Pharmaceutical Bioinformatics

  • Hardy, B., Apic, G., Carthew, P., Clark, D., Cook, D. et al. (2012). Toxicology Ontology Perspectives. ALTEX. Alternatives zu Tierexperimenten, vol. 29, ss. 139-156 [More information]
  • Harry, B., Apic, G., Carthew, P., Clark, D., Cook, D. et al. (2012). A toxicology ontology roadmap. ALTEX. Alternatives zu Tierexperimenten, vol. 29, ss. 129-137 [More information]
  • Alvarsson, J., Andersson, C., Spjuth, O., Larsson, R., Wikberg, J. (2011). Brunn: an open source laboratory information system for microplates with a graphical plate layout design process. BMC Bioinformatics, vol. 12, ss. 179- [doi:10.1186/1471-2105-12-179] [More information]
  • O'Boyle, N., Guha, R., Willighagen, E., Adams, S., Alvarsson, J. et al. (2011). Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of Cheminformatics, BioMed Central. vol. 3, ss. 37- [doi:10.1186/1758-2946-3-37] [More information]
  • Spjuth, O., Eklund, M., Helgee, E., Boyer, S., Carlsson, L. (2011). Integrated Decision Support for Assessing Chemical Liabilities. Journal of chemical information and modeling, vol. 51, ss. 1840-1847 [doi:10.1021/ci200242c] [More information]
  • Spjuth, O., Eklund, M., Lapins, M., Junaid, M., Wikberg, J. (2011). Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV Drug Research Centre. Bioinformatics, Oxford: Oxford University Press. vol. 27, ss. 1719-1720 [doi:10.1093/bioinformatics/btr192] [More information]
  • Willighagen, E., Alvarsson, J., Andersson, A., Eklund, M., Lampa, S. et al. (2011). Linking the Resource Description Framework to cheminformatics and proteochemometrics. Journal of Biomedical Semantics, vol. 2, ss. 6- [doi:10.1186/2041-1480-2-S1-S6] [More information]

Research Profile

Name: Ola Spjuth
Title: PhD
Position: Researcher at the Department of Pharmaceutical Biosciences, Uppsala University

Affiliations

  • Application expert at Uppsala high performance computing center (UPPMAX)
  • Scientific coordinator for UPPNEX, the Swedish resource for next generation sequencing data management and analysis
  • Coordinator for the Complex Diseases community of the Swedish e-Science Research Center (SeRC), at the Karolinska Institute, Stockholm

Research interests
My research area is Pharmaceutical Bioinformatics, and especially the topics below:

Computational toxicology
My research in computational toxicology is geared towards in silico modeling of drug safety, as well as metabolite predictions. My work is carried out in close collaboration with AstraZeneca R&D, and has resulted in the MetaPrint2D method for predicting site-of-metabolism (where the body starts to metabolize drugs) and a system for combining multiple predictive models to make better informed decisions in dug safety assessments.

Data integration in life science
This part of my research focuses on the problem of data heterogeneity in the life sciences; how we can share and integrate data and services from different sources and combine them to answer complex research questions. For this to be possible we need standards for information sharing and interoperable software systems, and I have developed standards for quantitative structure-activity relationships (named QSAR-ML) as well as for asynchronous Web services (named XMPP), and applied this for analyzing omics-data.

The Bioclipse Platform
A general trend through my research is to simplify for scientists to access data, methods, and new technologies in Bioinformatics and e-Science. This has resulted in the Bioclipse workbench, and almost all of my research ends up as modules in Bioclipse which makes it easily accessible for the scientific community. The Bioclipse project has grown to an international collaboration with over 30 scientists contributing over the years, and I am currently coordinating this organization. Our recent developments relate to the problem of reproducible data analysis in the life sciences.

Colllaborations
Much of my research is driven by a close collaboration with AstraZeneca, providing use cases from the pharmaceutical industry's point of view. It is also an excellent test bed for our developed methods as they are validated and tested in real projects by specialists in the field.
I am also collaborating with the EU FP7 project OpenTox for distributed toxicology predictions, who has adopted Bioclipse as interface for their research.
Apart from this I have close contact with the European Bioinformatics Institute and Cambridge University for development of standards in cheminformatics.

Why work in research?
Working as a researcher you have a very open agenda, and the possibilities to pursue interesting projects in the direction you desire. There are always new things to learn, and the freedom to plan your own schedule combined with exploring and developing new methods within an important field (drug development) is a very interesting and rewarding experience.

My future
I think that given the new technological advances in life science with equipment delivering data at constantly increasing rates creates a large need for people with expertise in bioinformatics. It will be exciting to see how the pharmaceutical domain will take advantage of all this new information being made available, and how this will affect our view on diseases and hopefully enable us to develop new drugs. Personally I will try to establish my own research group in Sweden, focused on the abovementioned research in the field of Pharmaceutical Bioinformatics.

Personal interests
I enjoy sports of almost all types and play bandy in IK Tellus during winters, and a lot of golf during the summertime.
 

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