Analysis and visualization of gene expression data using Self-Organizing Maps. - Janne Nikkilä; Petri Törönen; Samuel Kaski; Jarkko Venna; Eero Castrén; Garry Wong (Neural Networks, 2002)

Trustworthiness and metrics in visualizing similarity of gene expression. - Samuel Kaski; Janne Nikkilä; Merja Oja; Jarkko Venna; Petri Törönen; Eero Castrén (BMC Bioinform., 2003)

Selection of informative clusters from hierarchical cluster tree with gene classes. - Petri Törönen (BMC Bioinform., 2004)

Theme discovery from gene lists for identification and viewing of multiple functional groups. - Petri Pehkonen; Garry Wong; Petri Törönen (BMC Bioinform., 2005)

Bayesian search of functionally divergent protein subgroups and their function specific residues. - Pekka Marttinen; Jukka Corander; Petri Törönen; Liisa Holm (Bioinform., 2006)

POXO: a web-enabled tool series to discover transcription factor binding sites. - Matti Kankainen; Petri Pehkonen; Päivi Rosenström; Petri Törönen; Garry Wong; Liisa Holm (Nucleic Acids Res., 2006)

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. - Petri Törönen; Pauli J. Ojala; Pekka Marttinen; Liisa Holm (BMC Bioinform., 2009)

Generation of Gene Ontology benchmark datasets with various types of positive signal. - Petri Törönen; Petri Pehkonen; Liisa Holm (BMC Bioinform., 2009)

Interspliced transcription chimeras: Neglected pathological mechanism infiltrating gene accession queries? - Martti Tolvanen; Pauli J. Ojala; Petri Törönen; Heidi Anderson; Jukka Partanen; Hannu Turpeinen (J. Biomed. Informatics, 2009)

Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions. - Petri Pehkonen; Garry Wong; Petri Törönen (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

GOParGenPy: a high throughput method to generate Gene Ontology data matrices. - Ajay Kumar; Liisa Holm; Petri Törönen (BMC Bioinform., 2013)

Gene set analysis: limitations in popular existing methods and proposed improvements. - Pashupati P. Mishra; Petri Törönen; Yrjö Leino; Liisa Holm (Bioinform., 2014)

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment. - Patrik Koskinen; Petri Törönen; Jussi Nokso-Koivisto; Liisa Holm (Bioinform., 2015)

Robust multi-group gene set analysis with few replicates. - Pashupati P. Mishra; Alan Medlar; Liisa Holm; Petri Törönen (BMC Bioinform., 2016)

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. - Alan Medlar; Petri Törönen; Liisa Holm (Nucleic Acids Res., 2018)

PANNZER2: a rapid functional annotation web server. - Petri Törönen; Alan Medlar; Liisa Holm (Nucleic Acids Res., 2018)

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

A New Approach to Multilabel Stratified Cross Validation with Application to Large and Sparse Gene Ontology Datasets. - Henri Tiittanen; Liisa Holm; Petri Törönen (CoRR, 2021)

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