen; Tarja Sironen; Olli Vapalahti; Teemu Smura; Ravi Kant 005 (BMC Bioinform., 2022)

Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. - Ilya Plyusnin; Liisa Holm; Petri Törönen (PLoS Comput. Biol., 2022)