Publications | gnTEAM

2016
- Extracting patient data from tables in clinical literature: Case study on extraction of BMI, weight and number of patients
  Nikola Milosevic, Cassie Gregson, Robert Hernandez, Goran Nenadic Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016): International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016). Rome; 2016
- Modelling and Extraction of Variability in Free-text Medication Prescriptions from an Anonymised Primary Care Electronic Medical Record Research Database
  George Karystianis; Therese Sheppard; William G Dixon; Goran Nenadic B M C Medical Informatics and Decision Making. BioMed Central Ltd.; 2016
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2015
- Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.
  Wu, Chengkun; Schwartz, Jean-Marc; Brabant, Georg; Peng, Shao-Liang; Nenadic, Goran BMC systems biology; 2015
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- Disentangling the multigenic and pleiotropic nature of molecular function.
  Stoney, Ruth A; Ames, Ryan M; Nenadic, Goran; Robertson, David L; Schwartz, Jean-Marc BMC systems biology; 2015
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- Temporal expression extraction with extensive feature type selection and a posteriori label adjustment
  Michele Filannino, Goran Nenadic Data & Knowledge Engineering. Elsevier BV * North-Holland; 2015
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- Contextualisation of Biomedical Knowledge through Large-scale Processing of Literature, Clinical Narratives and Social Media
  Nenadic, Goran Lecture Notes in Computer Science; 2015
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- Combining knowledge- and data-driven methods for de-identification of clinical narratives
  Dehghan, Azad; Kovacevic, Aleksandar; Karystianis, George ; Keane, John A; Nenadic, Goran Journal of Biomedical Informatics. Academic Press; 2015
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- Using local lexicalized rules to identify heart disease risk factors in clinical notes
  Karystianis, George; Dehghan, Azad; Kovacevic, Alexsandar ; Keane, John A ; Nenadic, Goran Journal of Biomedical Informatics. Academic Press; 2015
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- Ambiguity and variability of database and software names in bioinformatics
  Duck, Geraint ; Kovacevic, Aleksandar ; Robertson, David L; Stevens, Robert ; Nenadic, Goran Journal of Biomedical Semantics. BioMed Central Ltd.; 2015
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2014
- An ontological approach to knowledge management for sustainable nuclear decommissioning
  Wallbridge S, Lowe AJ, Keane JA, Nenadic G, Cooper J International Journal of Nuclear Knowledge Management. Inderscience Publishers; 2014
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- Text mining of cancer-related information: Review of current status and future directions
  Spasic I, Livsey J, Keane JA, Nenadic G International Journal of Medical Informatics. Elsevier Ireland Ltd; 2014
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- The pain interactome: connecting pain specific protein interactions
  Jamieson DG, Moss A, Kennedy M, Jones, S, Nenadic G, Robertson DL, Sidders B Pain. Elsevier BV; 2014
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- Extracting patterns of database and software usage from the bioinformatics literature
  Duck G, Nenadic G, Brass A, Robertson DL, Stevens R Bioinformatics. Oxford University Press; 2014
- Molecular profiling of thyroid cancer subtypes using large-scale text mining
  Wu C, Schwartz JM, Brabant G, Nenadic G B M C Medical Genomics. BioMed Central Ltd.; 2014
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- Extracting patterns of database and software usage from the bioinformatics literature
  Duck, Geraint; Nenadic, Goran; Brass, Andy; Robertson, David L; Stevens, Robert Bioinformatics. Oxford University Press; 2014
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- Mining Characteristics of Epidemiological Studies from Medline: A Case Study in Obesity
  George Karystianis, Iain Buchan, Goran Nenadic Journal of Biomedical Semantics. BioMed Central Ltd.; 2014
- Extraction and representation of key characteristics from epidemiological literature
  Karystianis, George The University of Manchester; 2014
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2013
- Cataloguing the biomedical world of pain through semi-automated curation of molecular interactions
  Jamieson DG, Roberts PM, Robertson DL, Sidders B, Nenadic G Database. Oxford University Press; 2013
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- bioNerDS: exploring bioinformatics’ database and software use through literature mining
  Duck G, Nenadic G, Brass A, Robertson DL, Stevens R B M C Bioinformatics. BioMed Central Ltd.; 2013
- PathNER: A tool for systematic identification of biological pathway mentions in the literature
  Wu C, Schwartz JM, Nenadic G: B M C Systems Biology. BioMed Central Ltd.; 2013
- Logical models of DNA damage induced pathways to cancer
  Tian, Kun The University of Manchester; 2013
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- bioNerDS: exploring bioinformatics’ database and software use through literature mining
  Geraint Duck, Goran Nenadic, Andy Brass, David L Robertson and Robert Stevens BMC Bioinformatics; 2013
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- Literature Mining Solutions for Life Science Research
  Jörg Hakenberg, Goran Nenadic, Dietrich Rebholz-Schuhmann, Jin-Dong Kim Advances in Bioinformatics; 2013
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- Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives
  Kovačević A, Dehghan A, Filannino M, Keane J, Nenadic G Journal of the American Medical Informatics Association; 2013
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2012
- Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database
  Daniel G. Jamieson, Martin Gerner, Farzaneh Sarafraz, Goran Nenadic, David L. Robertson Database; 2012
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- BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events
  Martin Gerner, Farzaneh Sarafraz, Casey M Bergman, Goran Nenadic Bioinformatics. Oxford University Press; 2012
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- Integrating text-mining approaches to identify entities and extract events from the biomedical literature
  Gerner, Lars Martin Anders The University of Manchester; 2012
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- Bayesian mixture models for frequent itemset mining
  He, Ruofei The University of Manchester; 2012
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- Finding Conflicting Statements in the Biomedical Literature
  Sarafraz, Farzaneh The University of Manchester; 2012
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- Topic Categorisation of Statements in Suicide Notes with Integrated Rules and Machine Learning
  Kovacevic, A., Dehghan, A., Keane, J., Nenadic, G. Biomedical Informatics Insight. Libertas Academica Ltd.; 2012
- Mining methodologies from NLP publications: A case study in automatic terminology recognition
  Kovacevic, A., Konjovic, Z., Milosavljevic, B., Nenadic., G Computer Speech & Language. Elsevier; 2012
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2011
- pubmed2ensembl: A resource for mining the biological literature on genes
  Baran, J., Gerner, M., Haeussler, M., Nenadic, G. and Bergman, C. M. PLoS One; 2011
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- Data shopping in an open marketplace: Introducing the Ontogrator Platform
  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. Standards in Genomic Sciences; 2011
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- Mining semantic networks of bioinformatics e-resources from the literature
  Hammad Afzal, James Eales, Robert Stevens, Goran Nenadic Journal of Biomedical Semantics; 2011
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2010
- Identification of Negated Regulation Events in the Literature: Exploring the Feature Space
  Farzaneh Sarafraz, Goran Nenadic Fourth International Symposium on Semantic Mining in Biomedicine (SMBM). Hinxton, UK; 2010
- Development of a Computerized Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage
  Stivaros S; Nenadic G; Zeng X; Laitt R; Hughes D; Williams T; Herwadakar A; Hutchinson C; Keane J; Jackson A. Proceedings of American Society of NeuroRadiologists 48th Annual Meeting: American Society of NeuroRadiologists 48th Annual Meeting (ASNR 2010). Boston, UK; 2010
- Early Phase Validation of a Decision Support System within the Exemplar of Aneurysmal Subarachnoid Haemorrhage
  Stivaros S; Nenadic G; Zeng X; Gledson A; Hutchinson C; Keane J; Jackson A. Proceedings of British Society of NeuroRadiologists Annual Conference (BSNR 2010) : British Society of NeuroRadiologists Annual Conference (BSNR 2010) . Glasgow, UK; 2010
- Decision Support Systems for Clinical Radiological Practice
  Stivaros S; Gledson A; Zeng X; Nenadic G; Keane J; Jackson A. British Journal of Radiology; 2010
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- Improving Clustering of Noisy Documents through Automatic Summarisation
  Seemab Latif, Mary McGee Wood, Goran Nenadic International Conference on Intelligent Text Processing and Computational Linguistics (CICLing). Iasi, Romania; 2010
- pubmed2ensembl: Linking Publications and Genes
  Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C. Genome Informatics (UK) 2010. Hinxton, UK; 2010
- Using SVMs with the Command Relation Features to Identify Negated Events in Biomedical Literature
  Sarafraz F, Nenadic G. Proceedings of the Workshop on Negation and Speculation in Natural Language Processing, 2010 : ACL Workshop on Negation and Speculation in Natural Language Processing. Uppsala, Sweden; 2010
- Gene mention normalization in full texts using GNAT and LINNAEUS
  Illes Solt, Martin Gerner, Philippe Thomas, Goran Nenadic, Casey M. Bergman, Ulf Leser, Jorg Hakenberg Proceedings of the BioCreative III Workshop: BioCreative III Workshop. Bethesda, Maryland, USA; 2010
- An Exploration of Mining Gene Expression Mentions and their Anatomical Locations from Biomedical Text
  Gerner M., Nenadic, G., Bergman, C. M Proceedings of the BioNLP 2010 Workshop: BioNLP 2010 Workshop. Uppsala, Sweden; 2010
- Medication Information Extraction with Linguistic Pattern Matching and Semantic Rules
  Spasic I, Sarafraz F, Keane JA, Nenadic G. J Am Med Inform Assoc. ; 2010
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- Biomedical Semantics: the Hub for Biomedical Research 2.0
  Rebholz-Schuhmann D, Nenadic G Journal of Biomedical Semantics; 2010
- LINNAEUS: A species name identification system for biomedical literature
  Gerner M., Nenadic, G., Bergman, C. M. BMC Bioinformatics. BioMed Central ; 2010
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2009
- Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances
  Sarafraz, F., Eales, J., Mohammadi, R., Dickerson, J., Robertson, D., Nenadic, G. BioNLP shared task 2009 ; 2009
- Towards Semantic Network of Bioinformatics Resources
  Afzal, H, Stevens, R., Nenadic, G. ISMB/ECCB 2009. Stockholm, Sweden; 2009
- Assigning Roles to Protein Mentions: the Case of Transcription Factors
  Yang, H., Keane, J., Bergman, C., Nenadic, G. Journal of Biomedical Informatics; 2009
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- Correlation between Human Assessment of Essays and ROUGE Evaluation of Essays’ Summaries
  Latif, S., McGee-Wood, M., Nenadic, G. Proceedings of the 8th International Symposium on Natural Language Processing: 8th International Symposium on Natural Language Processing; 2009
- A Text Mining Approach to the Prediction of Disease Status from Clinical Discharge Summaries
  Yang, H., Spasic, I., Keane, J., Nenadic, G Journal of the American Medical Informatics Association. BMJ Publishing Group; 2009
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- Mining Semantic Descriptions of Bioinformatics Web Resources from the Literature
  Afzal, Hammad; Stevens, Robert; Nenadic, Goran Proceedings of ESWC 2009: The Semantic Web: Research and Applications, 6th European Semantic Web Conference, ESWC 2009. Heraklion, Crete, Greece, . Springer; 2009
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2008
- Combining Lexical Profiling, Rules and Machine Learning for Disease Prediction from Hospital Discharge Summaries
  Yang, H., Spasic, I., Keane, J., Nenadic, G. Proc. of i2b2 Obesity Challenge 2008: i2b2 Obesity Challenge 2008; 2008
- Mining bioinformatics services terminology from literature
  H. Afzal, G.Nenadic MIB Interdisciplinary Research Conference. Manchester; 2008
- Computational Treatment Prediction of Subarachnoid Haemorrhage
  Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A. British Society of Neuroradiologists (BSNR) 2008. Manchester; 2008
- Development of a Language-based Bayesian Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage
  Stivaros, SM., Nenadic, G., Zeng, X., Keane, J., Jackson, A. BSNR 2008. London, UK; 2008
- Towards Terminology Extraction in Serbian
  Nenadic, G., Spasic, I. Formal Description of Slavic Languages. Peter Lang; 2008
- Building and Evaluating Resources for Biomedical Text Mining
  Building and Evaluating Resources for Biomedical Text Mining ; 2008
- Decision support system for treatment planning and outcome prediction in aneurysmal subarachnoid haemorrhage
  Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A. Computer Assisted Radiology and Surgery 2008. Barcelona; 2008
- Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary
  Afzal, H., Stevens, R., Nenadic, G. Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008). Turku, Finland; 2008
- Towards Standardisation of Named Entity Annotations in the Life Science Literature
  Rebholz-Schuhmann, D., Nenadic, G. Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008). Turku, Finland; 2008
- Lexical Profiling of Existing Web Directories to Support Fine-grained Topic-Focused Web Crawling
  Greenwood, M., Nenadic G. Workshop on Corpus Profiling for Information Retrieval and Natural Language Processing. London, UK. BCS; 2008
- Identification of transcription factor contexts in literature using machine learning approaches
  Yang, Hui; Nenadic, Goran; Keane, John A BMC Bioinformatics; 2008
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2007
- A cascaded approach to normalizing gene mentions in biomedical literature
  Yang, H., Nenadic, G., Keane, J. Bioinformation; 2007
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- Identification of transcription factor contexts in literature using machine learning approaches
  Yang, H; Nenadic, G; Keane, J A 2nd International Symposium on Languages in Biology and Medicine: 2nd International Symposium on Languages in Biology and Medicine. Singapore, SINGAPORE. Biomed Central Ltd; 2007
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2006
- Automatic Terminology Management in Biomedicine
  Ananiadou, S., Nenadic, G. Text Mining for Biology and Biomedicine. Artech House Books; 2006
- Towards a terminological resource for biomedical text mining
  Nenadic, G., Okazaki, N., Ananiadou, S. Language Resources and Evaluation 2006. ELRA; 2006
- Annotation and Disambiguation of Semantic Types in Biomedical Text: a Cascaded Approach to Named Entity Recognition
  Rebholz-Schuhmann, D., Kirsch, H., Gaudan, S., Arregui, M., Nenadic, G. NLPXML 2006 (EACL 2006); 2006
- IeXML: towards an annotation framework for biomedical semantic types enabling interoperability of text processing modules
  Rebholz-Schuhmann, D., Kirsch, H., Nenadic, G. Joint BioLINK and Bio-Ontologies SIG Meeting, ISMB 2006; 2006
- Mining Biomedical Terminology from Literature
  Ananiadou, S., Nenadic, G., Mima, H., Tsujii, J. Terminology, Computing and Translation. Gunther Narr Verlag; 2006
- Mining Semantically Related Terms from Biomedical Literature
  Nenadic, G., Ananiadou, S. ACM Transactions on Asian Language Information Processing (TALIP). ACM Transactions on Asian Language Information Processing (TALIP); 2006
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2005
- Mining Biomedical Abstracts: What’s in a Term?
  Nenadic, G., Spasic, I., Ananiadou, S. Lecture Notes in Artificial Intelligence, Vol. 3248: IJCNLP 2004. Springer; 2005
- Mining protein function from text using term-based support vector machines
  Rice, Simon B; Nenadic, Goran; Stapley, Benjamin J BMC Bioinformatics; 2005
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2004
- Exploring Balkanet Shared Ontology for Multilingual Conceptual Indexing
  Stamou, S., Nenadic, G., Christodoulakis, D. Proceedings of LREC 2004, ELRA, pp. 781-784; 2004
- Protein Function Assignment using Term-based Support Vector Machines. BioCreative Task Two 2004
  Rice, S., Nenadic, G., Stapley, B. Workshop on Critical Assessment of Information Extraction systems in Biology (BioCreAtiVe), Granada, Spain; 2004
- Mining Biomedical Abstracts: What’s in a Term?
  Nenadic, Goran; Spasic, Irena; Ananiadou, Sophia IJCNLP: Natural Language Processing - IJCNLP 2004, First International Joint Conference, Hainan Island, China, March 22-24, 2004, Revised Selected Papers. Springer; 2004
- Learning to Classify Biomedical Terms Through Literature Mining and Genetic Algorithms.
  Spasic, Irena; Nenadic, Goran; Ananiadou, Sophia IDEAL: Intelligent Data Engineering and Automated Learning - IDEAL 2004, 5th International Conference, Exeter, UK, August 25-27, 2004, Proceedings. Springer; 2004
- Term identification in the biomedical literature
  Krauthammer, Michael; Nenadic, Goran Journal of Biomedical Informatics; 2004
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- Term Identification in the Biomedical Literature.
  NENADIC G; KRAUTHAMMER M; Journal of Biomedical Informatics. Journal of Biomedical Informatics; 2004
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2003
- Terminology-driven Mining of Biomedical Literature
  Nenadic, Goran; Spasic, Irena; Ananiadou, Sophia SAC: Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), March 9-12, 2003, Melbourne, FL, USA. ACM; 2003
- An Integrated Term-Based Corpus Query System
  Manios, Kostas; Nenadic, Goran; Spasic, Irena; Ananiadou, Sophia EACL; 2003
- Terminology-driven Mining of Biomedical Literature
  Nenadic, Goran; Spasic, Irena; Ananiadou, Sophia Bioinformatics; 2003
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- Terminology-driven Mining of Biomedical Literature.
  NENADIC G; SPASIC I; ANANIADOU S; Bioinformatics. Bioinformatics; 2003
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2002
- Supervised Learning of Term Similarities
  Spasic, Irena; Nenadic, Goran; Manios, Kostas; Ananiadou, Sophia IDEAL: Intelligent Data Engineering and Automated Learning - IDEAL 2002, Third International Conference, Manchester, UK, August 12-14, Proceedings. Springer; 2002
- A Methodology for Terminology-based Knowledge Acquisition and Integration
  Mima, Hideki; Ananiadou, Sophia; Nenadic, Goran; Tsujii, Jun-ichi COLING; 2002
- Terminology-driven literature mining and knowledge acquisition in biomedicine
  Nenadic, Goran; Mima, Hideki; Spasic, Irena; Ananiadou, Sophia; Tsujii, Jun-ichi I. J. Medical Informatics; 2002
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