Selection of informative clusters from hierarchical cluster tree with gene classes

por Toronen, Petri
Publicado 2004

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

por Pehkonen, Petri, Wong, Garry, Törönen, Petri
Publicado 2005

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

por Törönen, Petri, Pehkonen, Petri, Holm, Liisa
Publicado 2009

PANNZER2: a rapid functional annotation web server

por Törönen, Petri, Medlar, Alan, Holm, Liisa
Publicado 2018

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences

por Plyusnin, Ilya, Holm, Liisa, Törönen, Petri
Publicado 2019

Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences

por Plyusnin, Ilya, Holm, Liisa, Törönen, Petri
Publicado 2022

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

por Kumar, Ajay Anand, Holm, Liisa, Toronen, Petri
Publicado 2013

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

por Medlar, Alan J, Törönen, Petri, Holm, Liisa
Publicado 2018

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

por Törönen, Petri, Ojala, Pauli J, Marttinen, Pekka, Holm, Liisa
Publicado 2009

Robust multi-group gene set analysis with few replicates

por Mishra, Pashupati P., Medlar, Alan, Holm, Liisa, Törönen, Petri
Publicado 2016

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana

por Kankainen, Matti, Brader, Günter, Törönen, Petri, Palva, E. Tapio, Holm, Liisa
Publicado 2006

POXO: a web-enabled tool series to discover transcription factor binding sites

por Kankainen, Matti, Pehkonen, Petri, Rosenstöm, Päivi, Törönen, Petri, Wong, Garry, Holm, Liisa
Publicado 2006

Trustworthiness and metrics in visualizing similarity of gene expression

por Kaski, Samuel, Nikkilä, Janne, Oja, Merja, Venna, Jarkko, Törönen, Petri, Castrén, Eero
Publicado 2003

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

por Li, Jing, Besseau, Sebastien, Törönen, Petri, Sipari, Nina, Kollist, Hannes, Holm, Liisa, Palva, E Tapio
Publicado 2013

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

por Pussila, Marjaana, Törönen, Petri, Einarsdottir, Elisabet, Katayama, Shintaro, Krjutškov, Kaarel, Holm, Liisa, Kere, Juha, Peltomäki, Päivi, Mäkinen, Markus J, Linden, Jere, Nyström, Minna
Publicado 2018

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

por Nykyri, Johanna, Niemi, Outi, Koskinen, Patrik, Nokso-Koivisto, Jussi, Pasanen, Miia, Broberg, Martin, Plyusnin, Ilja, Törönen, Petri, Holm, Liisa, Pirhonen, Minna, Palva, E. Tapio
Publicado 2012

Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study

por Mishra, Pashupati P., Hänninen, Ismo, Raitoharju, Emma, Marttila, Saara, Mishra, Binisha H., Mononen, Nina, Kähönen, Mika, Hurme, Mikko, Raitakari, Olli, Törönen, Petri, Holm, Liisa, Lehtimäki, Terho
Publicado 2020

The giant diploid faba genome unlocks variation in a global protein crop

por Jayakodi, Murukarthick, Golicz, Agnieszka A., Kreplak, Jonathan, Fechete, Lavinia I., Angra, Deepti, Bednář, Petr, Bornhofen, Elesandro, Zhang, Hailin, Boussageon, Raphaël, Kaur, Sukhjiwan, Cheung, Kwok, Čížková, Jana, Gundlach, Heidrun, Hallab, Asis, Imbert, Baptiste, Keeble-Gagnère, Gabriel, Koblížková, Andrea, Kobrlová, Lucie, Krejčí, Petra, Mouritzen, Troels W., Neumann, Pavel, Nadzieja, Marcin, Nielsen, Linda Kærgaard, Novák, Petr, Orabi, Jihad, Padmarasu, Sudharsan, Robertson-Shersby-Harvie, Tom, Robledillo, Laura Ávila, Schiemann, Andrea, Tanskanen, Jaakko, Törönen, Petri, Warsame, Ahmed O., Wittenberg, Alexander H. J., Himmelbach, Axel, Aubert, Grégoire, Courty, Pierre-Emmanuel, Doležel, Jaroslav, Holm, Liisa U., Janss, Luc L., Khazaei, Hamid, Macas, Jiří, Mascher, Martin, Smýkal, Petr, Snowdon, Rod J., Stein, Nils, Stoddard, Frederick L., Stougaard, Jens, Tayeh, Nadim, Torres, Ana M., Usadel, Björn, Schubert, Ingo, O’Sullivan, Donal Martin, Schulman, Alan H., Andersen, Stig Uggerhøj
Publicado 2023

A large-scale evaluation of computational protein function prediction

por Radivojac, Predrag, Clark, Wyatt T, Oron, Tal Ronnen, Schnoes, Alexandra M, Wittkop, Tobias, Sokolov, Artem, Graim, Kiley, Funk, Christopher, Verspoor, Karin, Ben-Hur, Asa, Pandey, Gaurav, Yunes, Jeffrey M, Talwalkar, Ameet S, Repo, Susanna, Souza, Michael L, Piovesan, Damiano, Casadio, Rita, Wang, Zheng, Cheng, Jianlin, Fang, Hai, Gough, Julian, Koskinen, Patrik, Törönen, Petri, Nokso-Koivisto, Jussi, Holm, Liisa, Cozzetto, Domenico, Buchan, Daniel W A, Bryson, Kevin, Jones, David T, Limaye, Bhakti, Inamdar, Harshal, Datta, Avik, Manjari, Sunitha K, Joshi, Rajendra, Chitale, Meghana, Kihara, Daisuke, Lisewski, Andreas M, Erdin, Serkan, Venner, Eric, Lichtarge, Olivier, Rentzsch, Robert, Yang, Haixuan, Romero, Alfonso E, Bhat, Prajwal, Paccanaro, Alberto, Hamp, Tobias, Kaßner, Rebecca, Seemayer, Stefan, Vicedo, Esmeralda, Schaefer, Christian, Achten, Dominik, Auer, Florian, Boehm, Ariane, Braun, Tatjana, Hecht, Maximilian, Heron, Mark, Hönigschmid, Peter, Hopf, Thomas A, Kaufmann, Stefanie, Kiening, Michael, Krompass, Denis, Landerer, Cedric, Mahlich, Yannick, Roos, Manfred, Björne, Jari, Salakoski, Tapio, Wong, Andrew, Shatkay, Hagit, Gatzmann, Fanny, Sommer, Ingolf, Wass, Mark N, Sternberg, Michael J E, Škunca, Nives, Supek, Fran, Bošnjak, Matko, Panov, Panče, Džeroski, Sašo, Šmuc, Tomislav, Kourmpetis, Yiannis A I, van Dijk, Aalt D J, Braak, Cajo J F ter, Zhou, Yuanpeng, Gong, Qingtian, Dong, Xinran, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Di Camillo, Barbara, Toppo, Stefano, Lan, Liang, Djuric, Nemanja, Guo, Yuhong, Vucetic, Slobodan, Bairoch, Amos, Linial, Michal, Babbitt, Patricia C, Brenner, Steven E, Orengo, Christine, Rost, Burkhard, Mooney, Sean D, Friedberg, Iddo
Publicado 2013

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

por Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T., Bankapur, Asma R., D’Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S., Kahanda, Indika, Verspoor, Karin M., Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M. E., Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T., Chapman, Samuel, BKC, Dukka, Khan, Ishita K., Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E., Hieta, Reija, Legge, Duncan, Lovering, Ruth C., Magrane, Michele, Melidoni, Anna N., Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L., Lee, David, Lees, Jonathan G., Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E., Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E., Pavlidis, Paul, Feng, Shou, Cejuela, Juan M., Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio C.E., del Pozo, Angela, Fernández, José M., Maietta, Paolo, Valencia, Alfonso, Tress, Michael L., Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W., van Dijk, Aalt D. J., Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C., Vencio, Ricardo Z. N., Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael J. E., Wass, Mark N., Huntley, Rachael P., Martin, Maria J., O’Donovan, Claire, Robinson, Peter N., Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C., Brenner, Steven E., Linial, Michal, Orengo, Christine A., Rost, Burkhard, Greene, Casey S., Mooney, Sean D., Friedberg, Iddo, Radivojac, Predrag
Publicado 2016