Journal articles

  • Irena Spasić, Padraig Corcoran, Andrei Gagarin, Andreas Buerki (2018) Head to head: Semantic similarity of multi-word terms. IEEE Access, in press [DOI: 10.1109/ACCESS.2018.2826224] [Web: FlexiTerm]
  • Irena Spasić (2018) Acronyms as an integral part of multi-word term recognition - A token of appreciation. IEEE Access, Vol. 6, pp. 8351-8363 [DOI: 10.1109/ACCESS.2018.2807122] [Web: FlexiTerm]
  • Kate Button, Kevin Nicholas, Monica Busse, Mark Collins, Irena Spasić (2018) Integrating self-management support for knee injuries into routine clinical practice: TRAK intervention design and delivery. Musculoskeletal Science & Practice, Vol. 33, pp. 53-60 [PMID: 29172113] [DOI: 10.1016/j.msksp.2017.11.002]
  • Irena Spasić, Lowri Williams, Andreas Buerki (2017) Idiom-based features in sentiment analysis: Cutting the Gordian knot. IEEE Transactions on Affective Computing, in press [DOI: 10.1109/TAFFC.2017.2777842] [Web: Idioment]
  • Alun Preece, Irena Spasić, Kieran Evans, David Rogers, William Webberley, Colin Roberts, Martin Innes (2017) Sentinel: A co-designed platform for semantic enrichment of social media streams. IEEE Transactions on Computational Social Systems, Vol. 5, No. 1, pp. 118-131 [DOI: 10.1109/TCSS.2017.2763684]
  • Emma Dunphy, Fiona Hamilton, Irena Spasić, Kate Button (2017) Acceptability of a digital health intervention alongside physiotherapy to support patients following anterior cruciate ligament reconstruction. BMC Musculoskeletal Disorders, Vol. 18, 471 [PMID: 29162071] [DOI: 10.1186/s12891-017-1846-0]
  • 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, 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] [Web: Idioment]
  • Irena Spasić, Kate Button, Anna Divoli, Satyam Gupta, Tamas Pataky, Diego Pizzocaro, Alun Preece, Robert van Deursen, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, Douglas 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, Douglas Kell (2013) Searching for kinetic parameters with KiPar. In W. Dubitzky, O. Wolkenhauer, H. Yokota, K.-H. Cho (Eds.): Encyclopedia of Systems Biology, Springer
  • Neil Swainston, Daniel Jameson, Peter Li, Irena Spasić, Pedro Mendes, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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

Books

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

External links