Systems Biology
Computational Systems Biology
Group Leader
Matej Orešič, Ph.D., Docent
matej.oresic (at) vtt.fi
Contact information
Matej Orešič
Chief Research Scientist
VTT Technical Research Centre of Finland
Tietotie 2
FIN-02044 VTT, Finland
+358-20-722 4491
+358-20-722 7071 (Attn. Matej Orešič)
Personnel
- Tapio Lönnberg
Biography:
Matej Orešič (b. 1967) received his diploma in physics in 1992 from University of Ljubljana (Slovenia) and Ph.D. in biophysics from Cornell University (USA, 1999). During his doctoral studies he focused on development of new methods for studies of systems with complex energy landscapes such as proteins, as well as on bioinformatics studies of correlations between synonymous codon usage and protein secondary structure. After Ph.D. he worked as bioinformatician at LION Bioscience Research (Boston, USA), where he was focusing on development of text mining methods for extraction of biologically important facts from literature and patents. In 2001 he joined Beyond Genomics, Inc. (Boston, USA), the pioneer of systems biology as applied to drug discovery, as principal scientist and head of computational biology and statistics. His work focused on systems biology methods for biomarker discovery and phenotype characterization in general, including processing and analysis of metabolomics and proteomic data, and data integration at multiple levels. In April 2003 Matej Orešič moved to Finland and joined VTT Technical Research Centre of Finland, where he leads the Quantitative Biology and Bioinformatics group (QBIX).
Description of the research:
We are exploring the ways to characterize and model biological systems, as well as apply those ways to and pursue our own interests in integrative physiology as related to metabolic diseases, cellular physiology, and more generally to mechanisms controlling the homeostasis of biological systems.
Our research primarily covers domains of computational systems biology, bioinformatics, and metabolomics.
More information:
Funding:
Academy of Finland, Tekes, EU.
Selected publications:
- G. Medina-Gomez, S. Gray, L. Yetukuri, K. Shimomura, M. Campbell, K. Curtis, S. Virtue, M. Jimenez-Linan, M. Blount, G. Yeo, M. Lopez, T. Seppänen-Laakso, F. M. Ashcroft, M. Orešič, and A. Vidal-Puig, PPAR gamma 2 prevents lipotoxicity by controlling adipose tissue expandability and peripheral lipid metabolism, PLoS Genet. 3: e64 (2007).
- M. Sysi-Aho, M. Katajamaa, L. Yetukuri, and M. Orešič, Normalization method for metabolomics data using optimal selection of multiple internal standards, BMC Bioinformatics 8: e93 (2007).
- M. Katajamaa and M. Orešič, Data processing for mass spectrometry-based metabolomics J. Chromatogr. A (2007), doi:10.1016/j.chroma.2007.04.021.
- L. Yetukuri, M. Katajamaa, G. Medina-Gomez, T. Seppänen-Laakso, A. Vidal Puig, and M. Orešič, Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis, BMC Systems Biology 1, e12 (2007).
- D. Damian, M. Orešič, E. Verheij, J. Meulman, J. Friedman, A. Adourian, N. Morel, A. Smilde, J. van der Greef, Applications of a new subspace clustering algorithm (COSA) in medical systems biology, Metabolomics 3 (2007). 10.1007/s11306-006-0045-z
- K. H. Pietiläinen, M. Sysi-Aho, A. Rissanen, T. Seppänen-Laakso, H. Yki-Järvinen, J. Kaprio, and M. Orešič, Acquired obesity is associated with changes in the serum lipidomic profile independent of genetic effects – a monozygotic twin study, PLoS ONE 2(2), e218 (2007).
- R. Laaksonen, M. Katajamaa, H. Päivä, M. Sysi-Aho, L. Saarinen, P. Junni, D. Lütjohann, J. Smet, R. Van Coster, T. Seppänen-Laakso, T. Lehtimäki, J. Soini, M. Orešič, A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin induced changes in muscle, PLoS ONE 1(1): e97 (2006).
- C. J. Lelliott, G. Medina-Gomez, N. Petrovic, A. Kis, H. M. Feldmann, M. Bjursell, N. Parker, K. Curtis, M. Campbell, P. Hu, D. Zhang, S. E. Litwin, V. G. Zaha, K. T. Fountain, S. Boudina, M. Jimenez-Linan, M. Blount, M. Lopez, A. Meirhaeghe, M. Bohlooly-Y, L. Storlien, M. Strömstedt, M. Snaith, M. Orešič, D. Abel, B. Cannon, A. Vidal-Puig, Ablation of PGC-1b results in defective mitochondrial activity, thermogenesis, hepatic function and cardiac performance, PLoS Biol. 4(11), e369 (2006).
- L. L. Elo, M. Katajamaa, R. Lund, M. Orešič, R. Lahesmaa, T. Aittokallio, Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays, OMICS A Journal of Integrative Biology 10, 369 -380 (2006).
- M. Orešič, A. Vidal-Puig, and V. Hänninen, Metabolomics approaches to phenotype characterization and applications to complex diseases, Expert Rev. Mol. Diagn. 6, 575-585 (2006).
- H. Rischer, M. Orešič, T. Seppänen Laakso, M. Katajamaa, F. Lammertyn, W. Ardiles Diaz, M. C. E. Van Montagu, D. Inzé, K.M. Oksman Caldentey, and A. Goossens, Gene to metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells, Proc. Natl. Acad. Sci. USA 103, 5614-5619 (2006).
- M. Katajamaa, J. Miettinen, and M. Orešič, MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data, Bioinformatics 22, 634-636 (2006).
- K. Curtis, M. Orešič, and A. Vidal-Puig, Pathways to analysis of microarray data, Trends Biotechnol. 8, 429-435 (2005).
- R. Moulder, J.-J. Filén, J. Salmi, M. Katajamaa, O. S. Nevalainen, M. Orešič, T. Aittokallio, R. Lahesmaa and T. Nyman, A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments, Proteomics 5, 2748-2760 (2005)
- M. Katajamaa and M. Orešič, Processing methods for differential analysis of LC/MS profile data, BMC Bioinformatics 6:179 (2005).
- P.V. Gopalacharyulu, E. Lindfors, C. Bounsaythip, T. Kivioja, L. Yetukuri, J. Hollmén, and M. Orešič, Data integration and visualization system for enabling conceptual biology, Bioinformatics 21, i177-i185 (2005).
- G. Medina-Gomez, S. Virtue, C. Lelliott, R. Boiani, M. Campbell, C. Christodoulides, C. Perrin, M. Jimenez-Linan, M. Blount, J. Dixon, D. Zhan, R. R. Thresher, S. Aparicio, M. Carlton, W. H. Colledge, M. I. Kettunen , T. Seppänen-Laakso, J. K. Sethi, S. O'Rahilly, K. Brindle, S. Cinti, M. Orešič, R. Burcelin and A. Vidal-Puig, The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific PPAR gamma 2 isoform, Diabetes 54, 1706-1716 (2005).
- M. Orešič, C. Clish, E. Davidov, E. Verheij, J. Vogels, L. M. Havekes, E. Neumann, S. Naylor , J. v.-d. Greef, T. Plasterer, Phenotype characterization using integrated gene, protein and metabolite profiling, Applied Bioinformatics 3, 205-217 (2004).
- E. J. Davidov, C. B. Clish, M. Orešič, M. Meys, W. Stochaj, P. Snell, G. Lavine, T. R. Londo, A. Adourian, X. Zhang, M. Johnston, N. Morel, E. W. Marple, T. N. Plasterer, E. Neumann, E. Verheij, J. T. W. E. Vogels, L. M. Havekes, J. v-d Greef and S. Naylor, Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model, OMICS A Journal of Integrative Biology 8, 267-288 (2004).
- K.M. Oksman-Caldentey, D. Inzé and M. Orešič, Connecting genes to metabolites by a systems biology approach, Proc. Natl. Acad. Sci. USA 101, 9949-9950 (2004).