Nano Systems Biology
  1. Background
  2. Contact
  3. Publications

Professor Werner Dubitzky

Professor of Bioinformatics

Academic and Professional Qualifications

- 1991: MSc Electrical Engineering, FH Augsburg, Augsburg, Germany
- 1997: PhD Artificial Intelligence, University of Ulster

Career History

- Professor of Bioinformatics, University of Ulster
- Head of Data Mining Group, German Cancer Research Center
- Lecturer, University of Ulster
- Research Fellow, University of Ulster

Short Biography

I was awarded an MSc in electrical and communication engineering from the Augsburg University of Applied Science, Germany, in 1991 and a Ph.D. in artificial intelligence and machine learning from the University of Ulster, Northern Ireland, UK, in 1997.

From January 2000 to December 2001 I spearheaded the data mining developments at the Intelligent Bioinformatics Systems Group at the German Cancer Research Center, Heidelberg, Germany. Since 2002 I hold the Chair of Bioinformatics at the Biomedical Sciences Research Institute, Faculty of Life and Health Science, at the University of Ulster at Coleraine, Northern Ireland, UK.

You find a detailed curriculum vitae here

Teaching & Learning Activities

MSc in Systems Biology (100% online course)

Apply here:

This course is designed for students and researchers with a life science background wanting to learn more about the formal concepts and tools facilitating the modeling, analysis and simulation of biological systems.

Aims/audience: Equip learners with conceptual and practical knowledge of the methods and tools of systems biology. Emphasis is placed on solving concrete problems based on the programming language R. No prior programming knowledge is required, as R programming is fully covered in the course.

Content/structure: The MSc consists of 8 taught modules (15 credit points each) plus a research project worth 60 credit points. It is also possible to exit with a PgCert award after completion of 4 modules and a PgDip award after eight modules.

Content delivery: Fully online. Each module is assessed 100% by coursework/assignments (online discussions, coursework, essays, etc.). There is no requirement to be on campus.

Registration: In principle, registration is open untilSeptember 2014. If you make sure to get a place, it is better to apply sooner. If in doubt, please contact me.,

Contact: Professor Werner Dubitzky.
- Email:
- Phone: +44 7739 723 424 (mobile, WhatsApp)
- Phone: +44 28 70124478 (office)
- Skype: grobgestein

Prospectus: Formal details (including fees) are found in the Ulster Prospectus.

Course Leaflet: (PDF)

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Research Activities and Interests

Call for papers for special issue in Briefings in Bioinformatics on Computational Systems Biomedicine. Call for papers: PDF

Call for papers for special issue in Computation (open access journal) on Multiscale Modeling and Simulation in Computational Biology. Notice, manuscripts will be published in the journal’s regular issues as soon as they are accepted by the peer-review process. More

My current research interests are in the area of multiscale modelling and simulation in biology (see the MAPPER project) and reverse-engineering of gene-regulation network models. A main challenge in reverse-engineering is the inference of reliable mechanistic network structure (as opposed to producing a good dynamic response to new input data) from gene expression data.

I have published my Google Scholar citations here


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Professor Werner Dubitzky


Professor Werner Dubitzky - Publications

Number of items: 47.

Alexandru, Mizeranschi, Zheng, Huiru, Thompson, Paul and Dubitzky, Werner (2015) Evaluating a common semi-mechanistic mathematical model of gene-regulatory networks. BMC Systems Biology 2015, 9(Supp (S2).

Mizeranschi, Alexandru, Zheng, Huiru, Thompson, Paul and Dubitzky, Werner (2014) A multi-model reverse-engineering algorithm for large gene regulation networks. In: The IEEE International Conference on Bioinformatics and Biomedicine 2014 (BIBM 2014), Belfast, UK. IEEE. 510-514

Mizeranschi, Alexandru, Kennedy, Noel, Zheng, Huiru, Thompson, Paul and Dubitzky, Werner (2014) Automated reverse-engineering of gene regulatory networks based on semi-mechanistic rate laws. In: The 5th International Workshop on Integrative Data Analysis in Systems Biology, Belfast, UK. IEEE. 1-8

Zheng, Huiru, Dubitzky, Werner, Hu, Xiaohua, Hao,, Jin-Kao, Berrar, Daniel P., Cho, Kwang-Hyun, Wang, Yadong and Gilbert, David R. Gilbert:, eds. (2014) Proceedings of 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014). 612 pp. IEEE Computer Society. ISBN ISBN 978-1-4799-5669-2

Borgdorff, J., Belgacem, M.B., Bona-Casas, C., Fazendeiro, L., Groen, D., Hoenen, O., Mizeranschi, A., Suter, J.L., Coster, D., Coveney, P.V., Dubitzky, Werner, Hoekstra, A.G., Strand, P. and Chopard, B. (2014) Performance of distributed multiscale simulations. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 372 (221).

Gao, Jean X. and Dubitzky, Werner (2014) Data mining in bioinformatics, biomedicine, and healthcare informatics.

Mizeranschi, Alexandru, Kennedy, Noel, Thompson, Paul, Zheng, Huiru and Dubitzky, Werner (2014) The influence of network topology on reverse-engineering of gene-regulatory networks. In: International Conference on Computational Science (ICCS 2014), Cairns, Australia. Elsevier. 410-421

Dubitzky, Werner, Wolkenhauer, Olaf, Yokota, Hiroki and Cho, Kwang-Hyun, eds. (2013) Encyclopedia of systems biology. 2367 pp. Springer. ISBN 978-1-4419-9862-0

Mizeranschi, Alexandru, Thompson, Paul, Zheng, Huiru and Dubitzky, Werner (2013) Reverse-engineering of gene regulation models from multi-condition experiments. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Singapore. IEEE. 112-119

Kennedy, Noel, Mizeranschi, Alexandru, Thompson, Paul, Zheng, Huiru and Dubitzky, Werner (2013) Reverse engineering of gene regulation models from multi-condition experiments. In: Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2013 IEEE Symposium on. IEEE. 112-119

Wang, Chong, Beyerlein, Peter, Pospisil, Heike, Krause, Antje, Nugent, Chris D and Dubitzky, W (2012) An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,, 9 (1). pp. 40-51.

Dubitzky, Werner, Kötter, Tobias, Schmidt, Oliver and Berthold, Michael (2012) Towards creative information exploration based on Koestler's concept of bisociation. In: Bisociative Knowledge Discovery. Springer, pp. 11-32. ISBN 978-3-642-31829-0

Schmidt, Oliver, Kranjc, Janez, Mozetic, Igor, Thompson, Paul and Dubitzky, Werner (2012) Bisociative exploration of biological and financial literature with using clustering. In: Bisociative Knowledge Discovery. Springer, pp. 438-451. ISBN 978-3-642-31829-0

Kennedy, Noel, Thompson, Paul, Zheng, HR and Dubitzky, Werner (2011) Multi-scale modelling of the bile acid and xenobiotic system,. In: Int’l Conference on Bioinformatics and Computational Biology, Las Vegas, USA. Worldcomp. 499-505

Dubitzky, Werner (2011) Toward a system-centric global knowledge management approach to discovering (organizing and sharing) scientific knowledge from large-scale data. OMICS: A Journal of Integrative Biology, 15 (4). pp. 243-246.

Dubitzky, Werner (2011) Challenges in bioinformatics and computational biology.

Swain, Martin, Coti, Camille, Mandel, Johannes and Dubitzky, Werner (2011) A topology-aware evolutionary algorithm for reverse-engineering gene regulatory networks. In: Large-scale computing techniques for complex system simulations. Wiley-VCH, pp. 141-162. ISBN 978-0-470-59244-1

Dubitzky, Werner, Krzysztof, Kurowski and Schott, Bernhard, eds. (2011) Large-scale computing techniques for complex system simulations. 220 pp. Wiley-IEEE Computer Society Press. ISBN 978-0-470-59244-1

Dubitzky, Werner, Southgate, Jannifer and Fuss, Hendrik, eds. (2011) Understanding the dynamics of biological systems: Lessons learned from integrative systems biology. 238 pp. Springer. ISBN 978-1-4419-7963-6

Swain, Martin T, Mandel, Johannes J and Dubitzky, Werner (2010) Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks. BMC Bioinformatics, 11 (459).

Swain, Martin, Silva, Cândida, Loureiro-Ferreira, Nuno, Ostropytskyy, Vitaliy, Brito, João, Riche, Olivier, Stahl, Frederick, Dubitzky, Werner and Brito, Rui M M (2010) P-found: Grid-enabling distributed repositories of protein folding and unfolding simulations for data mining. Future Generation Computer Systems, 26 (3). pp. 424-433.

Hill, T. R., Cotter, A. A., Mitchell, S., Boreham, C. A., Dubitzky, W, Murray, L., Strain, JJ, Flynn, A., Robson, P. J., Wallace, Julie, Kiely, M. and Cashman, K. D. (2010) Vitamin D status and parathyroid hormone relationship in adolescents and its association with bone health parameters: analysis of the Northern Ireland Young Heart’s Project. Osteoporosis International, 21 (4). pp. 695-700.

Krzystof, Kurowski, De Back, Walter, Dubitzky, Werner, Gulyás, Laszlo, Kampis, George, Mamonski, Mariusz, Szemes, Gabor and Martin, Swain (2009) Complex system simulations with QosCosGrid. In: Int’l Conference on Computational Science 2009, Baton Rouge, LA, USA. Springer. Vol 5544 387-396

Stankovski, Vlado, Trnkoczy, Jernej, Swain, Martin, Dubitzky, Werner, Kravtsov, Valentin, Schuster, Assaf, Niessen, Thomas, Wegener, Dennis, May, Michael, Röhm, Matthias and Franke, Jürgen (2008) Digging Deep into the Data Mine with DataMiningGrid. IEEE INTERNET COMPUTING, 12 (6). pp. 69-76.

Hill, Tom R., Cotter, Alice A., Mitchell, Sarah, Boreham, Colin A., Dubitzky, W, Murray, Liam, Strain, JJ, Flynn, Albert, Robson, Paula J., Wallace, Julie, Kiely, Mairead and Cashman, Kevin D. (2008) Vitamin D status and its determinants in adolescents from the Northern Ireland Young Hearts 2000 cohort. BRITISH JOURNAL OF NUTRITION, 99 (5). pp. 1061-1067.

Cashman, Kevin D., Hill, Tom R., Cotter, Alice A., Boreham, Colin A., Dubitzky, Werner, Murray, Liam, Strain, JJ, Flynn, Albert, Robson, Paula J., Wallace, Julie and Kiely, Mairead (2008) Low vitamin D status adversely affects bone health parameters in adolescents. American Journal of Clinical Nutrition, 87 (4). pp. 1039-1044.

Stankovski, Vlado, Swain, Martin, Kravtsov, Valentin, Niessen, Thomas, Wegener, Dennis, Kindermann, Joerg and Dubitzky, Werner (2008) Grid-enabling data mining applications with DataMiningGrid: An architectural perspective. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING THEORY METHODS AND APPLICATIONS, 24 (4). pp. 259-279.

Fuss, Hendrik, Dubitzky, Werner, Downes, Stephen and Kurth, Mary Jo (2008) Src family kinases and receptors: Analysis of three activation mechanisms by dynamic systems modeling. BIOPHYSICAL JOURNAL, 94 (6). pp. 1995-2006.

Wang, C, Beyerlein, P, Hammer, P, Krause, A, Nugent, C and Dubitzky, Werner (2008) Allosteric Interaction of Rapid Delayed Rectifier Protein and Its Role in Cardiac Repolarization. In: COMPUTERS IN CARDIOLOGY 2008, VOLS 1 AND 2, Bologna, Italy. . 589-592

Fuss, Hendrik, Dubitzky, Werner, Downes, Stephen and Kurth, Mary Jo (2007) Deactivation of src family kinases: Hypothesis testing using a Monte Carlo sensitivity analysis of systems-level properties. JOURNAL OF COMPUTATIONAL BIOLOGY, 14 (9). pp. 1185-1200.

Gilbert, David, Fuss, Hendrik, Gu, Xu, Orton, Richard, Robinson, Steve, Vyshemirsky, Vladislav, Kurth, Mary Jo, Downes, Stephen and Dubitzky, Werner (2006) Computational methodologies for modelling, analysis and simulation of signalling networks. BRIEFINGS IN BIOINFORMATICS, 7 (4). pp. 339-353.

Dubitzky, Werner, Berrar, Daniel and Hack, Catherine (2006) Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics, 7. pp. 373.

Fuss, Hendrik, Dubitzky, Werner, Downes, Stephen and Kurth, Mary Jo (2006) Bistable switching and excitable behaviour in the activation of Src at mitosis. BIOINFORMATICS, 22 (14). pp. E158-E165.

Berrar, D, Bradbury, I and Dubitzky, Werner (2006) Avoiding model selection bias in small-sample genomic datasets. BIOINFORMATICS, 22 (10). pp. 1245-1250.

Fuss, H, Dubitzky, Werner, Downes, Stephen and Kurth, MJ (2005) Mathematical models of cell cycle regulation. BRIEFINGS IN BIOINFORMATICS, 6 (2). pp. 163-177.

Berrar, D, Sturgeon, B, Bradbury, I, Downes, Stephen and Dubitzky, Werner (2005) Survival trees for analyzing clinical outcome in lung adenocarcinomas based on gene expression profiles: Identification of neogenin and diacylglycerol kinase alpha expression as critical factors. JOURNAL OF COMPUTATIONAL BIOLOGY, 12 (5). pp. 534-544.

Wang, Hui and Dubitzky, Werner (2005) A flexible and robust similarity measure based on contextual probability. In: International Joint Conference on Artificial Intelligence, Edinburgh. . 27-32

Berrar, Daniel, Hack, Catherine and Dubitzky, Werner (2005) Knowledge discovery in biology and biotechnology texts: a review of techniques, evaluation strategies, and applications.. Critical reviews in biotechnology, 25 (1-2). pp. 31-52.

Berrar, Daniel, Hack, Catherine and Dubitzky, W (2005) Knowledge Discovery in Biology and Biotechnology Texts: A Review of Techniques, Evaluation Strategies, and Applications. Critical Reviews in Biotechnology, 25 (1-2). pp. 31.

Berrar, Daniel, Sturgeon, B, Bradbury, I, Downes, Stephen and Dubitzky, Werner (2005) Integration of microarray data for a comparative study of classifiers and identification of marker genes. In: METHODS OF MICROARRAY DATA ANALYSIS IV, Durham, NC. . 147-162

O'Donoghue, P, Dubitzky, W, Lopes, P, Berrar, D, Lagan, K, Hassan, D, Bairner, A and Darby, Paul (2004) An evaluation of qualitative and quantitative methods of predicting the 2002 FIFA World Cup. Journal of Sport Sciences, 22 (6). pp. 513-514.

Bi, YX, Bell, D, Wang, H, Guo, GD and Dubitzky, Werner (2004) Classification decision combination for text categorization: An experimental study. In: DATABASE AND EXPERT SYSTEMS APPLICATIONS, PROCEEDINGS, Zaragoza, Spain. . 222-231

Dubitzky, Werner and Azuaje, FJ (2003) AI in the life sciences. ARTIFICIAL INTELLIGENCE REVIEW, 20 (1-2). pp. 7-11.

Sturgeon, B, McCourt, D, Cowper, J, Palmer, FL, McClean, SI and Dubitzky, W (2003) Can the Grid Help to Solve the Data Integration Problems in Molecular Biology?. In: 3rd IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2003), Tokyo, Japan. IEEE Computer Society. 594-600

Wang, Hui, Dubitzky, Werner, Duntsch, Ivo and Bell, David (1999) A lattice machine approach to automated casebase design: Marrying lazy and eager learning. In: International Joint Conference on Artificial Intelligence. . 254-259

Dubitzky, W, Mariotti, D, Hyland, M and McLaughlin, JAD (1998) A neural network approach to plasma emission interpretation. In: International Society for Computers and their Applications 11TH International Conference on Computer Applications in Industry and Engineering, Las Vegas, USA. . 47-50

Buchner, AG, Dubitzky, Werner, Schuster, A, Lopes, P, O'Donoghue, P, Hughes, John, Bell, DA, Adamson, Kenneth, White, JA, Anderson, JMCC and Mulvenna, Maurice (1997) Corporate Evidential Decision Making in Performance Prediction Domains. In: Thirteenth Conference on Uncertainty in Artificial Intelligence (UAI1997), Providence, RI, USA. UAI.

This list was generated on Sun Jul 23 21:38:02 2017 BST.