petri toronen
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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
Analysis of gene expression data using self‐organizing maps
P Törönen, M Kolehmainen, G Wong, E Castrén
FEBS letters 451 (2), 142-146, 1999
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), 1-19, 2016
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), 1-23, 2019
PANNZER2: a rapid functional annotation web server
P Törönen, A Medlar, L Holm
Nucleic acids research 46 (W1), W84-W88, 2018
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
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), 1-13, 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
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
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
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
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
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
DALI shines a light on remote homologs: One hundred discoveries
L Holm, A Laiho, P Törönen, M Salgado
Protein Science 32 (1), e4519, 2023
Theme discovery from gene lists for identification and viewing of multiple functional groups
P Pehkonen, G Wong, P Törönen
BMC bioinformatics 6 (1), 1-18, 2005
Selection of informative clusters from hierarchical cluster tree with gene classes
P Toronen
BMC bioinformatics 5, 1-19, 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
PANNZER—a practical tool for protein function prediction
P Törönen, L Holm
Protein Science 31 (1), 118-128, 2022
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), 1-27, 2009
Analysis and visualization of gene expression data using self-organizing maps
S Kaski, J Nikkilä, P Törönen, E Castren, G Wong
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