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2011

Articles

  • Arighi, Cecilia, Phoebe Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michele Gwinn Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman and Cathy H Wu. BioCreative III Interactive Task: an Overview.. BMC Bioinformatics, special issue on BioCreative III. 2011. (accepted for publication).


  • Rinaldi, Fabio, Kaarel Kaljurand and Rune Sætre. Terminological resources for Text Mining over Biomedical Scientific Literature. Journal of Artificial Intelligence in Medicine. 2011. (accepted for publication in June).


  • Kocbek, Simon, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou and Jun'ichi Tsujii. AGRA: Analysis of Gene Ranking Algorithms. In Jonathan Wren et al. (Eds.), . Oxford Bioinformatics. Journal Department, Great Clarendon Street, OXFORD, OX2 6DP, UK, Oxford University Press, March 2011.


Conferences

  • Kocbek, Simon, Gregor Stiglic, Igor Pernek, Peter Kokol, Jun'ichi Tsujii, Rune Sætre, Jin-Dong Kim, Yoshimasa Tsuruoka and Sophia Ananiadou. Analysis of Gene Ranking Algorithms with Extraction of Relevant Biomedical Concepts from Pubmed Publications. In Jerlin Camilus Merlin and Sahar Al Seesi (Eds.), IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS). Orlando, Florida, IEEE, Feb 3‐5 2011.


2010

Articles

  • Wang Yue, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii.. Improving the Inter-corpora Compatibility for Protein Annotations. Journal of Bioinformatics and Computational Biology (JBCB). 8(5). October 2010. DOI: 10.1142/S0219720010004999 .


  • Ohta, Tomoko, Matsuzaki, Takuya, Okazaki, Naoaki, Miwa, Makoto, Saetre, Rune, Pyysalo, Sampo and Tsujii, Jun'ichi. Medie and Info-pubmed: 2010 update. BMC Bioinformatics. 11(Suppl 5). pp. P7, 2010. DOI:10.1186/1471-2105-11-S5-P7.


  • Riedel, Sebastian, Rune Sætre, Hong-Woo Chun, Toshihisa Takagi and Jun'ichi Tsujii. Bio-Molecular Event Extraction with Markov Logic. In Jin-Dong Kim (Eds.), . Computational Intelligence. Special Issue. Edmonton, Alberta, Canada T6G 2E8, 2010. (to appear).


  • Miwa, Makoto, Rune Sætre, Jin-Dong Kim, and Jun'ichi Tsujii. Event Extraction with Complex Event Classification Using Rich Features. Journal of Bioinformatics and Computational Biology (JBCB) . 8(1). pp. 131--146, February 2010.


  • Sætre, Rune, Kazuhiro Yoshida, Makoto Miwa, Takuya Matsuzaki, Yoshinobu Kano and Junichi Tsujii. Extracting Protein-Interactions from Text with the Unified AkaneRE Event Extraction System. Transactions on Computational Biology and Bioinformatics (TCBB), BioCreative II.5 Special Issue. 7. pp. 46pp, IEEE/ACM, 2010.


Conferences

  • Miwa, Makoto, Yusuke Miyao, Rune Sætre and Jun'ichi Tsujii. Entity-Focused Sentence Simplification for Relation Extraction. In the 23rd International Conference on Computational Linguistics (COLING 2010). pp. 788-796, August 2010.


  • Okazaki, Naoaki, Han-Cheol Cho, Rune Sætre, Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii. The gene normalization and intractive systems of the University of Tokyo in the BioCreative III challenge. In the Proceedings of BioCreative III. pp. 125-130, 2010.


2009

Articles

  • Wang, Yue, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo and Jun'ichi Tsujii. Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinformatics. 10(403). Dec. 2009. ISSN: 1471-2105.


  • Miyao, Yusuke, Kenji Sagae, Rune Sætre, Takuya Matsuzaki and Jun'ichi Tsujii. Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction. Bioinformatics. 25(3). pp. 394-400, Oxford University Press, February 2009.


  • Miwa, Makoto, Rune Sætre, Yusuke Miyao, and Jun'ichi Tsujii. Protein-Protein Interaction Extraction by Leveraging Multiple Kernels and Parsers. International Journal of Medical Informatics. 78(12). pp. e39--e46, April 2009. Mining of Clinical and Biomedical Text and Data Special Issue.


Conferences

  • Matsuoka, Yukiko, Samik Ghosh, Norihiko Kikuchi, Rune Sætre, Brian Kemper, Naoaki Okazaki, Sophia Ananiadou, Jun'ichi Tsujii and Hiroaki Kitano. Community Platform for Pathway Model Building. In the 10th International Conference on Systems Biology. pp. 139-140, Stanford University, September 2009. Poster 3.073.


  • Miwa, Makoto, Rune Sætre, Jin-Dong Kim, and Jun'ichi Tsujii. Event Extraction with Complex Event Classification using Rich Features. In the 3rd International Symposium on Languages in Biology and Medicine (LBM 2009). pp. 11--19, November 2009. (Honorable Mention Award).


  • Sætre, Rune, Kazuhiro Yoshida, Makoto Miwa, Takuya Matsuzaki, Yoshinobu Kano and Jun'ichi Tsujii. AkaneRE Relation Extraction: Protein Interaction and Normalization in the BioCreAtIvE II.5 Challenge. In the BioCreative II.5 Workshop 2009 special session | Digital Annotations. Madrid, Spain, pp. 33, CNIO, October 2009.


  • Sætre, Rune, Makoto Miwa, Kazuhiro Yoshida and Jun'ichi Tsujii. From Protein-Protein Interaction to Molecular Event Extraction. In the Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop. pp. 103--106, June 2009.
    [PDF]

  • Miwa, Makoto, Rune Sætre, Yusuke Miyao, and Jun'ichi Tsujii. A Rich Feature Vector for Protein-Protein Interaction Extraction from Multiple Corpora. In the Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing. Singapore, pp. 121--130, Association for Computational Linguistics, August 2009.


  • Wang, Yue, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii. Demystifying protein annotations: toward increasing the compatibility of different corpora. In the Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM 2009). Jeju Island, South Korea, pp. 103-108, November 2009.


2008

Articles

  • Leitner, Florian, Martin Krallinger, Carlos Rodriguez-Penagos, Joerg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hsi-Chuan Hung, William W. Lau, Calvin A. Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A. Baumgartner, Jr., Lawrence Hunter, Barry Haddow, Michael Matthew, Xinglong Wang, Patrick Ruch, Frederic Ehrler, Arzucan Ozgur, Gunes Erkan, Dragomir R. Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander and Alfonso Valencia. Introducing Meta-Services for Biomedical Information Extraction. Genome Biology. 9(S2). pp. S6, 2008. Special Issue on the BioCreative Challenge Evaluation.


Conferences

  • Sætre, Rune, Brian Kemper, Kanae Oda, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano, Sophia Ananiadou and Jun'ichi Tsujii. PathText/payao development: Text/pathway annotations. In the 9th International Conference on Systems Biology (ICSB), Abstract book. Gothenburg, Sweden, pp. 191-192, 22-28 August 2008. DS3-3-52.
    [PPT]

  • Sætre, Rune, Kenji Sagae and Jun'ichi Tsujii. Syntactic features for protein-protein interaction extraction. In the Christopher J.O. Baker and Su Jian (Eds.), Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007). ISSN 1613-0073319. Singapore, pp. 6.1-6.14, CEUR Workshop Proceedings (CEUR-WS.org), January 2008.


  • Sætre, Rune, B. Kemper, K. Oda, N. Okazaki, Y. Matsuoka, N. Kikuchi, H. Kitano, Y. Tsuruoka, S. Ananiadou and J. Tsujii. PathText: Text Mining Tools Integrated with Biological Pathway. In the Genomes to Systems Conference 2008 Handbook. Manchester, UK, pp. 65, The Consortium for Post-Genome Science, 17-19 March 2008.
    [PDF]

  • Matsuoka, Yukiko, Norihiro Kikuchi, Rune Sætre, Brian Kemper, Naoaki Okazaki, Haruka Sugimura, Akemi Hayama, Sophia Ananiadou, Jun'ichi Tsujii and Hiroaki Kitano. SB-012 'PAYAO': Web community tagging system to SBML models. In the Genomes to Systems Conference 2008 Handbook. Manchester, UK, pp. 91, The Consortium for Post-Genome Science, 17-19 March 2008.


  • Miyao, Yusuke, Rune Sætre, Kenji Sagae, Takuya Matsuzaki and Jun'ichi Tsujii. Task-Oriented Evaluation of Syntactic Parsers and Their Representations. In the Proceedings of ACL-08:HLT. Columbus, OH, pp. 46-54, June 2008.


  • Kano, Yoshinobu, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro Matsubayashi, Sophia Ananiadou and Jun'ichi Tsujii. Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example. In the Proceedings of The Pacific Symposium on Biocomputing (PSB). (13). Hawaii, USA, pp. 616-627, January 2008.


  • Sætre, Rune, B. Kemper, K. Oda, N. Okazaki, Y. Matsuoka, N. Kikuchi, H. Kitano, Y. Tsuruoka, S. Ananiadou and J. Tsujii. Connecting Text Mining and Pathways using the PathText Resource. In the Proceedings of the 2008 Language Resources and Evaluation Conference (LREC 2008). Marrakech, Morocco, May 2008.
    [PDF]

  • Kano, Yoshinobu, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Keiichiro Fukamachi, Yusuke Miyao, Yoshimasa Tsuruoka, Sophiha Ananiadou and Jun'ichi Tsujii. Towards Data And Goal Oriented Analysis: Tool Inter-Operability And Combinatorial Comparison. In the Proceedings of the 3rd International Joint Conference on Natural Language Processing. Hyderabad, India, pp. 859-864, January 2008.


  • Wang, Yue, Kazuhiro Yoshida, Jin-Dong Kim, Rune Sætre and Jun'ichi Tsujii. Raising the Compatibility of Heterogeneous Annotations: A Case Study on Protein Mention Recognition. In the Proceedings of the BioNLP workshop of the 46th Annual Meeting of the Association for Computational Linguistics (ACL 2008). Columbus, Ohio, pp. 118-–119, June 2008. BioNLP 2008: Current Trends in Biomedical Natural Language.


  • Kano, Yoshinobu, Ngan Nguyen, Rune Sætre, Keiichiro Fukamachi, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Sophia Ananiadou and Jun'ichi Tsujii. Sharable type system design for tool inter-operability and combinatorial comparison. In the Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL). Hong Kong, pp. 122-129, January 2008.


  • Miwa, Makoto, Rune Sætre, Yusuke Miyao, Tomoko Ohta and Jun'ichi Tsujii. Combining Multiple Layers of Syntactic Information for Protein-Protein Interaction Extraction. In the Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008). Turku, Finland, pp. 101--108, September 2008.


  • Wang, Yue, Jin-Dong Kim, Rune Sætre and Jun'ichi Tsujii. Exploring the Compatibility of Heterogeneous Protein Annotations Toward Corpus Integration. In the Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008). Turku, Finland, pp. 117--124, September 2008.


  • Pyysalo, Sampo, Rune Sætre, Jun'ichi Tsujii and Tapio Salakoski. Why Biomedical Relation Extraction Results are Incomparable and What to do about it. In Tapio Salakoski, Dietrich Rebholz-Schuhmann and Sampo Pyysalo (Eds.), Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland. pp. 149--152, Turku Centre for Computer Science (TUCS), 2008.


  • Sagae, Kenji, Yusuke Miyao, Rune Sætre and Jun'ichi Tsujii. Evaluating the Effects of Treebank Size in a Practical Application for Parsing. In the Software Engineering, Testing, and Quality Assurance for Natural Language Processing. pp. 14--20, June 20 2008.


2007

Articles

  • Sætre, Rune, Martin T. Ranang, Tonje S. Steigedal, Kamilla Stunes, Kristine Misund, Liv Thommesen and Astrid Lægreid. WebProt: Online Mining and Annotation of Biomedical Literature using Google. In T.D. Pham et al. (Eds.), Advanced Computational Methods for Biocomputing and Bioimaging. 400 Oser Ave., Hauppauge NY 11788-3619, pp. 189-206, Nova Science Publishers, Inc., May 2007.
    [PDF]

Conferences

  • Chen, Yan Hua, Heri Ramampiaro, Astrid Lægreid and Rune Sætre. ProtIR prototype: abstract relevance for Protein-Protein Interaction in BioCreAtIvE2 Challenge, PPI-IAS subtask. In the Proceedings of BioCreAtIvE II: Critical Assessment of Information Extraction for Biology. Madrid, Spain, pp. 179-182, April 2007.
    [PDF]

  • Sætre, Rune, Kazuhiro Yoshida, Akane Yakushiji, Yusuke Miyao, Yuichiro Matsubayashi and Tomoko Ohta. AKANE System: Protein-Protein Interaction Pairs in BioCreAtIvE2 Challenge, PPI-IPS subtask. In the Proceedings of the Second BioCreative Challenge Evaluation Workshop. pp. 209--212, April 2007. CNIO.
    [PDF][PPT]

2006

Articles

  • Sætre, Rune, Harald Søvik, Tore Amble and Yoshimasa Tsuruoka. GeneTUC, GENIA and Google: Natural Language Understanding in Molecular Biology Literature. Dr. Corrado Priami (Eds.), . Transactions on Computational Systems Biology. Lecture Notes in BIology (LNBI)4070(V). pp. 68-82, Springer-Verlag, August 2006.
    [PDF]

PhD Theses

  • Sætre, Rune. GeneTUC: Natural Language Understanding in Medical Text. ISSN 1503-8181(ISBN 82-471-7865-6). NO-7491 Trondheim, Norway, pp. 1-155, June 2006.


2005

Conferences

  • Tveit, Amund, Rune Sætre, Astrid Lægreid and Tonje Strømmen Steigedal. ProtChew: Automatic Extraction of Protein Names from Biomedical Literature . In the BDME - International Workshop on Biomedical Data Engineering. Tokyo, Japan, pp. 1161-1161, IEEE Press (Electronic Publication), April 2005.
    [PDF]

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