Björn Olsson

Associate Professor of Bioinformatics

PhD, University of Exeter, UK, 2000.
MSc, University of Skövde, 1993.
BSc, University of Skövde, 1992.

Head of the Bioinformatics Research group.

Publications

Journal articles:

1. Carlsson J, Davidsson S, Helenius G, Karlsson M, Lubovac Z, Andrén O, Olsson B, Klinga-Levan K (in press) A miRNA signature that separates between normal and malignant prostate tissues. Cancer Cell International (to appear).
2. Österberg L, Levan K, Partheen K, Delle U, Olsson B, Sundfeldt K, Horvath G (2010) Specific Copy Number Alterations Associated with Docetaxel/Carboplatin Response in Ovarian Carcinomas. Anticancer Research 30: 4451-4458.
3. Synnergren J, Améen C, Lindahl A, Olsson B, Sartipy P (2010) Expression of microRNAs and their target mRNAs in human stem cell derived cardiomyocyte clusters and in heart tissue. Physiological Genomics Sep 14 (Epub ahead of print).
4. Carlsson J, Helenius G, Karlsson M, Lubovac Z, Andrén O, Olsson B, Klinga-Levan K (2010) Validation of suitable control genes for expression studies of miRNA in prostate cancer tissues. Cancer Genetics and Cytogenetics 202(2): 71-75.
5. Synnergren J, Heins N, Brolén G, Lindahl A, Hyllner J, Olsson B, Sartipy P, Björquist P (2010) Transcriptional profiling of human embryonic stem cells differentiating to definitive and primitive endoderm and further towards the hepatic lineage. Stem Cells and Development 19(7): 961-978.
6. Levan K, Partheen K, Österberg L, Olsson B, Delle U, Eklind S, Horvath G (2010) Identification of a Gene Expression Signature for Survival Prediction in Type I Endometrial Carcinoma. Gene Expression 14(6): 361-370.
7. Möllerström E, Delle U, Danielsson A, Parris T, Olsson B, Karlsson P, Helou K (2010) High-resolution genomic profiling to predict 10-year overall survival in node-negative breast cancer. Cancer Genetics and Cytogenetics 198(2): 78-89.
8. Österberg L, Levan K, Partheen K, Delle U, Olsson B, Sundfeldt K, Horvath G (2010) Potential predictive markers of chemotherapy resistance in stage III serous ovarian adenocarcinomas. BMC Cancer 9: 368.
9. Linde J, Olsson B, Lubovac Z (2009) Network Properties for Ranking Predicted miRNA Targets in Breast Cancer. Advances in Bioinformatics. Vol 2009, Article ID 182689.
10. Sartipy P, Hyllner J, Olsson B, Synnergren J (2009) Regulation of ’Stemness’ and Stem Cell Differentiation by MicroRNAs. IDrugs 12(8): 492-496.
11. Lindlöf A, Bräutigam B, Chawade A, Olsson O, Olsson B (2009) In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control. Bioinformatics 25(11): 1345-1348.
12. Karlsson S, Olsson B, Klinga-Levan, K (2009) Gene expression profiling predicts a three-gene signature of endometrial adenocarcinoma in a rat model. Cancer Cell International 9:12.
13. Synnergren J, Olsson B, Gamalielsson J (2009) Classification of information fusion methods in systems biology. In Silico Biology 9, 0007.
14. Synnergren J, Åkesson K, Dahlenborg K, Vidarsson H, Améen C, Steel D, Lindahl A, Olsson B, Sartipy P (2008) Molecular signature of cardiomyocite clusters derived from human embryonic stem cells. Stem Cells 26(7): 1831-1840.
15. Lindlöf A, Bräutigam M, Chawade A, Olsson O, Olsson B (2008) Evaluation of Combining Several Statistical Methods with a Flexible Cut-off for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets. Bioinformatics and Biology Insights 2: 215-237.
16. Synnergren J, Adak S, Englund MC, Giesler TL, Noaksson K, Lindahl A, Nilsson P, Nelson D, Abbot S, Olsson B, Sartipy P (2008) Cardiomyogenic gene expression profiling of differentiating human embryonic stem cells. Journal of Biotechnology 134: 162-170.
17. Karlsson E, Delle U, Danielsson A, Olsson B, Abel F, Karlsson P, Helou K (2008) Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer. BMC Cancer 8: 254.
18. Gamalielsson J and Olsson B (2008) Gene Ontology-based Semantic Alignment of Biological Pathways by Evolutionary Search. Journal of Bioinformatics and Computational Biology 6(4): 825-842.
19. Gamalielsson J, Olsson B (2008) GOSAP: Gene Ontology-based Semantic Alignment of Biological Pathways. International Journal of Bioinformatics Research and Applications 4(3): 274-294.
20. Chawade A, Bräutigam M, Lindlöf A, Olsson O, Olsson B (2007) Novel cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics 8: 304.
21. Adamovic T, Roshani L, Chen L, Schaffer BS, Helou K, Levan G, Olsson B, Shull JD (2007) Nonrandom pattern of aberrations in 17β-estradiol-induced rat mammary tumors: Indications of distinct pathways for tumor development. Genes, Chromosomes and Cancer 46(5): 459-469.
22. Karlsson E, Danielsson A, Delle U, Olsson B, Karlsson P, Helou K (2007) Chromosomal changes associated with clinical outcome in lymph-node negative breast cancer. Cancer Genetics and Cytogenetics 172(2): 139-146.
23. Synnergren J, Giesler TL, Adak S, Tandon R, Noaksson K, Lindahl A, Nilsson P, Nelson D, Olsson B, Englund MCO, Abbot S, Sartipy P (2007) Differentiating human embryonic stem cells express a unique housekeeping gene signature. Stem Cells 25: 473-480.
24. Chen L, Nordlander C, Behboudi A, Olsson B, Klinga Levan K (2006) Deriving Evolutionary Tree Models of the Oncogenesis of Endometrial Adenocarcinoma. International Journal of Cancer 120(2): 292-296.
25. Bräutigam M, Chawade A, Gharti-Chhetri G, Lindlöf A, Jonsson A, Jonsson R, Olsson B, Olsson O (2006) Development of a Swedish winter oat with gene technology and molecular breeding. Journal of the Swedish Seed Association 116(1-2): 23-35. 
26. Lubovac Z, Gamalielsson J, Olsson B (2006) Combining functional and topological properties to identify core modules in protein interaction networks. Proteins - Structure, Function and Bioinformatics 64(4): 948-959. 
27. Olsson B, Gawronska B, Erlendsson B (2006) Deriving pathway maps from text analysis using a grammar-based approach. Journal of Bioinformatics and Computational Biology 4(2): 483-502.
28. Bräutigam M, Lindlöf A, Zakhrabetkova S, Gharti-Chhetri G, Olsson B, Olsson O (2005) Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biology 5:18.
29. Gamalielsson J and Olsson B (2004) On the (lack of) robustness of gene expression data clustering. WSEAS Transactions on Biology and Biomedicine 1(2):198-204.
30. Eriksson R and Olsson B (2004) Adapting Genetic Regulatory Models by Genetic Programming, Biosystems 76(1-3): 217-227. 
31. Lindlöf A and Olsson B (2003) Genetic network inference: the effects of pre-processing. Biosystems 72(3):229-239. 
32. Narayanan A, Keedwell EC, Olsson B (2003) Artificial Intelligence Techniques for Bioinformatics. Applied Bioinformatics 1(4): 191-222. 
33. Jonsson P, Laurio K, Lubovac Z, Olsson B, Andersson ML (2002) Using functional annotation to improve clusterings of gene expression patterns. Information Sciences 145(3-4): 183-194. 
34. Lindlöf A and Olsson B (2002) Could correlation-based methods be used to derive genetic association networks? Information Sciences 146(1-4): 103-113. 
35. Olsson B and Laurio K (2002) Towards a comprehensive collection of diagnostic patterns for protein sequence classification. Information Sciences 143(1-4): 1-11. 
36. Olsson B, Laurio K, Gudjonsson L (2001) A Hybrid Method for Protein Sequence Modeling with Improved Accuracy. Information Sciences 139(1-2): 113-138. 
37. Olsson B (2001) Co-evolutionary search in asymmetric spaces. Information Sciences 133(3-4): 103-125.

Papers in conference proceedings:

Note: The following list does not include abstracts or posters. It only includes papers that were peer-reviewed (more or less thoroughly) and published in full length (typically 5-10 pages) in a printed conference proceedings book.

1. Synnergren J, Olsson B, Gamalielsson J (2008) A data integration method for exploring gene regulatory mechanisms. DTMBIO '08: Proceedings of the 2nd international workshop on data and text mining in bioinformatics. ACM, p. 81-84.
2. Zichner T, Lubovac Z, Olsson B (2008) Temporal analysis of oncogenesis using microRNA expression data. In Beyer A, Schroeder M (eds.), Proceedings of the German Conference on Bioinformatics 2008, Vol P-136, 128-137. Springer-Verlag.
3. Synnergren J, Gamaliesson J, Olsson B (2007) Mapping of the JDL Data Fusion Model to Bioinformatics. In Proceedings of the 2007 IEE International Conference on Systems Man and Cybernetics (SMC 2007), p. 1506-1511.
4. Gamalielsson J and Olsson B (2007) EGOSAP: Evolutionary Gene Ontology-Based Semantic Alignment of Biological Pathways. In Proceedings of MCCMB 2007.
5. Laurio K, Gamalielsson J, Svensson T, Jirstrand M, Olsson B (2007) Evolutionary search for improved path diagrams. In: E. Marchiori JH, Moore JC, Rajapakse (eds.), Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 5th European Conference. LNCS 4447: 114-121. Springer-Verlag.
6. Lubovac Z, Corne D, Gamalielsson J, Olsson B (2007) Weighted Cohesiveness for Identification of Functional Modules and their Interconnectivity. In: Hochreiter S and Wagner R (eds.), Bioinformatics Research and Development – First International Conference, BIRD ’07, LNBI 4414: 185-198. Springer-Verlag.
7. Lindlöf A, Bräutigam M, Chawade A, Olsson B, Olsson O (2007) Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis through Comparative Analysis of Multiple EST sets. In: Hochreiter S and Wagner R (eds.), Bioinformatics Research and Development – First International Conference, BIRD ’07, LNBI 4414: 48-65. Springer-Verlag.
8. Olsson B, Gawronska B, Erlendsson B, Lindlöf A, Dura E (2006) Automated text analysis of biomedical abstracts applied to the extraction of signaling pathways involved in plant cold-adaptation. In: Kolchanov N and Hofestädt R (eds.), Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure, vol. 3, 296-299. 
9. Gawronska B, Erlendsson B, Olsson B (2006) Towards an Automated Analysis of Biomedical Abstracts. In: Proceedings of the 3rd International Workshop on Data Integration in the Life Sciences 2006 (DILS2006), July 20-22, Cambridge, UK. 
10. Dura E, Gawronska B, Erlendsson B, Olsson B (2006) Towards Information Fusion in Pathway Evaluation: Encoding of Biological Relations in Research Articles. In: Proceedings of the 9th International Conference on Information Fusion (FUSION 2006), July 10-13, Florence, Italy. 
11. Gamalielsson J, Nilsson P, Olsson B (2006) A GO-based Method for Assessing the Biological Plausibility of Regulatory Hypotheses. In Alexandrov VN, van Albada GD, Sloot MA, Dongarra J (eds.), Proceedings of ICCS 2006: 6th International Conference on Computational Science, LNCS 3992: 879-886. Springer-Verlag. 
12. Lubovac Z, Olsson B, Gamalielsson J (2005) Combining topological characteristics and domain knowledge reveals functional modules in protein interaction networks, In Sagot M-F and Guimaraes KS, Proceedings of CompBioNets 2005 - Algorithms and Computational Methods for Biochemical and Evolutionary Networks, Lyon, France, December 5-7, 2005,  p. 93-106. College Publications. 
13. Olsson B, Nilsson P, Gawronska B, Persson A, Ziemke T, Andler SF (2005) An Information Fusion Approach to Controlling Complexity in Bioinformatics Research. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference, p. 299-304. IEEE Press.
14. Lubovac Z, Gamalielsson J, Olsson B (2005) Exploring protein networks with a semantic similarity measure across the Gene Ontology. Proceedings of the 6th International Symposium on Computational Biology and Genome Informatics, p. 1203-1208. Association for Intelligent Machinery.
15. Gawronska B, Erlendsson B, Olsson B (2005) Tracking biological relations in texts: a Referent Grammar based approach. Proceedings of the workshop 'Biomedical Ontologies and Text Processing,' 4th European Conference on Computational Biology (ECCB05), 15-22. 
16. Andler SF, Niklasson L, Olsson B, Persson A, Planstedt T, de Vin LJ, Wangler B, Ziemke T (2005) Information Fusion from Databases, Sensors and Simulations. Proceedings of the 29th Annual NASA/IEEE Software Engineering Workshop. 
17. Eriksson R and Olsson B (2004) On the Performance of Evolutionary Algorithms with Life-Time Adaptation in Dynamic Fitness Landscapes. In Proceedings of the 2004 IEEE Congress on Evolutionary Computation, p. 1293-1300. IEEE Press.
18. Gawronska B, Olsson B, de Vin L (2004) Natural Language Technology in Multi-Source Information Fusion. In Proceedings of the International IPSI-2004k Conference. Published on CD with ISBN 86-7466-117-3. 
19. Rahpeymai N, Olsson B, Andersson ML (2003) Microarray-based diagnosis of breast cancer using decision trees. In Chen K, Chen S-H, Chen H-D, Chiu DKY, Das S, Duro R, Jiang Z, Kasabov N, Kerre E, Leong HV, Li Q, Lu M, Ventura D, Wang PP, Wu J (eds.), Proceedings of the 7th International Conference on Computational Biology and Genome Informatics,  p. 978-982. Association of Intelligent Machinery. 
20. Olsson B, Berndtsson B, Lundell B, Hansson J (2003) Running research-oriented final year projects for CS and IS students, In Proceedings of the 34th Annual SIGCSE Technical Symposium on Computer Science Education,  p. 79-83. ACM Press. 
21. Eriksson R and Olsson B (2002) On the Behavior of Evolutionary Global-Local Hybrids with Dynamic Fitness Functions, In Merelo Guervós JJ, Adamidis P, Beyer H-G, Fernández-Villacañas J-L, Schwefel H-P (eds.), Parallel Problem Solving from Nature - PPSN VII,  p. 13-22. Springer-Verlag. 
22. Gamalielsson J and Olsson B (2002) Using Evolutionary Algorithms to Evaluate Simplified Models for Protein Structure Prediction, In Caulfield HJ, Chen S-H, Cheng H-D, Duro R, Honavar V, Kerre EE, Lu M, Grana Romay M, Shih TK, Ventura D, Wang PP, Yang Y, Proceedings of The Sixth Joint Conference on Information Sciences,  p. 602-605. Association for Intelligent Machinery. 
23. Lubovac Z, Olsson B, Jonsson P, Laurio K, Andersson ML (2001) Biological and statistical evaluation of gene expression profiles, In D'Attellis CE, Kluev VV, Mastorakis NE (eds.), Proceedings of Mathematics and Computers in Biology and Chemistry 2001,  p. 149-155. WSES Press. 
24. Olsson B and Laurio K (2001) Towards a comprehensive collection of diagnostic patterns for protein sequence classification. In Wu CH, Wang PP, Wang JTL (eds.), Proceedings of the Atlantic Symposium on Computational Biology, Genome Information Systems and Technology,  p. 59-63. Association for Intelligent Machinery. 
25. Olsson B (2000) NK-landscapes as test functions for evaluation of host-parasite algorithms. In Schoenhauer M, Deb K, Rudolph G, Yao X, Lutton E, Merelo JJ, Schwefel H-P (eds.), Parallel Problem Solving from Nature - PPSN VI,  p. 487-496. Springer-Verlag. 
26. Jacobsson H and Olsson B (2000) An Evolutionary Algorithm for Inversion of ANNs. In Wang PP (ed.), Proceedings of the Fifth Joint Conference on Information Sciences, p. 1070-1073. Association for Intelligent Machinery. 
27. Gudjonsson L, Laurio K, Olsson B (2000) Combining Discrete and Probabilistic Methods Improves Accuracy in Sequence Modeling. In Wang PP (ed.), Proceedings of the Fifth Joint Conference on Information Sciences, p. 790-793. Association for Intelligent Machinery. 
28. Olsson B (2000) Co-evolutionary Search in Asymmetric Spaces. In Wang PP (ed.), Proceedings of the Fifth Joint Conference on Information Sciences, p. 1040-1043. Association for Intelligent Machinery. 
29. Olsson B (1999) Using Evolutionary Algorithms in the Design of Protein Fingerprints. In Banzhaf W, Daida RE, Eiben AE, Garzon MH, Honavar V, Jakiela M, Smith RE (eds.), GECCO-99: Proceedings of the Genetic and Evolutionary Computation Conference,  p. 1636-1642. Morgan Kaufmann. 
30. Olsson B and Laurio, K (1998) Discovery of Diagnostic Patterns from Protein Sequence Databases. In Quafafou M and Zytkow J (eds.), Principles of Knowledge Discovery and Data Mining, p. 167-175. Springer-Verlag.
31. Olsson B (1998) A Host-Parasite Genetic Algorithm for Asymmetric Tasks. In Nedellec C and Rouveirol C (eds.), Machine Learning: ECML98, p. 346-351. Springer-Verlag.
32. Olsson B (1998) Evaluation of a Simple Host-Parasite Genetic Algorithm. In Porto VW, Saravanan N, Waagen D, Eiben AE (eds.), Evolutionary Programming VII,  p. 53-62. Springer-Verlag. 
33. Eriksson R and Olsson B (1997) Cooperative Coevolution in Inventory Control Optimisation. In Smith GD, Steele NC, Albrecht RF (eds.), Artificial Neural Networks and Genetic Algorithms: Proceedings of ICANNGA 97, p. 583-587. Springer-Verlag. 
34. Olsson B (1996) Optimization Using A Host-Parasite Model with Variable-Size Distributed Populations. In Proceedings of the 1996 IEEE 3rd International Conference on Evolutionary Computation, p. 295-299. IEEE Press.

Books and book chapters:

1. Gamalielsson J and Olsson B (2004) Evaluating Protein Structure Prediction Models with Evolutionary Algorithms. Information Processing with Evolutionary Algorithms. 129-143. Graña M, Duro R, d'Anjou A, Wang PP. Springer-Verlag.
2. Berndtsson M, Hansson J, Olsson B, Lundell B (2002) Planning and implementing your final year project - with success!, Springer-Verlag. 
3. Lundh D, Olsson B, Narayanan, A (eds.) (1997) Biocomputing and Emergent Computation. World Scientific.