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Jun'ichi Tsujii

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Tingting Mu; Jun'ichi Tsujii; John Yannis Goulermas; Sophia Ananiadou
Proximity-based frameworks for generating embeddings from multi-output data.
Sampo Pyysalo; Jun'ichi Tsujii; Han-Cheol Cho; Makoto Miwa; Tomoko Ohta; Sophia Ananiadou
Event extraction across multiple levels of biological organization.
Sampo Pyysalo; Rafal Rak; Bruno Sobral; Dan Sullivan; Jun'ichi Tsujii; Chunxia Wang; Chunhong Mao; Tomoko Ohta; Sophia Ananiadou
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.

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All Publications

2012: Tingting Mu; Jun'ichi Tsujii; John Yannis Goulermas; Sophia Ananiadou
Proximity-based frameworks for generating embeddings from multi-output data.
IEEE transactions on pattern analysis and machine intelligence 2012;34(11):2216-32.
2012: Sampo Pyysalo; Jun'ichi Tsujii; Han-Cheol Cho; Makoto Miwa; Tomoko Ohta; Sophia Ananiadou
Event extraction across multiple levels of biological organization.
Bioinformatics (Oxford, England) 2012;28(18):i575-i581.
2012: Sampo Pyysalo; Rafal Rak; Bruno Sobral; Dan Sullivan; Jun'ichi Tsujii; Chunxia Wang; Chunhong Mao; Tomoko Ohta; Sophia Ananiadou
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.
BMC bioinformatics 2012;13 Suppl 11():S2.
2011: Xinglong Wang; Ian Barrett; Ian Dix; Tim French; Iain McKendrick; Jun'ichi Tsujii; Sophia Ananiadou
Automatic extraction of angiogenesis bioprocess from text.
Bioinformatics (Oxford, England) 2011;27(19):2730-7.
2011: Yoshimasa Tsuruoka; Kaisei Hamamoto; Makoto Miwa; Jun'ichi Tsujii; Sophia Ananiadou
Discovering and visualizing indirect associations between biomedical concepts.
Bioinformatics (Oxford, England) 2011;27(13):i111-9.
2011: Simon Kocbek; Rune Sætre; Gregor Stiglic; Jin-Dong Kim; Igor Pernek; Yoshimasa Tsuruoka; Peter Kokol; Sophia Ananiadou; Jun'ichi Tsujii
AGRA: analysis of gene ranking algorithms.
Bioinformatics (Oxford, England) 2011;27(8):1185-6.
2011: Yoshinobu Kano; Halil Kilicoglu; Jin-Dong Kim; Makoto Miwa; Mariana Neves; Tomoko Ohta; Alberto Pascual-Montano; Sampo Pyysalo; Dragomir R Radev; Sebastian Riedel; Christophe Roeder; Rune Sætre; Tapio Salakoski; Sophia Ananiadou; Sabine Bergler; Jari Björne; Ekaterina Buyko; Hong-Woo Chun; K Bretonnel Cohen; Filip Ginter; Udo Hahn; Lawrence Hunter; Yves Van de Peer; Sofie Van Landeghem; Thomas Van Parys; Karin Verspoor; Arzucan Özgür; Jun'ichi Tsujii
U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC bioinformatics 2011;12():481.
2011: BalaKrishna Kolluru; Lezan Hawizy; Peter Murray-Rust; Jun'ichi Tsujii; Sophia Ananiadou
Using workflows to explore and optimise named entity recognition for chemistry.
PloS one 2011;6(5):e20181.
2011: Sophia Ananiadou; Dan Sullivan; William Black; Gina-Anne Levow; Joseph Gillespie; Chunhong Mao; Sampo Pyysalo; BalaKrishna Kolluru; Jun'ichi Tsujii; Bruno Sobral
Named entity recognition for bacterial Type IV secretion systems.
PloS one 2011;6(3):e14780.
2010: Tomoko Ohta; Sampo Pyysalo; Jin-Dong Kim; Jun'ichi Tsujii
A re-evaluation of biomedical named entity-term relations.
Journal of bioinformatics and computational biology 2010;8(5):917-28.
2010: Yue Wang; Jin-Dong Kim; Rune Saetre; Sampo Pyysalo; Tomoko Ohta; Jun'ichi Tsujii
Improving the inter-corpora compatibility for protein annotations.
Journal of bioinformatics and computational biology 2010;8(5):901-16.
2010: Yoshinobu Kano; Paul Dobson; Mio Nakanishi; Jun'ichi Tsujii; Sophia Ananiadou
Text mining meets workflow: linking U-Compare with Taverna.
Bioinformatics (Oxford, England) 2010;26(19):2486-7.
2010: Rune Saetre; Kazuhiro Yoshida; Makoto Miwa; Takuya Matsuzaki; Yoshinobu Kano; Jun'ichi Tsujii
Extracting protein interactions from text with the unified AkaneRE event extraction system.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2010;7(3):442-53.
2010: Sophia Ananiadou; Sampo Pyysalo; Jun'ichi Tsujii; Douglas B Kell
Event extraction for systems biology by text mining the literature.
Trends in biotechnology 2010;28(7):381-90.
2010: Jari Björne; Filip Ginter; Sampo Pyysalo; Jun'ichi Tsujii; Tapio Salakoski
Complex event extraction at PubMed scale.
Bioinformatics (Oxford, England) 2010;26(12):i382-90.
2010: Brian Kemper; Takuya Matsuzaki; Yukiko Matsuoka; Yoshimasa Tsuruoka; Hiroaki Kitano; Sophia Ananiadou; Jun'ichi Tsujii
PathText: a text mining integrator for biological pathway visualizations.
Bioinformatics (Oxford, England) 2010;26(12):i374-81.
2010: Naoaki Okazaki; Sophia Ananiadou; Jun'ichi Tsujii
Building a high-quality sense inventory for improved abbreviation disambiguation.
Bioinformatics (Oxford, England) 2010;26(9):1246-53.
2010: Xinglong Wang; Jun'ichi Tsujii; Sophia Ananiadou
Disambiguating the species of biomedical named entities using natural language parsers.
Bioinformatics (Oxford, England) 2010;26(5):661-7.
2010: Makoto Miwa; Rune Saetre; Jin-Dong Kim; Jun'ichi Tsujii
Event extraction with complex event classification using rich features.
Journal of bioinformatics and computational biology 2010;8(1):131-46.
2009: Makoto Miwa; Rune Saetre; Yusuke Miyao; Jun'ichi Tsujii
Protein-protein interaction extraction by leveraging multiple kernels and parsers.
International journal of medical informatics 2009;78(12):e39-46.
2009: Yoshinobu Kano; William A Baumgartner; Luke McCrohon; Sophia Ananiadou; K Bretonnel Cohen; Lawrence Hunter; Jun'ichi Tsujii
U-Compare: share and compare text mining tools with UIMA.
Bioinformatics (Oxford, England) 2009;25(15):1997-8.
2009: Yusuke Miyao; Kenji Sagae; Rune Saetre; Takuya Matsuzaki; Jun'ichi Tsujii
Evaluating contributions of natural language parsers to protein-protein interaction extraction.
Bioinformatics (Oxford, England) 2009;25(3):394-400.
2009: Yue Wang; Jin-Dong Kim; Rune Saetre; Sampo Pyysalo; Jun'ichi Tsujii
Investigating heterogeneous protein annotations toward cross-corpora utilization.
BMC bioinformatics 2009;10():403.
2008: Yoshimasa Tsuruoka; Jun'ichi Tsujii; Sophia Ananiadou
FACTA: a text search engine for finding associated biomedical concepts.
Bioinformatics (Oxford, England) 2008;24(21):2559-60.
2008: Yoshimasa Tsuruoka; Jun'ichi Tsujii; Sophia Ananiadou
Accelerating the annotation of sparse named entities by dynamic sentence selection.
BMC bioinformatics 2008;9 Suppl 11():S8.
2008: Kanae Oda; Jin-Dong Kim; Tomoko Ohta; Daisuke Okanohara; Takuya Matsuzaki; Yuka Tateisi; Jun'ichi Tsujii
New challenges for text mining: mapping between text and manually curated pathways.
BMC bioinformatics 2008;9 Suppl 3():S5.
2008: Yoshinobu Kano; Ngan Nguyen; Rune Saetre; Kazuhiro Yoshida; Yusuke Miyao; Yoshimasa Tsuruoka; Yuichiro Matsubayashi; Sophia Ananiadou; Jun'ichi Tsujii
Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008;():616-27.
2008: Jin-Dong Kim; Tomoko Ohta; Jun'ichi Tsujii
Corpus annotation for mining biomedical events from literature.
BMC bioinformatics 2008;9():10.
2007: Yoshimasa Tsuruoka; John McNaught; Jun'ichi Tsujii; Sophia Ananiadou
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.
Bioinformatics (Oxford, England) 2007;23(20):2768-74.
2006: Sophia Ananiadou; Douglas B Kell; Jun'ichi Tsujii
Text mining and its potential applications in systems biology.
Trends in biotechnology 2006;24(12):571-9.
2006: Hong-Woo Chun; Yoshimasa Tsuruoka; Jin-Dong Kim; Rie Shiba; Naoki Nagata; Teruyoshi Hishiki; Jun'ichi Tsujii
Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts.
BMC bioinformatics 2006;7 Suppl 3():S4.
2006: Hong-Woo Chun; Yoshimasa Tsuruoka; Jin-Dong Kim; Rie Shiba; Naoki Nagata; Teruyoshi Hishiki; Jun'ichi Tsujii
Extraction of gene-disease relations from Medline using domain dictionaries and machine learning.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():4-15.
2005: Irena Spasic; Sophia Ananiadou; Jun'ichi Tsujii
MaSTerClass: a case-based reasoning system for the classification of biomedical terms.
Bioinformatics (Oxford, England) 2005;21(11):2748-58.
2004: Yoshimasa Tsuruoka; Jun'ichi Tsujii
Improving the performance of dictionary-based approaches in protein name recognition.
Journal of biomedical informatics 2004;37(6):461-70.
2003: Jin-Dong Kim; T Ohta; Y Tateisi; Jun'ichi Tsujii
GENIA corpus--semantically annotated corpus for bio-textmining.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i180-2.
2002: Goran Nenadić; Hideki Mima; Irena Spasić; Sophia Ananiadou; Jun'ichi Tsujii
Terminology-driven literature mining and knowledge acquisition in biomedicine.
International journal of medical informatics 2002;67(1-3):33-48.
2001: A Yakushiji; Y Tateisi; Y Miyao; Jun'ichi Tsujii
Event extraction from biomedical papers using a full parser.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():408-19.