[2013] [2012] [2011] [2010] [2009] [2008]
[2007] [2006] [2005] [2004] [2003] [2002]



  • Gomez-Paramio I, Nenadic G, Clayton-Smith J: CliMGuiDeS: online platform to develop clinical management guidelines for rare conditions, The European Human Genetics Conference 2015, Glasgow

  • Demetriou G, Nenadic G, Read W, Stevens R, Winter J: The BioHub Ontology for Sustainable Bio-Feedstocks, The 4th UK Ontology Network Meeting, 2015

  • Liptrot T, Karystianis G, Nenadic G, Keane J, Livsey J, Barker-Hewitt M, O'Hara C: Using natural language processing to automatically extract cancer outcomes data from clinical notes, The UK National Cancer Outcomes Conference 2015, Belfast, 2015.

  • Newman J, Noble P-J.M., Nenadic G, Radford A.D., Walker D, Bacon J, Jones PH: Mining Clinical Text Notes to Facilitate Surveillance of Alabama Rot, BSAVA Congress, 2015

  • Newman J, O'Brien L, Mooney A, Noble P-J.M, Nenadic G, Jones PH, Casey R, Adamantos S, Radford AD: Fireworks: don't leave it too late, BSAVA Congress, 2015

  • Newman J, Noble P-J.M, Nenadic G, Radford AD, Jones PH: Clinical text mining: the cutting edge of computer science meets the coalface of small animal veterinary practice, The Association for Veterinary Teaching and Research Work (AVTRW), 2015


  • Filannino M, Nenadic G: Using machine learning to predict temporal orientation of search engines' queries in the Temporalia challenge, Proceedings of the 11th NTCIR Conference, pp.438-442 (link)

  • Spasic I, Livsey J, Keane JA, Nenadic G: Text mining of cancer-related information: Review of current status and future directions, Int. J. Med. Inform. (2014), doi:, (link)

  • Wu C, Schwartz JM, Brabant G, Nenadic G: Molecular profiling of thyroid cancer subtypes using large-scale text mining, BMC Medical Genomics 2014 7:S3, doi:10.1186/1755-8794-7-S3-S3 (link)

  • Filannino M, Nenadic G: Mining temporal footprints from Wikipedia, Proc. of 1st AHA! Workshop on Information Discovery in Text (COLING 2014) (link)

  • Jamieson DG, Moss A, Kennedy M, Jones, S, Nenadic G, Robertson DL, Sidders B: The pain interactome: connecting pain specific protein interactions, Pain, DOI: 10.1016/j.pain.2014.06.020 (link)

  • Duck G, Nenadic G, Brass A, Robertson DL, Stevens R: Extracting patterns of database and software usage from the bioinformatics literature, Bioinformatics 2014, 30:17, doi:10.1093/bioinformatics/btu471 (link)

  • Zaki Ali MM, Nenadic G, Theodoulidis B: Identification of Multi-Focal Questions in Question and Answer Reports, in Proc. of NLDB 2014, LNCS vol.8455, pp. 126-137, Springer, Montpellier, France

  • Karystianis G, Buchan I, Nenadic G: Mining Characteristics of Epidemiological Studies from Medline: A Case Study in Obesity. Journal of Biomedical Semantics 2014, 5:22, doi:10.1186/2041-1480-5-22 (link)

  • Wallbridge S, Lowe AJ, Keane JA, Nenadic G, Cooper J: An ontological approach to knowledge management for sustainable nuclear decommissioning, International Journal of Nuclear Knowledge Management 2014 Vol. 6 No. 3, pp 1999-216, DOI: 10.1504/IJNKM.2014.058924 (link)


  • Tian D, Gledson A, Antoniades A, Aristodimou A, Ntalaperas D, Sahay R, Pan J, Stivaros S, Nenadic G, Zeng XJ, Keane JA: A Bayesian Association Rule Mining Algorithm, In Proc. of 2013 IEEE International Conference on Systems, Man, and Cybernetics

  • Dehghan A, Keane JA, Nenadic G: Challenges in Clinical Named Entity Recognition for Decision Support, In Proc. of 2013 IEEE International Conference on Systems, Man, and Cybernetics, pp. 947-951, doi: 10.1109/SMC.2013.166

  • Wu C, Schwartz JM, Nenadic G: PathNER: A tool for systematic identification of biological pathway mentions in the literature, BMC Systems Biology 2013, 7(Suppl 3):S2 (link)

  • Duck G, Nenadic G, Robertson DL, Stevens R: What is bioinformatics made from? A survey of database and software usage through full-text mining, ISMB/ECCB 2013 (poster)

  • Filannino M, Brown G, Nenadic G: ManTIME: Temporal expression identification and normalization in the TempEval-3 challenge, Proc. of TempEval-3 (link)

  • Duck G, Nenadic G, Brass A, Robertson DL, Stevens R: bioNerDS: exploring bioinformatics' database and software use through literature mining BMC Bioinformatics 2013, 14:194 (link)

  • Jamieson DG, Robertson DL, Sidders B, Nenadic G: Exploring the biomedical world of neuropathic pain through molecular interactions, NeuPSig (2013) (poster)

  • Jamieson DG, Roberts PM, Robertson DL, Sidders B, Nenadic G: Cataloguing the biomedical world of pain through semi-automated curation of molecular interactions, Database 2013: bat033 doi:10.1093/database/bat033 (link)

  • Kovacevic A, Dehghan A, Filannino M, Keane J, Nenadic G: Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives, J Am Med Inform Assoc, doi:10.1136/amiajnl-2013-001625 (link)

  • Hakenberg J, Nenadic G, Rebholz-Schuhmann D, Kim JD: Literature Mining Solutions for Life Science Research, Advances in Bioinformatics, vol. 2013, 2013. doi:10.1155/2013/320436


  • Gerner M, Sarafraz F, Bergman CB, Nenadic G. BioContext: an integrated text mining system for large-scale extraction and contextualisation of biomolecular events. Bioinformatics (2012) 28 (16): 2154-2161. doi: 10.1093/bioinformatics/bts332 (link)

  • Duck G, Stevens R, Robertson D, Nenadic G. Ambiguity and variability of database and software names in bioinformatics. SMBM 2012, pages 2-9 (2012) (link)

  • Kovacevic A, Dehghan A, Filannino M, Keane JA, Nenadic, G: Extraction of temporal expressions, events and relations from clinical narratives using rules and machine-learning. the Sixth i2b2 Workshop on Challenges in NLP for Clinical Data, November 2012 (poster)

  • Jamieson DG, Gerner M, Sarafraz F, Nenadic G, Robertson DL: Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. Database 2012; doi: 10.1093/database/bas023 (link)

  • Duck G, Brass A, Nenadic G, Robertson DL, Stevens R: Exploring Bioinformatics' Database and Software Use through Literature Mining. ECCB 2012 (poster)

  • Wu C, Schwartz JM, Nenadic G: Systematic Identification of Biological Pathway Mentions in Biomedical Literature: a Case Study of Thyroid Cancer. ECCB 2012 (poster)

  • Jamieson DG, Robertson DL, Nenadic G: Contextualising and exploring human-pathogen molecular interactions through full-scale biomedical text mining, ISMB 2012, Long Beach CA (2012) (poster)

  • Filannino M: Temporal expression normalisation in natural language texts.

  • Kovacevic A, Konjovic Z, Milosavljevic B, Nenadic G: Mining methodologies from NLP publications: A case study in automatic terminology recognition. Computer Speech & Language, Volume 26, Issue 2 (2012) (link)

  • Kovacevic A, Dehghan A, Keane JA, Nenadic G: Topic Categorisation of Statements in Suicide Notes with Integrated Rules and Machine Learning. J Biomed Informatics Insight. (2012) (link)


  • Karystianis, G., Buchan, I., Nenadic, G. Mining Characteristics of Epidemiological Studies from Medline: A Case Study in Obesity. Languages in Biology and Medicine (2011)

  • Jamieson, D., Robertson, DL., Nenadic, G.. Task-specific Protein Tagging: an Experiment with BANNER on HIV-1/human interaction text. Languages in Biology and Medicine (2011) (poster)

  • 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, Vol 4, No 2 (2011) (link)

  • Baran, J., Gerner, M., Haeussler, M., Nenadic, G. and Bergman, C. M.pubmed2ensembl: A resource for mining the biological literature on genes. PLoS One 6(9) (2011): e24716. (link)

  • Lu, Z., et al. The gene normalization task in BioCreative III. BMC Bioinformatics 12(Suppl 8): S1. (link)

  • Hakenberg, J., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., Gonzalez, G., Nenadic, G. and Bergman, C. M. The GNAT library for local and remote gene mention normalization. Bioinformatics 27(19) (2011): 2769-71. (link)

  • Afzal H, J. Eales, R. Stevens, G. Nenadic: Mining Semantic Networks of Bioinformatics Web Resources from the Literature, J Biomed Semantics 2 Suppl 1:S4 (2011) (link)


  • Stivaros S; Gledson A; Zeng X; Nenadic G; Keane J; Jackson A.: Decision Support Systems for Clinical Radiological Practice, British Journal of Radiology 83 (2010), 904-914 (link)

  • Sarafraz F, Nenadic G: Identification of Negated Regulation Events in the Literature: Exploring the Feature Space, Proc. of 4th International Symposium on Semantic Mining in Biomedicine (SMBM 2010) (link)

  • 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)

  • Latif S, McGee-Wood M, Nenadic G: Improving Clustering of Noisy Documents through Automatic Summarisation, International Conference on Intelligent Text Processing and Computational Linguistics (CICLing)

  • Gerner M., Nenadic, G., Bergman, C. M.: LINNAEUS: A Species Name Identification System for Biomedical Literature, BMC Bioinformatics 11:85 (link)

  • 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

  • Rebholz-Schuhmann D, Nenadic G: Biomedical Semantics: the Hub for Biomedical Research 2.0, J Biomed Semantics. 2010;1(1):1 (link)

  • 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):532-5 (link)

  • 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 (link)

  • Solt I, Gerner M, Thomas P, Nenadic G, Bergman CM, Leser U,Hakenberg J. Gene mention normalization in full texts using GNAT and LINNAEUS. Proceedings of the BioCreative III Workshop. (link)

  • 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 (link)

  • Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C: pubmed2ensembl: Linking Publications and Genes, Genome Informatics (UK) 2010 (poster)



  • 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

  • Greenwood, M., Nenadic, G.: Lexical Profiling of Existing Web Directories to Support Fine-grained Topic-Focused Web Crawling , Proc. of Corpus Profiling for IR and NLP Workshop, London, p. 42-49

  • Afzal, H., Stevens, R., Nenadic, G.: Mining bioinformatics services terminology from literature , Proc. of IBRC 2008, Manchester Interdisciplinary Biocentre (pdf)

  • Eales JM, Pinney JW, Stevens RD, Robertson DL.: Methodology capture: discriminating between the "best" and the rest of community practice , BMC Bioinformatics, Vol.9:359 (pdf)

  • Rebholz-Schuhmann, D., Nenadic, G.: Towards Standardisation of Named Entity Annotations in the Life Science Literature, in Proc. of Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), p. 167-169

  • Afzal, H., Stevens, R., Nenadic, G.: Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary, Proc. of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pp. 5-12 (pdf)

  • Eales JM, Stevens RD, Robertson DL.: Full-Text Mining: Linking Practice, Protocols and Articles in Biological Research , BioLINK SIG, ISMB, Toronto (pdf)

  • Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A.: Decision support system for treatment planning and outcome prediction in aneurysmal subarachnoid haemorrhage, Computer Assisted Radiology and Surgery 2008, Barcelona

  • Gledson, A., Keane, J.: Measuring Topic Homogeneity and its Application to Dictionary-based Word Sense Disambiguation, Proc. of Coling 2008, Manchester, pp. 273-280 (pdf)

  • Gledson, A.: Measuring Topic Homogeneity and its Application to Dictionary-based Word Sense Disambiguation, PhD Thesis, University of Manchester

  • Gledson, A., Keane, J.: Using Web-Search Results to Measure Word Group Similarity , Proc. of Coling 2008, Manchester, pp 281-288 (pdf)

  • Latif, S., Wood, M: Text Pre-processing for Document Clustering , Proc. of the 13th Natural Language and Information Systems conference (NLDB 2008), pp. 358-359 (pdf)

  • Latif, S.: Text Pre-processing for Document Clustering, Proc. of the 11th Annual CLUK Research Colloquium (CLUK 2008)

  • Yang, H., Nenadic, G., Keane, J.: Identification of transcription factor contexts in literature using machine learning approaches, BMC Bioinformatics, 9(Suppl 3):S11.(pdf)

  • Nenadic, G., Spasic, I.: Towards Terminology Extraction in Serbian, Zybatow G. et al. (eds.). Formal Description of Slavic Languages: The Fifth Conference, Leipzig 2003. Peter Lang: Frankfurt am Main, 2008

  • Nenadic, G.: Mining associations and roles: role of feature extraction, Proc. of Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, Dagstuhl Seminar Proceedings 08131, 2008

  • Ananiadou, S., Monachini, M., Nenadic, G., Su, J. (Eds): Building and Evaluating Resources for Biomedical Text Mining, Proceedings of an LREC 2008 Workshop p71, 2008

  • 1.Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A.: Decision support system for treatment planning and outcome prediction in aneurysmal subarachnoid haemorrhage, Computer Assisted Radiology and Surgery 2008 (Poster), Barcelona

  • 1.Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A.: Computational Treatment Prediction of Subarachnoid Haemorrhage, British Society of Neuroradiologists (BSNR) 2008 (Poster), Manchester



  • Latif, S., Khan,S.: Correlations and Associations Analysis for Identification and Prediction of Relationships and Their Activeness , Proc. of 2nd IEEE International Conference on Information and Communication Technologies: from Theory to Applications (ICTTA 2006) Damascus, Syria (pdf)

  • Rebholz-Schuhmann, D., Kirsch, H., Nenadic, G.: IeXML: towards an annotation framework for biomedical semantic types enabling interoperability of text processing modules, Proceedings of Joint BioLINK and Bio-Ontologies SIG Meeting, ISMB 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, Proceedings of NLPXML 2006, EACL 2006

  • Nenadic, G., Okazaki, N., Ananiadou, S.: Towards a terminological resource for biomedical text mining, Proceedings of LREC 2006, ELRA

  • Nenadic, G., Ananiadou, S.: Mining Semantically Related Terms from Biomedical Literature, ACM Transactions on ALIP (Special Issue on Text Mining and Management in Biomedicine) Vol. 5, No. 1, pp.22-43. (pdf)

  • Ananiadou, S., Nenadic, G: Automatic Terminology Management in Biomedicine, Chapter in ?Text Mining for Biology and Biomedicine?, S. Ananiadou and J. McNaught (Eds.), Artech House Books, London, pp. 67-98

  • Ananiadou, S., Nenadic, G., Mima, H., Tsujii, J.: Mining Biomedical Terminology from Literature, Chapter in ?Terminology, Computing and Translation?, P. ten Hacken (Ed.), Gunther Narr Verlag, T?bingen, 2006, pp. 117-140



  • Krauthammer, M., Nenadic, G.: Term Identification in the Biomedical Literature, Journal of Biomedical Informatics (Special Issue on Named Entity Recognition in Biomedicine), Vol. 37(6):512-526.(pdf)

  • Nenadic, G.: Creating Digital Language Resources, Review of the National Centre for Digitisation, Vol. 5, 19-30.(pdf)

  • Nenadic, G., Spasic, I., Ananiadou, S.: Mining Term Similarities from Corpora,Terminology Vol. 10, No. pp.. 55-80. (pdf)

  • Nenadic, G., Ananiadou, S., McNaught, J.: Enhancing Automatic Term Recognition through Recognition of Variation, Proceedings of COLING 2004, Geneva, Switzerland, pp. 604-610

  • Spasic, I., Nenadic, G., Ananiadou, S.: Learning to Classify Biomedical Terms through Literature Mining and Genetic Algorithms, in Yang, ZR et al. (Eds.): Intelligent Data Engineering and Automated Learning (IDEAL'04), Lecture Notes in Computer Science, Vol. 3177, Springer Verlag, pp. 345-351

  • Stamou, S., Nenadic, G., Christodoulakis, D.: Exploring Balkanet Shared Ontology for Multilingual Conceptual Indexing, Proceedings of LREC 2004, ELRA, pp. 781-784

  • Rice, S., Nenadic, G., Stapley, B.: Protein Function Assignment using Term-based Support Vector Machines ? BioCreative Task Two 2004, Workshop on Critical Assessment of Information Extraction systems in Biology (BioCreAtiVe), Granada, Spain