Publications

Journals and International Conferences

Aitken S., Kilpatrick, A.M. and Akman O.E. (2015) Dizzy-Beats: a Bayesian Evidence analysis tool for systems biology Bioinformatics doi: 10.1093/bioinformatics/btv062

Aitken S. and Akman O.E. (2013) Nested sampling for parameter inference in systems biology: application to an exemplar circadian model. BMC Syst Biol. 7:72. doi: 10.1186/1752-0509-7-72.

Kilpatrick A.M., Ward B., Aitken S. (2013) MCOIN: a novel heuristic for determining transcription factor binding site motif width. Algorithms Mol Biol. 8(1):16. doi: 10.1186/1748-7188-8-16

Aitken S., Alexander R.D., Beggs J.D. (2013) A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation. J R Soc Interface 10(86):20130438 doi: 10.1098/rsif.2013.0438

De Ferrari, L., Aitken, S., van Hemert, J. and Goryanin, I. (2012) EnzML: Multi-label prediction of enzyme classes using InterPro signatures. BMC Bioinformatics 13:61. doi:10.1186/1471-2105-13-61

Aitken, S., Alexander, D.A. and Beggs, J.D. (2011) Modelling reveals kinetic advantages of co-transcriptional splicing. PLoS Computational Biology 7(10): e1002215. doi:10.1371/journal.pcbi.1002215

Schmidt, U., Basyuk, E., Robert, M-C., Yoshida, M., Villemin, J-P., Auboeuf, D., Aitken, S. and Bertrand, E. (2011) Real-time imaging of co-transcriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. Journal of Cell Biology 193(5): 819. doi:10.1083/jcb.201009012

Daly,R., Shen,Q. and Aitken,S. (2011) Learning Bayesian Networks: Approaches and Issues. The Knowledge Engineering Review 26:2 99-127. doi: 10.1017/S0269888910000251

Tirmizi, S. H., Aitken, S., Moreira, D. A., Mungall, C., Sequeda, J., Shah, N. H. and Miranker, D. P. (2011) Mapping between the OBO and OWL ontology languages. Journal of Biomedical Semantics 2 (Suppl):S3. doi:10.1186/2041-1480-2-S1-S3

Aitken, S., Robert, M-C., Alexander, D.A., Goryanin, I., Bertrand, E. and Beggs, J. D. (2010) Processivity and coupling in messenger RNA transcription. PLoS ONE 5(1): e8845. doi:10.1371/journal.pone.0008845

Aitken, S., Dang, K. and Bard, J. (2009) On the Design of BioSphere: A Grid Portal for Collaborative Ontology Creation. Proc. International Workshop on Portals for the Life Sciences (IWPLS), September 2009.

Daly, R., Edwards, K.D., O ' Neill, J.S., Aitken, S., Millar, A.J. and Girolami, M. (2009) Using higher-order dynamic Bayesian networks to model periodic data from the circadian clock of Arabidopsis Thaliana. Proc. Fourth IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2009), Lecture Notes in Bioinformatics, vol. 5780:67-78. on-line article

De Ferrari, L., Aitken, S., van Hemert, J. and Igor Goryanin (2009) A model of social collaboration in Molecular Biology knowledge bases. Proc. 6th Conference of the European Social Simulation Association (ESSA) September 2009. on-line article

Moreira, D.A., Mungall, C.J., Shah, N.H., Aitken, S., Richter, J.-D., Redmond, T. and Musen, M.A. (2009) The NCBO OBOF to OWL Mapping. Article available from Nature Precedings

Bard J.B., Lam M.S., and Aitken, S. (2008) A bioinformatics approach for identifying candidate transcriptional regulators of mesenchyme-to-epithelium transitions in mouse embryos. . Developmental Dynamics Vol. 237 (10) :2748-2754. on-line abstract.

Aitken, S., Chen, Y. and Bard J. (2008) OBO Explorer: An Editor for Open Biomedical Ontologies in OWL Bioinformatics 24(3):443-444; doi:10.1093/bioinformatics/btm593

Aitken, S. and Chen, Y. (2008) COBrA and COBrA-CT: Ontology engineering tools In Anatomy Ontologies for Bioinformatics Principles and Practice Burger, A., Davidson, D. and Baldock, R. (Eds.) Springer ISBN: 978-1-84628-884-5.

Aitken, S., Chen, Y., Webber, B., Fan, W. and Bard J. (2007) Managing the transition from OBO to OWL: The COBrA-CT Bio-Ontology Tools. Proc. UK e-Science All-Hands Meeting 2007 :94-101. on-line article

De Ferrari, L. and Aitken, S. (2006) Mining housekeeping genes with a Naive Bayes classifier. BMC Genomics 7:277 doi:10.1186/1471-2164-7-277

Daly, R., Shen, Q., and Aitken, S. (2006). Speeding up the learning of equivalence classes of Bayesian network structures. In A. P. del Pobil (Ed.), Proceedings of the Tenth IASTED International Conference on Artificial Intelligence and Soft Computing, (pages 34-39). ACTA Press.

Daly, R., Shen, Q. and Aitken, S. (2006) Using ant colony optimisation in learning Bayesian network equivalence classes. Proceedings of the 2006 UK Workshop on Computational Intelligence:111-118.

Jirapech-Umpai, T. and Aitken, S. (2005) Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes. BMC Bioinformatics 6:148 doi:10.1186/1471-2105-6-148

Aitken, S. (2005) Formalising concepts of species, sex and developmental stage in anatomical ontologies. Bioinformatics. 21(11):2773-2779; doi:10.1093/bioinformatics/bti409

Aitken, S., Korf, R., Webber, B. and Bard, J. (2005) COBrA: A Bio-Ontology Editor. Bioinformatics. 21(6):825-826; doi: 10.1093/bioinformatics/bti097

Potter S. and Aitken S. (2005) A Semantic Service Environment: A Case Study in Bioinformatics. Proceedings European Semantic Web Conference 2005. doi: 10.1007/b136731

Aitken S. (2005) An ontological account of action in processes and plans. Knowledge-Based Systems 18 (6) :295-305. doi:10.1016/j.knosys.2005.04.001

Parkinson, H., Aitken, S., Baldock, R.A, Bard, J.B.L., Burger, A., Hayamizu, T.F., Rector, A., Ringwald, M., Rogers, J., Rosse, C., Stoeckert Jr, C.J. and Davidson, D.(2005) The SOFG anatomy entry list (SAEL): an annotation tool for functional genomics data. Comparative and Functional Genomics Volume 5, Issue 6-7, 2004 :521-527. doi: 10.1002/cfg.434

Atkinson, J., Mellish, C. and Aitken, S. (2004) Combining Information Extraction with Genetic Algorithms for Text Mining IEEE Intelligent Systems 19 (3) :22-30. on-line abstract

Aitken, J.S., Webber, B.L. and Bard J.B.L. (2004) Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations. Pacific Symposium on Biocomputing 9 Big Island, Hawaii, January 6-10 2004 :166-177. on-line article ( local copy )

Atkinson, J., Mellish, C. and Aitken, S. (2003) A Semantically-Guided and Domain-Independent Evolutionary Model for Knowledge Discovery from Texts. IEEE Transactions on Evolutionary Computation December 2003, Vol 7, No. 6 pp.546-560. 10.1109/TEVC.2003.819262

Aitken, S. and Curtis, J. (2002) A Process Ontology Proceedings of the 13th International Conference on Knowledge Engineering and Knowledge Management (EKAW 02), ed. Gómez-Pérez, A., Springer Verlag :108-113. on-line article

Aitken, J.S. (2002) Learning Information Extraction Rules: An Inductive Logic Programming approach Proceedings of the 15th European Conference on Artificial Intelligence Ed. van Harmelen, F., IOS Press, Amsterdam. on-line article

Aitken, S. and Melham, T. (2000) An Analysis of Errors in Interactive Proof Attempts. Interacting with Computers, 12 (6) :565-586.

Wheeler, R. and Aitken, S. (2000) Multiple Algorithms for Fraud Detection. Knowledge-Based Systems Journal, 13 (2-3) :93-99. doi: 10.1016/S0950-7051(00)00050-2

Aitken, J.S., and Sklavakis, D. (1999) Integrating Problem-Solving Methods into Cyc. Proceedings of the 16th International Joint Conference on Artificial Intelligence, ed. Dean, T., Stockholm, 3-6th August 1999, Morgan Kaufmann. on-line article

Aitken, J.S., Gray, P., Melham, T., and Thomas, M. (1998) Interactive Theorem Proving: An Empirical Study of User Activity. Journal of Symbolic Computation, 25 :263-284. on-line article

Abecker, A., Aitken, S., Schmalhofer, F., and Tschaitschian, B. (1998) KARATEKIT: Tools for the Knowledge-Creating Company. Proceedings of the Eleventh Workshop on Knowledge Acquisition, Modeling and Management, KAW 98,Banff, Canada, 1998.

Aitken, J.S. (1996) Problem Solving in Interactive Proof: A Knowledge-Modelling Approach. Proceedings of the 12th European Conference on Artificial Intelligence, ed. Wahlster, W., Budapest, 11-16th August 1996, John Wiley & Sons, pp. 335-339. on-line article

Aitken, J.S., Schmalhofer, F., and Shadbolt, N. (1995) A Knowledge Level Analysis of Multi-Agent Systems. Lecture Notes in Artificial Intelligence No. 890, Springer Verlag :179-190. Proceedings of the ECAI '94 workshop on Agent Theories, Architectures and Languages.

Schmalhofer, F., Aitken, J.S., and Bourne, L.E. (1994) Beyond the Knowledge Level: Descriptions of Rational Behaviour for Sharing and Reuse. Lecture Notes in Artificial Intelligence No. 867 :83-103. Proceedings of the European Knowledge Acquisition Workshop 1994.

Aitken, J.S., Reichgelt, H.R., and Shadbolt, N. (1994) Resolution Theorem Proving in Reified Modal Logics. Journal of Automated Reasoning 12 (1) :109-136. on-line abstract

Aitken, J.S. and Shadbolt, N. (1993) Knowledge Level Planning. InCurrent Trends in AI planning Eds. Bäckström, C. and Sandewall, E., IOS Press, Proceedings of the European Scheduling and Planning Workshop 1993.

Anderson, K., Aitken, S., Macleod, J.E.S., and Moran, F. (1990) Variation of Breath Sound and Airway Calibre Induced by Histamine Challenge. American Review of Respiratory Disease 141 :1147-1150. on-line abstract

Aitken, S., Anderson, K., Macleod, J.E.S., and Moran, F. (1989) The Correlation of Breath Sound Power Spectrum and FEV1. Original Investigations (abstracts) Proceedings XVI World Congress of Diseases of the Chest, Boston, October 30th-3rd November 1989, pp. 258S.

Anderson, K., Aitken, S., Macleod, J.E.S., and Moran, F. (1988) Lung Sound Transmission and Reliability of Chest Signs. Lancet 1988, Vol. 2 :228. doi:10.1016/S0140-6736(88)92343-4

Refereed Workshop Proceedings and Poster Abstracts (Selected)

Aitken, S. (2009) Grid technology for collaborative ontology development. Article in the OMII Newsletter, March 2009

Aitken, S. Dang, K. and Bard, J. (2009) Grid technology for collaborative ontology development. 3rd International Biocuration Conference Poster available from Nature Precedings http://dx.doi.org/10.1038/npre.2009.3186.1

Aitken, S. and Bard J. (2008) Ontology views for collaborative ontology creation: The BioSphere Portal. Proc. UK e-Science All-Hands Meeting September 2008. on-line presentation

Aitken, S., Chen, Y., Webber, B., Fan, W. and Bard, J. (2007) Bio-ontologies in OWL: Editing, sharing and curating. Poster ISMB 2007 on-line poster

Aitken, S., Jirapech-Umpai, T. and Daly, R. (2005) Inferring gene regulatory networks from classified microarray data:Initial results BioSysBio 05 Edinburgh 2005 www.biomedcentral.com/1471-2105/6/S3/S4

Luger, S., Aitken, S. and Webber, B. (2005) Automated Terminological and Structural Analysis of Human-Mouse Anatomical Ontology Mappings BioSysBio 05 Edinburgh 2005 www.biomedcentral.com/1471-2105/6/S3/P19

Luger, S., Aitken, S. and Webber, B. (2005) Human-Mouse Anatomical Ontology Mapping: Terminological and Structural Support. (Poster) ISMB 05 Michigan 2005

Luger, S., Aitken, S. (2004) Cross-species Mapping between Anatomical Ontologies Based on Lexico-syntactic Properties (Poster) ISMB 04 July 31 - August 4 2004, Glasgow

Luger, S., Aitken, S. and Webber B. (2004) Cross-species Mapping between Anatomical Ontologies: Terminological and Structural Support Bio-Ontology Workshop 30 July 2004 ISMB 04, Glasgow on-line poster

Aitken, S. (2003) A Cross-Species Anatomy Resource XSPAN: Models of Anatomy in the Gene Ontology. International Conference on Bioinformatics (Abstracts), Penang, Malaysia, 8-10 September 2003 on-line article

Atkinson-Abutridy, J., Mellish, C. and Aitken, S. (2002) An Evolutionary Genre-Based and Domain-Independent Approach for High-Level Knowledge Discovery from Texts. AAAI Spring Symposium Technical Report SS-02-06, Harabagiu, S.M. and Chaudhri, V. (eds.)

Potter, S. and Aitken, S. (2001) An Expert System for Evaluating the Knowledge Potential of Databases. The 21st SGES International Conference on Knowledge Based Systems and Applied Artificial Intelligence. on-line article

Aitken, S. and Reid, S. (2000) Evaluation of an Ontology-Based Information Retrieval Tool Workshop on the Applications of Ontologies and Problem-Solving Methods, (eds) Gómez-Pérez, A., Benjamins, V.R., Guarino, N., and Uschold, M. European Conference on Artificial Intelligence 2000, Berlin. on-line article

Aitken, S. (1998) Extending the HPKB-Upper-Level Ontology: Experiences and observations. Workshop on the Applications of Ontologies and Problem-Solving Methods, (eds) Gómez-Pérez, A. and Benjamins, V.R., European Conference on Artificial Intelligence 1998, Brighton, August 24-25 :11-15. on-line article

Aitken, J.S. and Gray, P. (1997) Providing Relevant Feedback by Critiquing. Proceedings of User Interface Design for Theorem Provers, 1997, Yves Bertot (ed), Sophia-Antipolis, September 1997 :1-8.

Aitken, J.S., Gray, P., Melham, T., and Thomas, M. (1996) Phases, Modes and Information Flow in Theory Development. Proceedings of User Interface Design for Theorem Provers, 1996, Nicholas Merriam (ed), York, July 1996 :1-8.

Aitken, J.S., Bourne, L.E., and Schmalhofer, F. (1994) Descriptions of Rational Behaviour for Sharing and Reuse: The Sisyphus Task. Proceedings of the 4th KADS Users Meeting, GMD, Bonn, 24-25th March 1994, Arbeitspapier der GMD 832.

Aitken, S., Kühn, O., Shadbolt, N., and Schmalhofer, F. (1993) A conceptual model of hierarchical skeletal planning and its formalisation. Proceedings of the 3rd KADS Users Meeting, Siemens AG, München, 8-9th March 1993 :229-247.

Technical Reports

Wheeler, R. and Aitken, S. (1998) An Investigation into Adaptive Fraud Risk Assessment. Technical Report, AIAI, University of Edinburgh, 131.2/Phase 2/report1.0, August 1998.

Aitken, S. A Survey of Artificial Intelligence Techniques in Finance. (1998) Technical Report, AIAI, University of Edinburgh, Inst-Dev-CBR/report/1 Version 1, August 1998.

Polyak, S. and Aitken, S. (1998) Technical Report, AIAI, University of Edinburgh, Manufacturing Process Interoperability Scenario. AIAI-PR-68, April 1998.

Aitken, S. and Tate, A. (1997) Process Modelling of the TIE 97-1 Demonstration: Modelling Complex Technologies Using ACP Terminology. Technical Report, AIAI, University of Edinburgh, ISAT-AIAI/TR/6, December 1997.

Aitken, S. Gray, P., Melham, T., and Thomas, M. (1997) ITP Project Anthology. Technical Report, Department of Computing Science, University of Glasgow, TR-1997-36, November 1997.

Aitken, S. (1996) An Analysis of Errors in Interactive Proof Attempts. Technical Report, Department of Computing Science, University of Glasgow, TR-1996-27, August 1996.