Journal articles

  • Irena Spasić, Bo Zhao, Christopher Jones, Kate Button (2015) KneeTex: An ontology-driven system for information extraction from MRI reports. Journal of Biomedical Semantics, Vol. 6, 34 [PMID: 26347806] [DOI: 10.1186/s13326-015-0033-1] [Web: KneeTex]
  • Lowri Williams, Christian Bannister, Michael Arribas-Ayllon, Alun Preece and Irena Spasić (2015) The role of idioms in sentiment analysis. Expert Systems with Applications, Vol. 42, No. 21, pp. 7375-7385 [DOI: 10.1016/j.eswa.2015.05.039]
  • Irena Spasić, Kate Button, Anna Divoli, Satyam Gupta, Tamas Pataky, Diego Pizzocaro, Alun Preece, Robert van Deursen and Chris Wilson (2015) TRAK application suite: A web-based intervention for delivering standard care for the rehabilitation of knee conditions. JMIR Research Protocols, Vol. 4, No. 4, e122 [PMID: 26474643] [DOI: 10.2196/resprot.4091]
  • Kate Button, Paulien Roos, Irena Spasić, Paul Adamson and Robert van Deursen (2015) The clinical effectiveness of self-care interventions with an exercise component to manage knee conditions: A systematic review. The Knee, pp. 360-371 [PMID: 26056046] [DOI: 10.1016/j.knee.2015.05.003]
  • Irena Spasić, Jacqueline Livsey, John Keane and Goran Nenadić (2014) Text mining of cancer-related information: review of current status and future directions. International Journal of Medical Informatics, Vol. 83, No. 9, pp. 605-623 [PMID: 25008281] [DOI: 10.1016/j.ijmedinf.2014.06.009]
  • Christian Bannister, Craig Currie, Alun Preece and Irena Spasić (2014) Automatic development of clinical prediction models with genetic programming: A case study in cardiovascular disease. Value in Health, Vol. 17, No. 3, pp. A200-A201 [DOI: 10.1016/j.jval.2014.03.1171]
  • Simon Moore, Claire O'Brien, Mohammed Fasihul Alam, David Cohen, Kerenza Hood, Chao Huang, Laurence Moore, Simon Murphy, Rebecca Playle, Vaseekaran Sivarajasingam, Irena Spasić, Anne Williams and Jonathan Shepherd (2014) All-Wales licensed premises intervention (AWLPI): a randomised controlled trial to reduce alcohol-related violence. BMC Public Health, Vol. 14, 21 [PMID: 24405575] [DOI: 10.1186/1471-2458-14-21]
  • Christian Bannister, Chris Poole, Sara Jenkins-Jones, Christopher Morgan, Glyn Elwyn, Irena Spasić and Craig Currie (2014) External validation of the UKPDS risk engine in incident type 2 diabetes: a need for new type 2 diabetes-specific risk equations. Diabetes Care, Vol. 37, No. 2, pp. 537-545 [PMID: 24089541] [DOI: 10.2337/dc13-1159]
  • Irena Spasić, Mark Greenwood, Alun Preece, Nick Francis and Glyn Elwyn (2013) FlexiTerm: A flexible term recognition method. Journal of Biomedical Semantics, Vol. 4, 27 [PMID: 24112363] [DOI: 10.1186/2041-1480-4-27] [Web: FlexiTerm]
  • Kate Button, Robert W. van Deursen, Larisa Soldatova and Irena Spasić (2013) TRAK ontology: Defining standard care for the rehabilitation of knee conditions. Journal of Biomedical Informatics, Vol. 46, No. 4, pp. 615-625 [PMID: 23665300] [DOI: 10.1016/j.jbi.2013.04.009] [BioPortal: 3210] [Web: TRAK]
  • Kieran Smallbone, Hanan Messiha, Kathleen Carroll, Catherine Winder, Naglis Malys, Warwick Dunn, Ettore Murabito, Neil Swainston, Joseph Dada, Farid Khan, Pinar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil Hayes, Daniel Jameson, David Broomhead, Stephen Oliver, Simon Gaskell, John McCarthy, Norman Paton, Hans Westerhoff, Douglas Kell and Pedro Mendes (2013) A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Letters, Vol. 587, No. 17, pp. 2832-2841 [PMID: 23831062] [DOI: 10.1016/j.febslet.2013.06.043]
  • Irena Spasić, Peter Burnap, Mark Greenwood and Michael Arribas-Ayllon (2012) A naive Bayes approach to topic classification in suicide notes. Biomedical Informatics Insights, Vol. 5, Suppl. 1, pp. 87-97 [PMID: 22879764] [DOI: 10.4137/BII.S8945]
  • Peter Li, Joseph Dada, Daniel Jameson, Irena Spasić, Neil Swainston, Kathleen Carroll, Warwick Dunn, Farid Khan, Hanan Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, David Broomhead, Carole Goble, Simon Gaskell, Douglas Kell, Hans Westerhoff, Pedro Mendes and Norman Paton (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics, Vol. 11, 582 [PMID: 21114840] [DOI: 10.1186/1471-2105-11-582]
  • Irena Spasić, Farzaneh Sarafraz, John Keane and Goran Nenadić (2010) Medication information extraction with linguistic pattern matching and semantic rules. Journal of the American Medical Informatics Association, Vol. 17, No. 5, pp. 532-535 [PMID: 20819858] [DOI: 10.1136/jamia.2010.003657]
  • Joseph Dada, Irena Spasić, Norman Paton and Pedro Mendes (2010) SBRML: a markup language for associating systems biology data with models. Bioinformatics, Vol. 26, No. 7, pp. 932-938 [PMID: 20176582] [DOI: 10.1093/bioinformatics/btq069]
  • Irena Spasić, Evangelos Simeonidis, Hanan Messiha, Norman Paton and Douglas Kell (2009) KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics, Vol. 25, No. 11, pp. 1404-1411 [PMID: 19336445] [DOI: 10.1093/bioinformatics/btp175]
  • Hui Yang, Irena Spasić, John Keane and Goran Nenadić (2009) A text mining approach to the prediction of a disease status from clinical discharge summaries. Journal of the American Medical Informatics Association, Vol. 16, No. 4, pp. 596-600 [PMID: 19390098] [DOI: 10.1197/jamia.M3096]
  • Marie Brown, Warwick Dunn, Paul Dobson, Yogendra Patel, Cate Winder, Sue Francis-McIntyre, Paul Begley, Kathleen Carroll, David Broadhurst, Andy Tseng, Neil Swainston, Irena Spasić, Royston Goodacre and Douglas Kell (2009) Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. The Analyst, Vol. 134, No. 7, pp. 1322-1332 [PMID: 19562197] [DOI: 10.1039/b901179j]
  • Markus J. Herrgård, Neil Swainston, Paul Dobson, Warwick B. Dunn, K. Yalçin Arga, Mikko Arvas, Nils Blüthgen, Simon Borger, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Peter Li, Wolfram Liebermeister, Monica L. Mo, Ana Paula Oliveira, Dina Petranović, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasić, Dieter Weichart, Roger Brent, David S. Broomhead, Hans V. Westerhoff, Betül Kirdar, Merja Penttilä, Edda Klipp, Bernhard Ø. Palsson, Uwe Sauer, Stephen G. Oliver, Pedro Mendes, Jens Nielsen and Douglas B. Kell (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, Vol. 26, No. 10, pp. 1155-1160 [PMID: 18846089] [DOI: 10.1038/nbt1492]
  • Irena Spasić, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas Kell and Norman Paton (2008) Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinformatics, Vol. 9, Suppl. 5, S5 [PMID: 18460187] [DOI: 10.1186/1471-2105-9-S5-S5]
  • Warwick Dunn, David Broadhurst, David Ellis, Marie Brown, Anthony Halsall, Steven O'Hagan, Irena Spasić, Andrew Tseng and Douglas Kell (2008) A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols. International Journal of Epidemiology, Vol. 37, pp. i23-i30 [PMID: 18381390] [DOI: 10.1093/ije/dym281]
  • Warwick Dunn, David Broadhurst, Sasalu Deepak, Mamta Buch, Garry McDowell, Irena Spasić, David Ellis, Nicholas Brooks, Douglas Kell and Ludwig Neyses (2007) Serum metabolomics reveals many novel metabolic markers of heart failure, including pseudouridine and 2-oxoglutarate. Metabolomics, Vol. 3, No. 4, pp. 413-426 [DOI: 10.1007/s11306-007-0063-5]
  • Susanna-Assunta Sansone, Daniel Schober, Helen Atherton, Oliver Fiehn, Helen Jenkins, Philippe Rocca-Serra, Denis Rubtsov, Irena Spasić, Larisa Soldatova, Chris Taylor, Andy Tseng, Mark Viant and the Ontology Working Group Members (2007) Metabolomics Standards Initiative - Ontology Working Group: Work in progress. Metabolomics, Vol. 3, No. 3, pp. 249-256 [DOI: 10.1007/s11306-007-0069-z]
  • Irena Spasić, Warwick Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen Oliver and Douglas Kell (2006) MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. BMC Bioinformatics, Vol. 7, 281 [PMID: 16753052] [DOI: 10.1186/1471-2105-7-281]
  • Stephen Wilkinson, Irena Spasić and David Ellis (2006) Genomes to Systems 3. Metabolomics, Vol. 2, No. 3, pp. 165-170 [DOI: 10.1007/s11306-006-0030-6]
  • Irena Spasić, Sophia Ananiadou, John McNaught and Anand Kumar (2005) Text mining and ontologies in biomedicine: making sense of raw text. Briefings in Bioinformatics, Vol. 6, No. 3, pp. 239-251 [PMID: 16212772] [DOI: 10.1093/bib/6.3.239]
  • Douglas Kell, Marie Brown, Hazel Davey, Warwick Dunn, Irena Spasić and Stephen Oliver (2005) Metabolic footprinting and systems biology: the medium is the message. Nature Reviews Microbiology, Vol. 3, No. 7, pp. 557-565 [PMID: 15953932] [DOI: 10.1038/nrmicro1177]
  • Irena Spasić, Sophia Ananiadou and Junichi Tsujii (2005) MaSTerClass: a case-based reasoning system for the classification of biomedical terms. Bioinformatics, Vol. 21, No. 11, pp. 2748-2758 [PMID: 15728115] [DOI: 10.1093/bioinformatics/bti338]
  • Marie Brown, Warwick Dunn, David Ellis, Royston Goodacre, Julia Handl, Joshua Knowles, Steve O'Hagan, Irena Spasić and Douglas Kell (2005) A Metabolome pipeline: from concept to data to knowledge. Metabolomics, Vol. 1, No. 1, pp. 39-51 [DOI: 10.1007/s11306-005-1106-4]
  • Irena Spasić and Sophia Ananiadou (2004) Using automatically learnt verb selectional preferences for classification of biomedical terms. Journal of Biomedical Informatics, Vol. 37, No. 6, pp. 483-497 [PMID: 15542021] [DOI: 10.1016/j.jbi.2004.08.002]
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2004) Mining term similarities from corpora. Terminology, Vol. 10, No. 1, pp. 55-80 [DOI: 10.1075/term.10.1.04nen]
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2003) Terminology-driven mining of biomedical literature. Bioinformatics, Vol. 19, No. 8, pp. 938-943 [PMID: 12761055] [DOI: 10.1093/bioinformatics/btg105]
  • Goran Nenadić, Hideki Mima, Irena Spasić, Sophia Ananiadou and Junichi Tsujii (2002) Terminology-based literature mining and knowledge acquisition in biomedicine. International Journal of Medical Informatics, Vol. 67, No. 1-3, pp. 33-48 [PMID: 12460630] [DOI: 10.1016/S1386-5056(02)00055-2]

Book chapters

  • Irena Spasić and Douglas Kell (2013) Searching for kinetic parameters with KiPar. In W. Dubitzky, O. Wolkenhauer, H. Yokota and K.-H. Cho (Eds.): Encyclopedia of Systems Biology, Springer
  • Neil Swainston, Daniel Jameson, Peter Li, Irena Spasić, Pedro Mendes and Norman Paton (2010) Integrative information management for systems biology. In P. Lambrix and G. Kemp (Eds.): Data Integration in the Life Sciences, LNCS 6254, Springer, pp. 164-178 [DOI: 10.1007/978-3-642-15120-0_13]
  • Marco Masseroli, Norman Paton and Irena Spasić (2010) Search computing and the life sciences. In S. Ceri and M. Brambilla (Eds.): Search Computing Challenges and Directions, LNCS 5950, Springer, pp. 291-306 [DOI: 10.1007/978-3-642-12310-8_15]
  • Goran Nenadić and Irena Spasić (2008) Towards automatic terminology extraction in Serbian. In G. Zybatow et al. (Eds.): Formal Description of Slavic Languages, Peter Lang, Frankfurt/Main
  • Irena Spasić and Sophia Ananiadou (2005) A flexible measure of contextual similarity for biomedical terms. In R. Altman et al. (Eds.): Pacific Symposium on Biocomputing - PSB 2005. World Scientific Publishing Company, Singapore, pp. 197-208 [PMID: 15759626]
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2005) Mining biomedical abstracts: what is in a term?. In K.Y. Su et al. (Eds.): Natural Language Processing - IJCNLP 2004. LNAI 3248, Springer, pp. 797-806
  • Irena Spasić, Goran Nenadić and Sophia Ananiadou (2004) Learning to classify biomedical terms through literature mining and genetic algorithms. In Z.R. Yang et al. (Eds.): Intelligent Data Engineering and Automated Learning - IDEAL 2004. LNCS 3177, Springer, pp. 345-351
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2003) Reducing lexical ambiguity in Serbo-Croatian by using genetic algorithms. In P. Kosta et al. (Eds.): Investigations into Formal Slavic Linguistics. Linguistik International, Peter Lang, Frankfurt, pp. 287-298
  • Irena Spasić, Goran Nenadić, Kostas Manios and Sophia Ananiadou (2002) Supervised learning of term similarities. In Hujun Yin et al. (Eds.): Intelligent Data Engineering and Automated Learning - IDEAL 2002. LNCS 2412, Springer, pp. 429-434
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2002) Term clustering using a corpus-based similarity measure. In P. Sojka et al. (Eds.): Text, Speech and Dialogue - TSD 2002. LNAI 2448, Springer, pp. 151-154
  • Irena Spasić and Gordana Pavlović-Lažetić (2001) Syntactic structures in a sublanguage of Serbian for querying relational databases. In G. Zybatow et al. (Eds.): Current Issues in Formal Slavic Linguistics. Peter Lang, Frankfurt/Main, pp. 478-488
  • Goran Nenadić and Irena Spasić (2000) The recognition and acquisition of compound names from corpora. In D. Christodoulakis (Ed.): Natural Language Processing - NLP 2000. LNAI 1835, Springer, pp.38-48
  • Goran Nenadić and Irena Spasić (1999) The acquisition of some lexical constraints from corpora. In V. Matousek et al. (Eds.): Text, Speech and Dialogue - TSD 1999. LNAI 1692, Springer, pp. 115-120

Conference papers

  • Xiangfeng Dai, Irena Spasić and Frédéric Andrès (2017) A framework for automated rating of online reviews against the underlying topics, in Proceedings of the Annual ACM Southeast Conference, Kennesaw State University, Georgia, USA, pp. 164-167
  • Steven Neale, Irena Spasić, Jennifer Needs, Gareth Watkins, Steve Morris, Tess Fitzpatrick, L Marshall and Dawn Knight (2017) The CorCenCC crowdsourcing app: A bespoke tool for the user-driven creation of the national corpus of contemporary Welsh, in Proceedings of the 9th International Corpus Linguistics Conference, Birmingham, UK
  • Kieran Evans, Andrew Jones, Alun Preece, Francisco Quevedo, David Rogers, Irena Spasić, Ian Taylor, Vlado Stankovski, Salman Taherizadeh, Jernej Trnkoczy, George Suciu, Victor Suciu, Paul Martin, Junchao Wang and Zhiming Zhao (2015) Dynamically reconfigurable workflows for time-critical applications, in Proceedings of the 10th Workshop on Workflows in Support of Large-Scale Science, Austin, Texas, USA
  • Lakhveer Bhachu, Larisa Soldatova, Irena Spasić and Kate Button (2014) Mobile application KneeCare to support knee rehabilitation, Science and Information Conference, London, UK
  • Mark Greenwood, Glyn Elwyn, Nick Francis, Alun Preece and Irena Spasić (2013) Automatic extraction of personal experiences from patients' blogs: A case study in chronic obstructive pulmonary disease, Third International Conference on Social Computing and its Applications, Karlsruhe, Germany, pp. 377-382
  • Peter Burnap, Irena Spasić, W. Alex Gray, Jeremy Hilton, Omer Rana and Glyn Elwyn (2012) Protecting patient privacy in distributed collaborative healthcare environments by retaining access control of shared information, in Proceedings of 14th International Conference on Collaboration Technologies and Systems, Denver, Colorado, USA, pp. 490-497 [Springer best paper runner up]
  • Hui Yang, Irena Spasić, John Keane and Goran Nenadić (2008) Combining lexical profiling, rules and machine learning for disease prediction from hospital discharge summaries, in Proceedings of 2nd i2b2 Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data, Washington DC, USA
  • Irena Spasić, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas Kell, Norman Paton and the Ontology Working Group Members (2007) Facilitating the development of controlled vocabularies for metabolomics with text mining, in ISMB/ECCB Special Interest Group (SIG) Meeting Program Materials, Bio-Ontologies SIG Workshop, Vienna, Austria, pp. 103-106
  • Goran Nenadić, Simon Rice, Irena Spasić, Sophia Ananiadou and Benjamin Stapley (2003) Selecting text features for gene name classification: from documents to terms, in Proceedings of ACL Workshop on Natural Language Processing in Biomedicine, Sapporo, Japan, pp. 121-128
  • Irena Spasić, Goran Nenadić and Sophia Ananiadou (2003) Using domain-specific verbs for term classification, in Proceedings of ACL Workshop on Natural Language Processing in Biomedicine, Sapporo, Japan, pp. 17-24
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2003) Morpho-syntactic clues for terminological processing in Serbian, in Proceedings of EACL Workshop on Morphological Processing of Slavic Languages, Budapest, Hungary, pp. 79-86
  • Irena Spasić, Goran Nenadić, Kostas Manios and Sophia Ananiadou (2003) An integrated term-based corpus query system, in Proceedings of 10th Conference of the European Chapter of the Association for Computational Linguistics, Budapest, Hungary, pp. 243-250
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2003) Terminology-driven mining of biomedical literature, in Proceedings of 18th Annual ACM Symposium on Applied Computing, Melbourne, Florida, USA
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2002) Automatic discovery of term similarities using pattern mining, in Proceedings of Second International Workshop on Computational Terminology - CompuTerm 2002, Taipei, Taiwan, pp. 43-49
  • Sophia Ananiadou, Goran Nenadić, Dietrich Schuhmann and Irena Spasić (2002) Term-based literature mining from biomedical texts, ISMB Text Data Mining SIG, Edmonton, Canada
  • Irena Spasić, Goran Nenadić and Sophia Ananiadou (2002) Tuning context features with genetic algorithms, in Proceedings of 3rd International Conference on Language, Resources and Evaluation, Las Palmas, Spain, pp. 2048-2054
  • Goran Nenadić, Irena Spasić and Sophia Ananiadou (2002) Automatic acronym acquisition and management within domain-specific texts, in Proceedings of 3rd International Conference on Language, Resources and Evaluation, Las Palmas, Spain, pp. 2155-2162
  • Irena Spasić, Goran Nenadić and Sophia Ananiadou (2002) A genetic algorithm approach to unsupervised learning of context features, in Proceedings of 5th National Colloquium for Computational Linguistics in the UK, Leeds, UK, pp. 12-19
  • Dubravka Pavličić and Irena Spasić (2001) The effects of irrelevant alternatives on the results of the TOPSIS method, in Proceedings of XXVIII Yugoslav Symposium on Operational Research SYM-OP-IS 2001, Belgrade, Serbia
  • Irena Spasić and Gordana Pavlović-Lažetić (2001) Object-oriented modelling in natural language communication with a relational database, in Selected Papers from 10th Congress of Yugoslav Mathematicians, Belgrade, Serbia, pp. 343-347
  • Olgica Bošković and Irena Spasić (1999) Graph theory and log-linear models, in Proceedings of XXVI Yugoslav Symposium on Operational Research SYM-OP-IS, Belgrade, Serbia
  • Irena Spasić (1996) Automatic foreign words recognition in a Serbian scientific or technical text, in Proceedings of Conference on Standardization of Terminology, Serbian Academy of Arts and Sciences, Belgrade, Serbia

Books

  • Irena Spasić and Predrag Janičić (2000) Theory of Algorithms, Languages and Automata. Faculty of Mathematics, Belgrade, Serbia
  • Miodrag Ivović, Branislav Boričić, Dragan Azdejković and Irena Spasić (1998) Practice Book in Mathematics. Faculty of Economics, Belgrade, Serbia
  • Miodrag Ivović, Branislav Boričić, Velimir Pavlović, Dragan Azdejković and Irena Spasić (1996) Mathematics through Examples and Exercises with Elements of Theory. Faculty of Economics, Belgrade, Serbia

External links