| A large-scale evaluation of computational protein function prediction P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ... Nature methods 10 (3), 221-227, 2013 | 1255 | 2013 |
| Analysis of gene expression data using self‐organizing maps P Törönen, M Kolehmainen, G Wong, E Castrén FEBS letters 451 (2), 142-146, 1999 | 772 | 1999 |
| DALI shines a light on remote homologs: One hundred discoveries L Holm, A Laiho, P Törönen, M Salgado Protein Science 32 (1), e4519, 2023 | 612 | 2023 |
| The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20 (1), 244, 2019 | 527 | 2019 |
| PANNZER2: a rapid functional annotation web server P Törönen, A Medlar, L Holm Nucleic acids research 46 (W1), W84-W88, 2018 | 518 | 2018 |
| An expanded evaluation of protein function prediction methods shows an improvement in accuracy Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ... Genome biology 17 (1), 184, 2016 | 485 | 2016 |
| Defense‐related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis J Li, S Besseau, P Törönen, N Sipari, H Kollist, L Holm, ET Palva New Phytologist 200 (2), 457-472, 2013 | 294 | 2013 |
| Trustworthiness and metrics in visualizing similarity of gene expression S Kaski, J Nikkilä, M Oja, J Venna, P Törönen, E Castrén BMC bioinformatics 4 (1), 48, 2003 | 228 | 2003 |
| Analysis and visualization of gene expression data using self-organizing maps J Nikkilä, P Törönen, S Kaski, J Venna, E Castrén, G Wong Neural networks 15 (8-9), 953-966, 2002 | 195 | 2002 |
| PANNZER—a practical tool for protein function prediction P Törönen, L Holm Protein Science 31 (1), 118-128, 2022 | 187 | 2022 |
| AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination AJ Medlar, P Törönen, L Holm Nucleic acids research 46 (W1), W479-W485, 2018 | 174 | 2018 |
| PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment P Koskinen, P Törönen, J Nokso-Koivisto, L Holm Bioinformatics 31 (10), 1544-1552, 2015 | 174 | 2015 |
| The giant diploid faba genome unlocks variation in a global protein crop M Jayakodi, AA Golicz, J Kreplak, LI Fechete, D Angra, P Bednář, ... Nature 615 (7953), 652-659, 2023 | 156 | 2023 |
| Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193 J Nykyri, O Niemi, P Koskinen, J Nokso-Koivisto, M Pasanen, M Broberg, ... PLoS Pathogens 8 (11), e1003013, 2012 | 137 | 2012 |
| Changes in gene expression in atherosclerotic plaques analyzed using DNA array MO Hiltunen, TT Tuomisto, M Niemi, JH Bräsen, TT Rissanen, P Törönen, ... Atherosclerosis 165 (1), 23-32, 2002 | 109 | 2002 |
| Antipsychotic drug treatment induces differential gene expression in the rat cortex O Kontkanen, P Törönen, M Lakso, G Wong, E Castrén Journal of neurochemistry 83 (5), 1043-1053, 2002 | 102 | 2002 |
| Theme discovery from gene lists for identification and viewing of multiple functional groups P Pehkonen, G Wong, P Törönen BMC bioinformatics 6 (1), 162, 2005 | 78 | 2005 |
| Selection of informative clusters from hierarchical cluster tree with gene classes P Toronen BMC bioinformatics 5 (1), 32, 2004 | 68 | 2004 |
| Bayesian search of functionally divergent protein subgroups and their function specific residues P Marttinen, J Corander, P Törönen, L Holm Bioinformatics 22 (20), 2466-2474, 2006 | 60 | 2006 |
| Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function P Törönen, PJ Ojala, P Marttinen, L Holm BMC bioinformatics 10 (1), 307, 2009 | 55 | 2009 |
