Dr Goran Nenadic - publications

2012

• Kovacevic, A., Konjovic, Z., Milosavljevic, B., Nenadic., G. Mining methodologies from NLP publications: A case study in automatic terminology recognition. Computer Speech & Language. 2012; 26(2): eScholarID:151544 | DOI:10.1016/j.csl.2011.09.001
• Kovacevic, A., Dehghan, A., Keane, J., Nenadic, G. Topic Categorisation of Statements in Suicide Notes with Integrated Rules and Machine Learning. Kovacevic, A., Dehghan, A., Keane, J., Nenadic, G. 2012; eScholarID:151547

2011

• Morrison, N., Hancock, D., Hirschman, L., Dawyndt, P., Verslyppe, B., Kyrpides, N.C., Kottmann R., Yilmaz, P., Glöckner, F. O., Grethe, J., Booth, T., Sterk, P., Nenadic, G., Field., D. Data shopping in an open marketplace: Introducing the Ontogrator Platform. Standards in Genomic Sciences. 2011; 4(2): 286-292. eScholarID:151549 | DOI:DOI:10.4056/sigs.1344279
• Hammad Afzal, James Eales, Robert Stevens, Goran Nenadic. Mining semantic networks of bioinformatics e-resources from the literature. Journal of Biomedical Semantics. 2011 March; 2((Suppl 1)): S4. eScholarID:122333 | DOI:10.1186/2041-1480-2-S1-S4
• Baran, J., Gerner, M., Haeussler, M., Nenadic, G. and Bergman, C. M. pubmed2ensembl: A resource for mining the biological literature on genes. PLoS One. 2011; 6(9): eScholarID:151611 | DOI:10.1371/journal.pone.0024716

2010

• Gerner M., Nenadic, G., Bergman, C. M. An Exploration of Mining Gene Expression Mentions and their Anatomical Locations from Biomedical Text. Proceedings of the BioNLP 2010 Workshop. 2010: -. eScholarID:113908
• Rebholz-Schuhmann D, Nenadic G. Biomedical Semantics: the Hub for Biomedical Research 2.0. Journal of Biomedical Semantics. 2010 March; 1(1): eScholarID:113904
• Stivaros S; Gledson A; Zeng X; Nenadic G; Keane J; Jackson A. Decision Support Systems for Clinical Radiological Practice. British Journal of Radiology. 2010; 83: 904-914. eScholarID:114000 | DOI:10.1259/bjr/33620087
• Stivaros S; Nenadic G; Zeng X; Laitt R; Hughes D; Williams T; Herwadakar A; Hutchinson C; Keane J; Jackson A. Development of a Computerized Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage. Proceedings of American Society of NeuroRadiologists 48th Annual Meeting. 2010: -. eScholarID:114015
• Stivaros S; Nenadic G; Zeng X; Gledson A; Hutchinson C; Keane J; Jackson A. Early Phase Validation of a Decision Support System within the Exemplar of Aneurysmal Subarachnoid Haemorrhage. Proceedings of British Society of NeuroRadiologists Annual Conference (BSNR 2010). 2010: -. eScholarID:114011
• Illes Solt, Martin Gerner, Philippe Thomas, Goran Nenadic, Casey M. Bergman, Ulf Leser, Jorg Hakenberg. Gene mention normalization in full texts using GNAT and LINNAEUS. Proceedings of the BioCreative III Workshop. 2010: -. eScholarID:113912
• Farzaneh Sarafraz, Goran Nenadic. Identification of Negated Regulation Events in the Literature: Exploring the Feature Space. 2010: -. eScholarID:114209
• Seemab Latif, Mary McGee Wood, Goran Nenadic. Improving Clustering of Noisy Documents through Automatic Summarisation. 2010: -. eScholarID:113984
• Gerner M., Nenadic, G., Bergman, C. M. LINNAEUS: A Species Name Identification System for Biomedical Literature. BMC Bioinformatics. 2010 February; 11(85): eScholarID:113903 | DOI:doi:10.1186/1471-2105-11-85
• Spasic I, Sarafraz F, Keane JA, Nenadic G. Medication Information Extraction with Linguistic Pattern Matching and Semantic Rules. J Am Med Inform Assoc. 2010; 17(5): 532-535. eScholarID:113906 | DOI:10.1136/jamia.2010.003657
• Sarafraz F, Nenadic G. Using SVMs with the Command Relation Features to Identify Negated Events in Biomedical Literature. Proceedings of the Workshop on Negation and Speculation in Natural Language Processing, 2010. 2010: -. eScholarID:113923
• Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C. pubmed2ensembl: Linking Publications and Genes. 2010: -. eScholarID:113965

2009

• Yang, H., Spasic, I., Keane, J., Nenadic, G. A Text Mining Approach to the Prediction of a Disease Status from Clinical Discharge Summaries. Journal of American Medical Informatics Association. 2009 October; 16(4): 596-600. eScholarID:50690 | DOI:10.1197/jamia.M3096
• Yang, H., Keane, J., Bergman, C., Nenadic, G. Assigning Roles to Protein Mentions: the Case of Transcription Factors. Journal of Biomedical Informatics. 2009; 42(5): 887-894. eScholarID:51871 | DOI:10.1016/j.jbi.2009.04.001
• Sarafraz, F., Eales, J., Mohammadi, R., Dickerson, J., Robertson, D., Nenadic, G. Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances. 2009: 115-118. eScholarID:51901
• Latif, S., McGee-Wood, M., Nenadic, G. Correlation between Human Assessment of Essays and ROUGE Evaluation of Essays' Summaries. Proceedings of the 8th International Symposium on Natural Language Processing. 2009: -. eScholarID:51855
• Afzal, H, Stevens, R., Nenadic, G. Towards Semantic Network of Bioinformatics Resources. 2009: -. eScholarID:51884
• Afzal, Hammad, Robert Stevens, and Goran Nenadic. Mining Semantic Descriptions of Bioinformatics Web Resources from the Literature. Proceedings of ESWC 2009. Springer: 2009: 535-549. eScholarID:2h819 | DOI:10.1007/978-3-642-02121-3_40

2008

• Building and Evaluating Resources for Biomedical Text Mining. 2008. eScholarID:51231
• Yang, H., Spasic, I., Keane, J., Nenadic, G. Combining Lexical Profiling, Rules and Machine Learning for Disease Prediction from Hospital Discharge Summaries. Proc. of i2b2 Obesity Challenge 2008. 2008: online-. eScholarID:68354
• Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A. Computational Treatment Prediction of Subarachnoid Haemorrhage. 2008: -. eScholarID:52005
• Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A. Decision support system for treatment planning and outcome prediction in aneurysmal subarachnoid haemorrhage. 2008: -. eScholarID:51214
• Stivaros, SM., Nenadic, G., Zeng, X., Keane, J., Jackson, A. Development of a Language-based Bayesian Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage. 2008: -. eScholarID:51274
• Greenwood, M., Nenadic G. Lexical Profiling of Existing Web Directories to Support Fine-grained Topic-Focused Web Crawling. London, UK: BCS: 2008: 42-49. eScholarID:50928
• H. Afzal, G.Nenadic. Mining bioinformatics services terminology from literature. 2008: -. eScholarID:68351
• Afzal, H., Stevens, R., Nenadic, G. Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary. 2008: 5-12. eScholarID:51088
• Rebholz-Schuhmann, D., Nenadic, G. Towards Standardisation of Named Entity Annotations in the Life Science Literature. 2008: 167-169. eScholarID:51075
• Nenadic, G., Spasic, I. Towards Terminology Extraction in Serbian. Formal Description of Slavic Languages. Frankfurt am Main, Peter Lang.2008: eScholarID:51255
• Yang H, Nenadic G, Keane J. Identification of transcription factor contexts in literature using machine learning approaches. BMC Bioinformatics. 2008; 9(S-3): eScholarID:1h345 | DOI:10.1186/1471-2105-9-S3-S11

2007

• Yang, H., Nenadic, G., Keane, J. A cascaded approach to normalizing gene mentions in biomedical literature. Bioinformation. 2007; 2(5): 197-206. eScholarID:51617

2006

• Rebholz-Schuhmann, D., Kirsch, H., Gaudan, S., Arregui, M., Nenadic, G. Annotation and Disambiguation of Semantic Types in Biomedical Text: a Cascaded Approach to Named Entity Recognition. 2006: 11-18. eScholarID:51447
• Ananiadou, S., Nenadic, G. Automatic Terminology Management in Biomedicine. In: S. Ananiadou and J. McNaught, ed. Text Mining for Biology and Biomedicine. London, Artech House Books.2006: eScholarID:51633
• Rebholz-Schuhmann, D., Kirsch, H., Nenadic, G. IeXML: towards an annotation framework for biomedical semantic types enabling interoperability of text processing modules. 2006: -. eScholarID:51432
• Ananiadou, S., Nenadic, G., Mima, H., Tsujii, J. Mining Biomedical Terminology from Literature. Terminology, Computing and Translation. Tubingen, Gunther Narr Verlag.2006: eScholarID:51416
• Nenadic, G., Ananiadou, S. Mining Semantically Related Terms from Biomedical Literature. ACM Transactions on Asian Language Information Processing (TALIP). 2006 March; 5(1): 1-22. eScholarID:1a9802 | DOI:10.1145/1131348.1131351
• Nenadic, G., Okazaki, N., Ananiadou, S. Towards a terminological resource for biomedical text mining. ELRA: 2006: 1071-1076. eScholarID:51463

2005

• Nenadic, G., Spasic, I., Ananiadou, S. Mining Biomedical Abstracts: What's in a Term?. Lecture Notes in Artificial Intelligence, Vol. 3248. Springer: 2005: 797-806. eScholarID:51552
• Rice S, Nenadic G, Stapley B. Mining protein function from text using term-based support vector machines. BMC Bioinformatics. 2005; 6(S-1): eScholarID:1h387 | DOI:10.1186/1471-2105-6-S1-S22

2004

• Nenadic, G. Creating digital language resources, The Review of National Centre for Digitsation, Belgrade. Vol. 5. 2004.
• Nenadic, G., Ananiadou, S, McNaught, J. Enhancing automatic term recognition through recognition of variation, 20th International Conference on Computational Linguistics (Coling 2004), Proc., Geneva. 2004. 604-610.
• Nenadic, G., Spasic, I, Ananiadou, S. Automatic discovery of term similarities using pattern mining, Terminology. Vol. 10 (1). 2004.
• Nenadic, G., Spasic, I, Ananiadou, S. Mining biomedical abstracts: what's in a term?, IJCNLP 2004, Proc.,. 2004. 247-254.
• Rice, S, Nenadic, G., Stapley, B. Protein function assignment using term-based support vector machines, BioCreative Task Two 2003, Workshop on Critical Assessment of Information Extraction systems in Biology (BioCreAtiVe), Granada, Spain. 2004.
• Spasic, I, Nenadic, G., Ananiadou, S. Learning to classify biomedical terms through literature mining and genetic algorithms, Intelligent Data Engineering and Automated Learning (IDEAL'04), Lecture Notes in Computer Science. Ed. Yang Z R et al. 2004. Springer Verlag. 345-351.
• Stamou, S, Nenadic, G., Christodoulakis, D. Exploring balkanet shared ontology for multilingual conceptual indexing, LREC 2004, Proc., Lisbon, Portugal. 2004. 781-784.
• NENADIC G; KRAUTHAMMER M. Term Identification in the Biomedical Literature. Journal of Biomedical Informatics. 2004 October; 37(6): 512-526. eScholarID:1a9803 | DOI:10.1016/j.jbi.2004.08.004
• Krauthammer M, Nenadic G. Term identification in the biomedical literature. Journal of Biomedical Informatics. 2004; 37(6): 512-526. eScholarID:1h388 | DOI:10.1016/j.jbi.2004.08.004
• Nenadic, Goran, Irena Spasic, and Sophia Ananiadou. Mining Biomedical Abstracts: What's in a Term?. IJCNLP. Springer: 2004: 797-806. eScholarID:2h821
• Spasic, Irena, Goran Nenadic, and Sophia Ananiadou. Learning to Classify Biomedical Terms Through Literature Mining and Genetic Algorithms. IDEAL. Springer: 2004: 345-351. eScholarID:2h820

2003

• Nenadic, G., Rice, S, Spasic, I, Ananiadou, S, Stapley, B. Selecting text features for gene name classification: from documents to terms, ACL 2003 Workshop on NLP in Biomedicine, Proc., Sapporo, Japan 2003. 2003. 121-128.
• Nenadic, G., Spasic, I, Ananiadou, S. Investigations into formal slavic linguistics, Reducing lexical ambiguity in Serbo-Croatian by using genetic algorithms. Ed. Kosta P et al. 2003. Linguistik International, Peter Lang, Frankfurt. 287-298.
• Nenadic, G., Spasic, I, Ananiadou, S. Morpho-syntactic clues for teminogical processing in serbian, Workshop on Morphological Processing of Slavic Languages EACL, Proc., Budapest, Hungary, 2003. 2003. 79-86.
• Nenadic, G., Spasic, I, Ananiadou, S. Terminology-driven mining of biomedical literature, 18th Annual ACM Symposium on Applied Computing, SAC 2003. 2003.
• Nenadic, G., Spasic, I, Ananiadou, S. Terminology-driven mining of biomedical literature, Bioinformatics. Vol. 19 (8). 2003.
• Spasic , I, Nenadic, G., Ananiadou, S. Term classification using domain-specific verb complementation patterns, ACL 2003 Workshop on NLP in Biomedicine, Proc., Sapporo, Japan 2003. 2003.
• Spasic, I, Nenadic, G., Keane, J., Ananiadou, S. Towards terminology extraction in serbian, 5th European Conference on Formal Description of Slavic Languages (FDSL-5), Proc., Leipzig, Germany 2003. 2003.
• Spasic, I, Nenadic, G., Manios, K, Ananiadou, S. An integrated term-based corpus query system, EACL 2003, Proc., Budapest, Hungary. 2003. 243-250.
• NENADIC G; SPASIC I; ANANIADOU S. Terminology-driven Mining of Biomedical Literature. Bioinformatics. 2003 May; 19(8): 938-943. eScholarID:1a9804 | DOI:10.1093/bioinformatics/btg105
• Manios, Kostas, Goran Nenadic, Irena Spasic, and Sophia Ananiadou. An Integrated Term-Based Corpus Query System. EACL. 2003: 243-250. eScholarID:2h822
• Nenadic G, Spasic I, Ananiadou S. Terminology-driven Mining of Biomedical Literature. Bioinformatics. 2003; 19(8): 938-943. eScholarID:1h389
• Nenadic, Goran, Irena Spasic, and Sophia Ananiadou. Terminology-driven Mining of Biomedical Literature. SAC. ACM: 2003: 83-87. eScholarID:2h823

2002

• Ananiadou, S, Nenadic, G. Automatic term management in biology, Workshop on Natural Language Processing and Ontology Building in Biology, Tokyo, Japan. February 18-20, 2002. 2002.
• Ananiadou, S, Nenadic, G., Schuhmann, D, Spasic, I. Term-based literature mining from biomedical texts, ISMB Text Data Mining SIG, Proc., Edmonton, Canada. 2002.
• Mima, H, Ananiadou, S, Nenadic, G., Tsujii, J. A methodology for terminology-based knowledge acquisition and integration, COLING 2002, Proc., Taipei, Taiwan 2002. 2002. 667-673.
• Mima, H, Ananiadou, S, Nenadic, G., Tsujii, J. TIMS - a workbench for ontology-based knowledge acquisition and integration, Workshop on Natural Language Processing in Biomedical applications, Proc., Nicosia, Cyprus 2002. 2002. 11-15.
• Mima, H, Ananiadou, S, Nenadic, G., Tsujii, J. XML tag information management system - a workbench for ontology-based knowledge acquisition and integration, Human Language Technology Conference (HLT 2002), Proc., San Diego, California, USA 2002. 2002. 274-279.
• Nenadic, G., Mima, H, Spasic, I, Ananiadou, S, Tsujii, J. Terminolology-based literature mining and knowledge acquisition in biomedicine, International Journal of Medical Informatics. Vol. 67 (1 - 3). 2002.
• Nenadic, G., Spasic, I, Ananiadou, S. Automatic acronym acquisition and term variation management within domain-specific texts, 3rd International Conference on Language, Resources and Evaluation (LREC-3) ELRA, Proc., Las Palmas de Gran Canaria, Spain. 2002. 2002. 2155-2162.
• Nenadic, G., Spasic, I, Ananiadou, S. Automatic discovery of term similarities using pattern mining, CompuTerm 2002, Proc., Taipai, Taiwan 2002. 2002. 43-49.
• Nenadic, G., Spasic, I, Ananiadou, S. Text speech and dialogue (TSD 2002) Lecture notes in artificial intelligence, Term clustering using a corpus-based similarity measure. Ed. Sojka P et al. 2002. Springer Verlag. 151-154.
• Spasic, I, Nenadic, G., Ananiadou, S. A genetic algorithm approach to unsupervised learning of context features, 5th National Colloquium for Computational Linguistics in the UK (CLUK-5), Proc., University of Leeds, UK, 2002. 2002. 12-19.
• Spasic, I, Nenadic, G., Ananiadou, S. Tuning context features with genetic algorithms, 3rd International Conference on Language, Resources and Evaluation (LREC-3) ELRA, Proc., Las Palmas de Gran Canaria, Spain 2002. 2002. 2048-2054.
• Spasic, I, Nenadic, G., Manios, K, Ananiadou, S. Intelligent data engineering and automated learning (IDEAL 02). Lecture notes in computer science, Supervised learning of term similarities. Ed. Yin H et al. 2002. Springer Verlag. 429-434.
• Mima, Hideki, Sophia Ananiadou, Goran Nenadic, and Jun-ichi Tsujii. A Methodology for Terminology-based Knowledge Acquisition and Integration. COLING. 2002: eScholarID:2h824
• Nenadic, Goran, Irena Spasic, and Sophia Ananiadou. Term Clustering Using a Corpus-Based Similarity Measure. TSD. Springer: 2002: 151-154. eScholarID:2h826
• Nenadic G, Mima H, Spasic I, Ananiadou S, Tsujii J. Terminology-driven literature mining and knowledge acquisition in biomedicine. I. J. Medical Informatics. 2002; 67(1-3): 33-48. eScholarID:1h390 | DOI:10.1016/S1386-5056(02)00055-2
• Spasic, Irena, Goran Nenadic, Kostas Manios, and Sophia Ananiadou. Supervised Learning of Term Similarities. IDEAL. Springer: 2002: 429-434. eScholarID:2h825

2001

• Ananiadou, S, Mima, H, Nenadic, G. Terminology management workbench for molecular biology, Information extraction in molecular biology. Ed. Van de Vet P et al. 2001. TWLT 19, Twente, The Netherlands, 2001. 7-12.
• Mima, H, Ananiadou, S, Nenadic, G. Improving knowledge acquisition through automatic term recognition, Advances in human-computer interaction (PC-HCI 2001), Proc., Typorama, Patras, Greece 2001. 2001. 177-182.
• Mima, H, Ananiadou, S, Nenadic, G. Text, speech and dialogue (TSD 2001) Lecture notes in artificial intelligence, The ATRACT workbench: automatic term recognition and clustering of terms. Ed. Matousek V et al. 2001. Springer Verlag. 126-133.
• Mima, Hideki, Sophia Ananiadou, and Goran Nenadic. The ATRACT Workbench: Automatic Term Recognition and Clustering for Terms. TSD. Springer: 2001: 126-133. eScholarID:2h827

2000

• Nenadic, Goran. Local Grammars and Parsing Coordination of Nouns in Serbo-Croatian. TSD. Springer: 2000: 57-62. eScholarID:2h829
• Nenadic, Goran, and Irena Spasic. Recognition and Acquisition of Compound Names from Corpora. Natural Language Processing. Springer: 2000: 38-48. eScholarID:2h828

1999

• Nenadic, Goran, and Irena Spasic. The Acquisition of Some Lexical Constraints from Corpora. TSD. Springer: 1999: 115-120. eScholarID:2h830