Publication list - NaCTeM Publications

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Stenetorp, P., Pyysalo, S. and Tsujii, J., SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation, in: Proceedings of the BioNLP 2011 Workshop, pages 136-145, Association for Computational Linguistics, 2011

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Wu, X., Matsuzaki, T. and Tsujii, J., Effective Use of Function Words for Rule Generalization in Forest-Based Translation, in: Proceedings of ACL-HLT 2011, pages 22-31, 2011

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Hatori, J., Murakami, A. and Tsujii, J., Multi-Topical Discussion Summarization using Structured Lexical Chains and Cue Words, in: Proceedings of CICLing 2011, Lecture Notes in Computer Science, pages 313-327, Springer, 2011

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Ananiadou, S., Thompson, P., Kano, Y., McNaught, J., Attwood, T. K., Day, P. J. R., Keane, J., Jackson, D. and Pettifer, S., Towards Interoperability of European Language Resources (2011), in: Ariadne, 67

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Zervanou, K., Korkontzelos, I., van den Bosch, A. and Ananiadou, S., Enrichment and Structuring of Archival Description Metadata, in: Proceedings of the 5th ACL Workshop on Language Technology for Cultural Heritage, Social Sciences, and Humanities, pages 44-53, 2011

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Batista-Navarro, R. and Ananiadou, S., Building a coreference-annotated corpus from the domain of biochemistry, in: Proceedings of BioNLP 2011, pages 83-91, 2011

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Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R., Nawaz, R. and Ananiadou, S., Detecting Experimental Techniques and Selecting Relevant Documents for Protein-Protein Interactions from Biomedical Literature (2011), in: BMC Bioinformatics, 12:Suppl 8(S11)

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Tsuruoka, Y., Miwa, M., Hamamoto, K., Tsujii, J. and Ananiadou, S., Discovering and visualizing indirect associations between biomedical concepts (2011), in: Bioinformatics, 27:13(i111-i119)

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Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J. and Ananiadou, S., Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry (2011), in: PLoS ONE, 6:5(e20181)

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Thomas, J., McNaught, J. and Ananiadou, S., Applications of text mining within systematic reviews (2011), in: Research Synthesis Methods, 2:1(1-14)

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Ananiadou, S., Sullivan, D., Black, W.J., Levow, G., Gillespie, J., Mao, C., Pyysalo, S., Kolluru, B., Tsujii, J. and Sobral, B., Named Entity Recognition for Bacterial Type IV Secretion Systems (2011), in: PLoS ONE, 6:3(e14780)

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Ohta, T., Matsuzaki, T., Okazaki, N., Miwa, M., SÃ¦tre, R., Pyysalo, S. and Tsujii, J., Medie and Info-pubmed: 2010 update (2010), in: BMC Bioinformatics, 11:Suppl 5(P7)

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Kocbek, S., SÃ¦tre, R., Stiglic, G., Kim, J.-D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., AGRA: Analysis of Gene Ranking Algorithms (2011), in: Bioinformatics, 27:8(1185-1186)

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Kolluru, B., Nakjang, S., Rupp, C. J., Hirt, R. P, Wipat, A. and Ananiadou, S., Automatic extraction of microorganisms and their habitats from free text using text-mining workflows, in: Proceedings of the International Symposium on Integrative Bioinformatics, 2011, 2011

Kano, Y., Nguyen, N. T. H., SÃ¦tre, R., Fukamachi, K., Yoshida, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., Sharable type system design for tool inter-operability and combinatorial comparison, in: Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL), pages 122--129, 2008

Soldatova, L. N., Kolluru, B., King, R. D., Qi, D. and Ananiadou, S., An ontology-based disambiguation of terms, in: Proceedings of the Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing, 2011

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Batista-Navarro, R. and Ananiadou, S., Discovering Potential Drugs by Extracting Biological Activities of Natural Products, in: Proceedings of the Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing, 2011

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Kocbek, S., SÃ¦tre, R., Stiglic, G., Kim, J.-D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from Pubmed publications, in: Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011

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Kano, Y., Miwa, M., Cohen, K. B., Hunter, L., Ananiadou, S. and Tsujii, J., U-Compare: a modular NLP workflow construction and evaluation system (2011), in: IBM Journal of Research and Development, 55:3(11:1 - 11:10)

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McEntyre, J. R., Ananiadou, S., Andrews, S., Black, W.J., Boulderstone, R., Buttery, P., Chaplin, D., Chevuru, S., Cobley, N., Coleman, L., Davey, P., Gupta, B., Haji-Gholam, L., Hawkins, C., Horne, A., Hubbard, S. J., Kim, J. -H., Lewin, I., Lyte, V., MacIntyre, R., Mansoor, S., Mason, L., McNaught, J., Newbold, E., Nobata, C., Ong, E., Pillai, S., Rebholz-Schuhmann, D., Rosie, H., Rowbotham, R., Rupp, C. J., Stoehr, P. and Vaughan, P., UKPMC: a full text article resource for the life sciences (2010), in: Nucleic Acids Research, 39:Suppl. 1(D58-D65)

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Ananiadou, S., Thompson, P. and Nawaz, R., Improving Search Through Event-based Biomedical Text Mining, in: Proceedings of the 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop, 2010

Nobata, C., Dobson, P., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B. and Ananiadou, S., Mining Metabolites: Extracting the Yeast Metabolome from the Literature (2011), in: Metabolomics, 7:1(94-101)

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Black, W.J., Rupp, C. J., Nobata, C., McNaught, J., Tsujii, J. and Ananiadou, S., High-Precision Semantic Search by Generating and Testing Questions, in: Proceedings of the UK e-Science All Hands Meeting, 2010

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Riedel, S., SÃ¦tre, R., Chun, H.-W., Takagi, T. and Tsujii, J., Bio-Molecular Event Extraction with Markov Logic (2011), in: Computational Intelligence, 27:4(558-582)

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Mu, T. and Ananiadou, S., Proximity-based graph embeddings for multi-label classification, in: Proceedings of the International Conference on Knowledge Discovery and Information Retrieval (KDIR 2010), 2010

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