Publication list - NaCTeM Publications

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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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Rupp, C. J., Thompson, P., Black, W.J., McNaught, J. and Ananiadou, S., A Specialised Verb Lexicon as the Basis of Fact Extraction in the Biomedical Domain, in: Proceedings of Interdisciplinary Workshop on Verbs: The Identification and Representation of Verb Features (Verb 2010), 2010

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Nawaz, R., Thompson, P. and Ananiadou, S., Event Interpretation: A Step towards Event-Centred Text Mining, in: Proceedings of the 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop, 2010

Nawaz, R., Thompson, P. and Ananiadou, S., Evaluating a meta-knowledge annotation scheme for bio-events, in: Proceedings of the Workshop on Negation and Speculation in Natural Language Processing, pages 69--77, 2010

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Kano, Y., Dobson, P., Nakanishi, M., Tsujii, J. and Ananiadou, S., Text Mining Meets Workflow: Linking U-Compare with Taverna (2010), in: Bioinformatics, 26:19(2486-2487)

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BjÃ¶rne, J., Ginter, F., Pyysalo, S., Tsujii, J. and Salakoski, T., Complex event extraction at PubMed scale (2010), in: Bioinformatics, 26:12(i382-i390)

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Miwa, M., Pyysalo, S., Hara, T. and Tsujii, J., A Comparative Study of Syntactic Parsers for Event Extraction, in: Proceedings of BioNLP 2010, ACL., pages 37--45, 2010

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Miwa, M., Miyao, Y., SÃ¦tre, R. and Tsujii, J., Entity-Focused Sentence Simplification for Relation Extraction, in: Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010), pages 788-796, 2010

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Miwa, M., Pyysalo, S., Hara, T. and Tsujii, J., Evaluating Dependency Representation for Event Extraction, in: Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010), pages 779-787, 2010

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SÃ¦tre, R., Yoshida, K., Miwa, M., Matsuzaki, T., Kano, Y. and Tsujii, J., Extracting Protein-Interactions from Text with the Unified AkaneRE Event Extraction System (2010), in: Transactions on Computational Biology and Bioinformatics (TCBB), BioCreative II.5 Special Issue, 7:3(442-453)

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