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Petri Törönen

  • PL 56 (Viikinkaari 5)

    00014

    Finland

19992018
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Publications 1999 2018

  • 28 Article
  • 2 Anthology or special issue
  • 1 Chapter
2018

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

Medlar, A. J., Törönen, P. & Holm, L., 2 Jul 2018, In : Nucleic Acids Research. 46, W1, p. W479-W485 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer

Pussila, M., Toronen, P., Einarsdottir, E., Katayama, S., Krjutskov, K., Holm, L., Kere, J., Peltomäki, P., Mäkinen, M. J., Linden, J. & Nyström, M., Jun 2018, In : Carcinogenesis. 39, 6, p. 788-797 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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PANNZER2: a rapid functional annotation web server

Törönen, P., Medlar, A. & Holm, L., 2 Jul 2018, In : Nucleic Acids Research. 46, W1, p. W84-W88 5 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 othersCao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Toronen, P., Koskinen, P., Holm, L., Chen, C-T., Hsu, W-L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., Dukka, B. K. C., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L-C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeno-Cortes, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernandez, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A. D. J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., 7 Sep 2016, In : Genome Biology. 17, 19 p., 184.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Robust multi-group gene set analysis with few replicates

Mishra, P. P., Medlar, A., Holm, L. & Törönen, P., 9 Dec 2016, In : BMC Bioinformatics. 17, 12 p., 526.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2015

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment

Koskinen, P., Törönen, P., Nokso-Koivisto, J. & Holm, L., 2015, In : Bioinformatics. 31, 10, p. 1544-1552 9 p.

Research output: Contribution to journalArticleScientificpeer-review

2014

Gene set analysis: limitations in popular existing methods and proposed improvements

Mishra, P., Törönen, P., Leino, Y. & Holm, L., 2014, In : Bioinformatics. 30, 19, p. 2747-2756 10 p., btu374.

Research output: Contribution to journalArticleScientificpeer-review

Oxidative Stress Components Explored in Anoxic and Hypoxic Global Gene Expression Data

Blokhina, O., Törönen, P. & Fagerstedt, K., 2014, Low-Oxygen Stress in Plants: Oxygen Sensing and Adaptive Responses to Hypoxia. Springer-Verlag, p. 19-40 20 p. (Plant Cell Monographs; vol. 21).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

2013

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., Pandey, G., Yunes, J. M., Talwalkar, A. S., Repo, S., Souza, M. L., Piovesan, D., Casadio, R., Wang, Z., Cheng, J., Fang, H. & 82 othersGoughl, J., Koskinen, P., Toronen, P., Nokso-Koivisto, J., Holm, L., Cozzetto, D., Buchan, D. W. A., Bryson, K., Jones, D. T., Limaye, B., Inamdar, H., Datta, A., Manjari, S. K., Joshi, R., Chitale, M., Kihara, D., Lisewski, A. M., Erdin, S., Venner, E., Lichtarge, O., Rentzsch, R., Yang, H., Romero, A. E., Bhat, P., Paccanaro, A., Hamp, T., Kassner, R., Seemayer, S., Vicedo, E., Schaefer, C., Achten, D., Auer, F., Boehm, A., Braun, T., Hecht, M., Heron, M., Hoenigschmid, P., Hopf, T. A., Kaufmann, S., Kiening, M., Krompass, D., Landerer, C., Mahlich, Y., Roos, M., Bjorne, J., Salakoski, T., Wong, A., Shatkay, H., Gatzmann, F., Sommer, I., Wass, M. N., Sternberg, M. J. E., Skunca, N., Supek, F., Bosnjak, M., Panov, P., Dzeroski, S., Smuc, T., Kourmpetis, Y. A. I., van Dijk, A. D. J., ter Braak, C. J. F., Zhou, Y., Gong, Q., Dong, X., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Di Camillo, B., Toppo, S., Lan, L., Djuric, N., Guo, Y., Vucetic, S., Bairoch, A., Linial, M., Babbitt, P. C., Brenner, S. E., Orengo, C., Rost, B., Mooney, S. D. & Friedberg, I., Mar 2013, In : Nature methods. 10, 3, p. 221-227 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis

Li, J., Besseau, S., Törönen, P., Sipari, N. H., Kollist, H., Holm, L. & Palva, E. T., Oct 2013, In : New Phytologist. 200, 2, p. 457–472 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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GOParGenPy: a high throughput method to generate Gene Ontology data matrices

Kumar, A. A., Holm, L. & Toronen, P., 8 Aug 2013, In : BMC Bioinformatics. 14, 242, 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2012

Revised Phylogeny and Novel Horizontally Acquired Virulence Determinants of the Model Soft Rot Phytopathogen Pectobacterium wasabiae SCC3193

Nykyri, J., Niemi, O. A., Koskinen, P., Nokso-Koivisto, J. P., Pasanen, M., Broberg, E. M., Plyusnin, I., Törönen, P., Holm, L., Pirhonen, M. & Palva, E. T., 2012, In : PLoS Pathogens. 8, 11 (e1003013), 18 p.

Research output: Contribution to journalArticleScientificpeer-review

2010

Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions

Pehkonen, P., Wong, G. & Törönen, P., 2010, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7, 1, p. 37-49 13 p.

Research output: Contribution to journalArticleScientificpeer-review

2009

Generation of Gene Ontology benchmark datasets with various types of positive signal

Törönen, P., Pehkonen, P. & Holm, L. U. T., 2009, In : BMC Bioinformatics. 10, 319, 14 s

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File

Interspliced transcription chimeras: neglected pathological mechanism infiltrating gene accession queries?

Tolvanen, M., Ojala, P. J., Törönen, P., Anderson, H., Partanen, J. & Turpeinen, H., 2009, In : Journal of Biomedical Informatics. 42, p. 382-389 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

Törönen, P., Ojala, P. J., Marttinen, P. & Holm, L. U. T., 2009, In : BMC Bioinformatics. 10, p. 307

Research output: Contribution to journalArticleScientificpeer-review

Open Access
File
2007

Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code?

Ojala, P., Kilpinen, S., Arola, L., Toronen, P., Bucher, E., Ojala, K., Iljin, K., Peltonen, M., Skotheim, R., Kleivi, K., Tolvanen, M., Autio, R., Somerharju, P., Kallioniemi, O. & Laitinen, S., Sep 2007, In : Chemistry and Physics of Lipids. 149, p. S86-S86 1 p.

Research output: Contribution to journalArticleScientificpeer-review

2006

Bayesian search of functionally divergent protein subgroups and their function specific residues

Marttinen, P., Corander, J., Törönen, P. & Holm, L., 2006, In : Bioinformatics. 22, 20, p. 2466-2474 9 p.

Research output: Contribution to journalArticleScientificpeer-review

2005

Theme discovery from gene lists for identification and viewing of multiple functional groups

Pehkonen, P., Wong, G. & Törönen, P., 2005, In : BMC Bioinformatics. 6, 162, 18 s

Research output: Contribution to journalArticleScientificpeer-review

2004

Brain-derived neurotrophic factor signaling modifies hippocampal gene expression during epileptogenesis in transgenic mice

Lähteinen, S., Pitkänen, A., Knuuttila, J., Törönen, P. & Castrén, E., 2004, In : European Journal of Neuroscience. 19, p. 3245-3254 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Effects of antidepressant drug imipramine on gene expression in rat prefrontal cortex

Knuuttila, J. E. A., Toronen, P. & Castren, E., 2004, In : Neurochemical Research. 29, p. 1235-1244 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Selection of informative clusters from hierarchical cluster tree with gene classes

Toronen, P., 25 Mar 2004, In : BMC Bioinformatics. 5, 19 p., 32.

Research output: Contribution to journalArticleScientificpeer-review

2003

Trustworthiness and metrics in visualizing similarity of gene expression

Kaski, S., Nikkila, J., Oja, M., Venna, J., Toronen, P. & Castren, E., 2003, In : BMC Bioinformatics. 4, 13 p.

Research output: Contribution to journalArticleScientificpeer-review

2002

Analysis and visualization of gene expression data using Self-Organizing Maps

Nikkila, J., Törönen, P., Kaski, S., Venna, J., Castren, E. & Wong, G., 2002, In : Neural Networks. 15, p. 953-966 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Antipsychotic drug treatment induces differential gene expression in the rat cortex

Kontkanen, O., Toronen, P., Lakso, M. A., Wong, G. & Castren, E., 2002, In : Journal of Neurochemistry. 83, p. 1043-1053 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Changes in gene expression in atherosclerotic plaques analyzed using DNA array

Hiltunen, MO., Tuomisto, TT., Niemi, M., Brasen, JH., Rissanen, TT., Toronen, P., Vajanto & Yla-Herttuala, S., Nov 2002, In : Atherosclerosis. 165, 1, p. 23-32 10 p., PII S0021-9150(02)00187-9.

Research output: Contribution to journalArticleScientificpeer-review

Exploratory Clustering Of Gene Expression Profiles Of Mutated Yeast Strains

Oja, M., Nikkilä, J., Törönen, P., Wong, G. & Kaski, S., 2002

Research output: Book/ReportAnthology or special issueScientificpeer-review

Synexpression analysis of ESTs in the rat brain reveals distinct patterns and potential drug targets

Marvanova, A., Storvik, M., Lakso, M., Wong, G., Marvanova, A., Toronen, P., Storvik, M., Lakso, M., Castren, E. & Wong, G., 2002, In : Molecular brain research : a section of Brain research devoted to the publication of molecular studies. 104, p. 176-183 8 p.

Research output: Contribution to journalArticleScientificpeer-review

2001

Analysis and Visualization of Gene Expression Data Using Self-Organizing Maps

Kaski, S., Nikkilä, J., Törönen, P., Castrén, E. & Wong, G., 2001

Research output: Book/ReportAnthology or special issueScientificpeer-review

1999

Analysis of gene expression data using self-organizing maps

Toronen, P., Kolehmainen, M., Wong, C. & Castren, E., 1999, In : FEBS Letters. 451, p. 142-146 5 p.

Research output: Contribution to journalArticleScientificpeer-review