Publications by authors named "Petri Toronen"

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Genome-wide DNA methylation profiles of colorectal tumors in Lynch syndrome and familial adenomatous polyposis.
Satu Mäki-Nevala, Anni Kauppinen, Alisa Olkinuora, Aleksi Laiho, Petri Törönen

Clin Epigenetics· August 2025

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3-D substructure search by transitive closure in AlphaFold database.
Hao Liu, Aleksi Laiho, Petri Törönen, Liisa Holm

Protein Sci· June 2025

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Mitotic abnormalities precede microsatellite instability in lynch syndrome-associated colorectal tumourigenesis.
Marjaana Pussila, Aleksi Laiho, Petri Törönen, Pauliina Björkbacka, Sonja Nykänen

EBioMedicine· May 2024

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Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity.
Jurgita Paukštytė, Rosa María López Cabezas, Yuehan Feng, Kai Tong, Daniela Schnyder

Mol Cell· September 2023

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The giant diploid faba genome unlocks variation in a global protein crop.
Murukarthick Jayakodi, Agnieszka A Golicz, Jonathan Kreplak, Lavinia I Fechete, Deepti Angra

Nature· March 2023

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DALI shines a light on remote homologs: One hundred discoveries.
Liisa Holm, Aleksi Laiho, Petri Törönen, Marco Salgado

Protein Sci· January 2023

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Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
Ilya Plyusnin, Liisa Holm, Petri Törönen

PLoS Comput Biol· June 2022

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PANNZER-A practical tool for protein function prediction.
Petri Törönen, Liisa Holm

Protein Sci· January 2022

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Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain.
Francesca Morello, Daniel Borshagovski, Mantas Survila, Laura Tikker, Samir Sadik-Ogli

Cell Rep· October 2020

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Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study.
Pashupati P Mishra, Ismo Hänninen, Emma Raitoharju, Saara Marttila, Binisha H Mishra

Biosci Rep· July 2020

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Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.
Ilya Plyusnin, Liisa Holm, Petri Törönen

PLoS Comput Biol· November 2019

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh

Genome Biol· November 2019

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PANNZER2: a rapid functional annotation web server.
Petri Törönen, Alan Medlar, Liisa Holm

Nucleic Acids Res· July 2018

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AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.
Alan J Medlar, Petri Törönen, Liisa Holm

Nucleic Acids Res· July 2018

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Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer.
Marjaana Pussila, Petri Törönen, Elisabet Einarsdottir, Shintaro Katayama, Kaarel Krjutškov

Carcinogenesis· May 2018

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Robust multi-group gene set analysis with few replicates.
Pashupati P Mishra, Alan Medlar, Liisa Holm, Petri Törönen

BMC Bioinformatics· December 2016

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea

Genome Biol· September 2016

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

Bioinformatics· May 2015

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Gene set analysis: limitations in popular existing methods and proposed improvements.
Pashupati Mishra, Petri Törönen, Yrjö Leino, Liisa Holm

Bioinformatics· October 2014

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Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis.
Jing Li, Sebastien Besseau, Petri Törönen, Nina Sipari, Hannes Kollist

New Phytol· October 2013

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GOParGenPy: a high throughput method to generate gene ontology data matrices.
Ajay Anand Kumar, Liisa Holm, Petri Toronen

BMC Bioinformatics· August 2013

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Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.
Johanna Nykyri, Outi Niemi, Patrik Koskinen, Jussi Nokso-Koivisto, Miia Pasanen

PLoS Pathog· April 2013

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A large-scale evaluation of computational protein function prediction.
Predrag Radivojac, Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes, Tobias Wittkop

Nat Methods· March 2013

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Heuristic Bayesian segmentation for discovery of coexpressed genes within genomic regions.
Petri Pehkonen, Garry Wong, Petri Törönen

IEEE/ACM Trans Comput Biol Bioinform· May 2010

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Generation of Gene Ontology benchmark datasets with various types of positive signal.
Petri Törönen, Petri Pehkonen, Liisa Holm

BMC Bioinformatics· October 2009

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