Jun'ichi Tsujii

Jun'ichi Tsujii

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Jun'ichi Tsujii

Jun'ichi Tsujii

Publications by authors named "Jun'ichi Tsujii"

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1PubMed Central Citations

Improving clinical named entity recognition in Chinese using the graphical and phonetic feature.

BMC Med Inform Decis Mak 2019 Dec 23;19(Suppl 7):273. Epub 2019 Dec 23.

National Centre of Text Mining, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/s12911-019-0980-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927114PMC
December 2019

Annotation and detection of drug effects in text for pharmacovigilance.

J Cheminform 2018 Aug 13;10(1):37. Epub 2018 Aug 13.

National Centre for Text Mining, School of Computer Science, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.

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http://dx.doi.org/10.1186/s13321-018-0290-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089860PMC
August 2018

Generalising semantic category disambiguation with large lexical resources for fun and profit.

J Biomed Semantics 2014 2;5:26. Epub 2014 Jun 2.

School of Computer Science, University of Manchester, Manchester, UK ; National Centre for Text Mining, University of Manchester, Manchester, UK ; Microsoft Research Asia, Beijing, People's Republic of China.

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http://dx.doi.org/10.1186/2041-1480-5-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107982PMC
August 2014

Proximity-based frameworks for generating embeddings from multi-output data.

IEEE Trans Pattern Anal Mach Intell 2012 Nov;34(11):2216-32

National Centre for Text Mining (NaCTeM), School of Computer Science, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1109/tpami.2012.20DOI Listing
November 2012

Event extraction across multiple levels of biological organization.

Bioinformatics 2012 Sep;28(18):i575-i581

National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436834PMC
September 2012

The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011.

BMC Bioinformatics 2012 Jun 26;13 Suppl 11:S1. Epub 2012 Jun 26.

Database Center for Life Science, Research Organization of Information and Science, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, Japan.

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http://dx.doi.org/10.1186/1471-2105-13-S11-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384256PMC
June 2012

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.

BMC Bioinformatics 2012 Jun 26;13 Suppl 11:S2. Epub 2012 Jun 26.

School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1186/1471-2105-13-S11-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384257PMC
June 2012

Automatic extraction of angiogenesis bioprocess from text.

Bioinformatics 2011 Oct 5;27(19):2730-7. Epub 2011 Aug 5.

National Centre for Text Mining, University of Manchester, Manchester, AstraZeneca, Alderley Park, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179660PMC
October 2011

An analysis of gene/protein associations at PubMed scale.

J Biomed Semantics 2011 Oct 6;2 Suppl 5:S5. Epub 2011 Oct 6.

Department of Computer Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1186/2041-1480-2-S5-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239305PMC
October 2011

Event extraction for DNA methylation.

J Biomed Semantics 2011 Oct 6;2 Suppl 5:S2. Epub 2011 Oct 6.

Department of Computer Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1186/2041-1480-2-S5-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239302PMC
October 2011

Discovering and visualizing indirect associations between biomedical concepts.

Bioinformatics 2011 Jul;27(13):i111-9

School of Information Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btr214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117364PMC
July 2011

AGRA: analysis of gene ranking algorithms.

Bioinformatics 2011 Apr 23;27(8):1185-6. Epub 2011 Feb 23.

Faculty of Health Sciences, University of Maribor, Maribor, Slovenia.

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http://dx.doi.org/10.1093/bioinformatics/btr097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072556PMC
April 2011

Extracting protein interactions from text with the unified AkaneRE event extraction system.

IEEE/ACM Trans Comput Biol Bioinform 2010 Jul-Sep;7(3):442-53

Department of Information Science, University of Tokyo, Tokyo, Japan.

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http://ieeexplore.ieee.org/document/5499452/
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http://dx.doi.org/10.1109/TCBB.2010.46DOI Listing
December 2010

Text mining meets workflow: linking U-Compare with Taverna.

Bioinformatics 2010 Oct 12;26(19):2486-7. Epub 2010 Aug 12.

Department of Computer Science, The University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944208PMC
October 2010

Improving the inter-corpora compatibility for protein annotations.

J Bioinform Comput Biol 2010 Oct;8(5):901-16

Department of Computer Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.

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http://dx.doi.org/10.1142/s0219720010004999DOI Listing
October 2010

A re-evaluation of biomedical named entity-term relations.

J Bioinform Comput Biol 2010 Oct;8(5):917-28

Department of Computer Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1142/s0219720010005014DOI Listing
October 2010

Event extraction for systems biology by text mining the literature.

Trends Biotechnol 2010 Jul 1;28(7):381-90. Epub 2010 Jun 1.

University of Manchester, Manchester M13 9PL, UK.

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https://linkinghub.elsevier.com/retrieve/pii/S01677799100007
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http://dx.doi.org/10.1016/j.tibtech.2010.04.005DOI Listing
July 2010

Complex event extraction at PubMed scale.

Bioinformatics 2010 Jun;26(12):i382-90

Department of Information Technology, University of Turku, Turku, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btq180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881365PMC
June 2010

Building a high-quality sense inventory for improved abbreviation disambiguation.

Bioinformatics 2010 May 25;26(9):1246-53. Epub 2010 Mar 25.

Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859134PMC
May 2010

Disambiguating the species of biomedical named entities using natural language parsers.

Bioinformatics 2010 Mar 6;26(5):661-7. Epub 2010 Jan 6.

National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828111PMC
March 2010

Event extraction with complex event classification using rich features.

J Bioinform Comput Biol 2010 Feb;8(1):131-46

Department of Computer Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan.

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http://dx.doi.org/10.1142/s0219720010004586DOI Listing
February 2010

Protein-protein interaction extraction by leveraging multiple kernels and parsers.

Int J Med Inform 2009 Dec 4;78(12):e39-46. Epub 2009 Jun 4.

Department of Computer Science, the University of Tokyo, Tokyo, Japan.

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http://linkinghub.elsevier.com/retrieve/pii/S138650560900076
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http://dx.doi.org/10.1016/j.ijmedinf.2009.04.010DOI Listing
December 2009

Investigating heterogeneous protein annotations toward cross-corpora utilization.

BMC Bioinformatics 2009 Dec 9;10:403. Epub 2009 Dec 9.

Department of Computer Science, School of Information Science and Technology, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1186/1471-2105-10-403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804683PMC
December 2009

U-Compare: share and compare text mining tools with UIMA.

Bioinformatics 2009 Aug 4;25(15):1997-8. Epub 2009 May 4.

Department of Computer Science, University of Tokyo Hongo 7-3-1, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712335PMC
August 2009

FACTA: a text search engine for finding associated biomedical concepts.

Bioinformatics 2008 Nov 4;24(21):2559-60. Epub 2008 Sep 4.

School of Computer Science, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572701PMC
November 2008

Themes in biomedical natural language processing: BioNLP08.

BMC Bioinformatics 2008 Nov 19;9 Suppl 11:S1. Epub 2008 Nov 19.

US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1186/1471-2105-9-S11-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586759PMC
November 2008

Accelerating the annotation of sparse named entities by dynamic sentence selection.

BMC Bioinformatics 2008 Nov 19;9 Suppl 11:S8. Epub 2008 Nov 19.

School of Computer Science, The University of Manchester, MIB, 131 Princess Street, Manchester M17DN, UK.

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http://dx.doi.org/10.1186/1471-2105-9-S11-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586757PMC
November 2008

New challenges for text mining: mapping between text and manually curated pathways.

BMC Bioinformatics 2008 Apr 11;9 Suppl 3:S5. Epub 2008 Apr 11.

Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.

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http://dx.doi.org/10.1186/1471-2105-9-S3-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2352872PMC
April 2008

Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.

Pac Symp Biocomput 2008 :616-27

Department of Computer Science, University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Tokyo.

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March 2008

Corpus annotation for mining biomedical events from literature.

BMC Bioinformatics 2008 Jan 8;9:10. Epub 2008 Jan 8.

Department of Computer Science, School of Information Science and Technology, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1186/1471-2105-9-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267702PMC
January 2008

Learning string similarity measures for gene/protein name dictionary look-up using logistic regression.

Bioinformatics 2007 Oct 12;23(20):2768-74. Epub 2007 Aug 12.

School of Computer Science, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm393DOI Listing
October 2007

Extraction of gene-disease relations from Medline using domain dictionaries and machine learning.

Pac Symp Biocomput 2006 :4-15

Tsujii Laboratory, Room 615, 7th Building of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.

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January 2007

Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts.

BMC Bioinformatics 2006 Nov 24;7 Suppl 3:S4. Epub 2006 Nov 24.

Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1186/1471-2105-7-S3-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764448PMC
November 2006

Improving the performance of dictionary-based approaches in protein name recognition.

J Biomed Inform 2004 Dec;37(6):461-70

CREST, Japan Science and Technology (JST) Agency, Honcho 4-1-8, Kawaguchi-shi, Saitama 332-0012, Japan.

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http://dx.doi.org/10.1016/j.jbi.2004.08.003DOI Listing
December 2004