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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (8):

• Predrag Radivojac, Wyatt T. Clark, Tal Ronnen Oron, Alexandra M. Schnoes, Tobias Wittkop Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M. Yunes, Ameet S. Talwalkar, Susanna Repo, Michael L. Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang, Julian Gough, Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm, Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones, Bhakt Limave, Harshal Inamdar, Avik Datta, Sunitha K. Manjari, Rajendra Joshi, Meghana Chitale, Daisuke Kihara, Andreas M. Lisewski, Serkan Erdin, Eric Venner, Olivier Lichtarge, Robert Rentzsch, Haixuan Yang, Alfonso E. Romero, Prajwal Bhat, Alberto Paccanaro, Tobias Hamp, Rebecca Kaßner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Jari Björne, Tapio Salakoski, Andrew Wong, Hagit Shatkay, Fanny Gatzmann, Ingolf Sommer, Mark N. Wass, Michael J. E. Sternberg, Nives Škunca, Fran Supek, Matko Bošnjak, Panče Panov, Sašo Džeroski, Tomislav Šmuc, Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Cajo J. F. ter Braak, Yuanpeng Zhou, Qingtian Gong, Xinran Dong, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Barbara Di Camillo, Stefano Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic Vucetic, Amos Bairoch, Michal Linial, Patricia C. Babbitt, Steven E. Brenner, Christine Orengo, Burkhard Rost, Sean D. Mooney, Iddo Friedberg, A Large-Scale Evaluation of Computational Protein Function Prediction. Nature methods 10, 221–227, 2013.
• Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer, Semantically linking molecular entities in literature through entity relationships. BMC bioinformatics 13, S6, 2012.
• Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets. Computational Intelligence 27, 541–557, 2011.
• Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, Kevin Cohen, Katrin Verspoor, Christophe Roeder, Lawrence Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, U-Compare Bio-Event Meta-Service: Compatible BioNLP Event Extraction Services. BMC Bioinformatics 12(1), 481, 2011.
• Jari Björne, Finter Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski, Complex Event Extraction at PubMed Scale . Bioinformatics (ISMB'2010 proceedings volume) 26, 382-390, 2010.
• Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski, All-paths Graph Kernel for Protein-Protein Interaction Extraction With Evaluation of Cross-Corpus Learning. BMC Bioinformatics 9 (Suppl 11), 2008.
• Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski, Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 9 (supplement 3)(6), 2008.
• Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, BioInfer: A Corpus for Information Extraction in the Biomedical Domain. BMC Bioinformatics 8(50), 2007.

Articles in proceedings (11):

• Jari Björne, Suwisa Kaewphan, Tapio Salakoski, UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge. In: Suresh Manandhar, Deniz Yuret (Eds.), Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013), 2, 651–659, Association for Computational Linguistics (ACL), 2013.
• Jari Björne, Sofie van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves van de Peer, Sophia Ananiadou, Tapio Salakoski, PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. In: Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian (Eds.), Proceedings of the 2012 Workshop on Biomedical Natural Language Processing (BioNLP 2012), 82–90, Association for Computational Linguistics, 2012.
• Jari Björne, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Drug-Drug Interaction Extraction with RLS and SVM Classifiers. In: Isabel Segura-Bedmar, Paloma Martinez, Daniel Sanchez-Cisneros (Eds.), Proceedings of the First Challenge task on Drug- Drug Interaction Extraction (DDIExtraction 2011), Ceur Workshop Proceedings, 35–42, CEUR Workshop Proceedings, 2011.
• Jari Björne, Tapio Salakoski, A Machine Learning Model and Evaluation of Text Mining for Protein Function Prediction. In: Iddo Friedberg, Michal Linial, Predrag Radivojac (Eds.), Automated Function Prediction Featuring a Critical Assessment of Function Annotations (AFP/CAFA) 2011, 7-8, Automated Function Prediction Featuring a Critical Assessment of Function Annotations (AFP/CAFA) 2011 - An ISMB Special Interest Group, 2011.
• Jari Björne, Tapio Salakoski, Generalizing Biomedical Event Extraction. In: Proceedings of the BioNLP Shared Task 2011 Workshop, 183--191, Association for Computational Linguistics, 2011.
• Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski, Scaling up Biomedical Event Extraction to the Entire PubMed. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp. 28-36, 2010.
• Juho Heimonen, Jari Björne, Tapio Salakoski, Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, 108--116, Association for Computational Linguistics, 2010.
• Jari Björne, Filip Ginter, Juho Heimonen, Sampo Pyysalo, Tapio Salakoski, Learning to Extract Biological Event and Relation Graphs. In: Proceedings of the 17th Nordic Conference of Computational Linguistics NODALIDA 2009, NEALT Proceedings Series Vol. 4 (2009), 18-25, Northern European Association for Language Technology (NEALT), 2009.
• Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Extracting Complex Biological Events with Rich Graph-Based Feature Sets. In: Jun'ichi Tsujii (Ed.), Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 10–18, Association for Computational Linguistics (ACL), 2009.
• Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski, A Graph Kernel for Protein-Protein Interaction Extraction. In: Sophia Ananiadou K. Bretonnel Cohen John Pestian Jun'ichi Tsujii Dina Demner-Fushman, Bonnie Webber (Eds.), Proceedings of ACL-08: HLT BioNLP 2008 Workshop: Current Trends in Biomedical Natural Language Processing, 1–9, The Association for Computational Linguistics, 2008.
• Jari Björne, Sampo Pyysalo, Filip Ginter, Tapio Salakoski, How Complex are Complex Protein-protein Interactions?. In: Proceedings of SMBM 2008, 2008.

Ph.D. thesis (1):

• Jari Björne, Biomedical Event Extraction with Machine Learning. TUCS Dissertations 178. 2014.

Technical reports (1):

• Filip Ginter, Sampo Pyysalo, Jari Björne, Juho Heimonen, Tapio Salakoski, BioInfer Relationship Annotation Manual. TUCS Technical Reports 806, Turku Centre for Computer Science, 2007.