Matej Orešič

Research Professor, Systems Biology and Bioinformatics

Phone: +358-20-722-4491
Fax: +358-20-722-7071
Email: matej.oresic@vtt.fi

VTT Technical Research Centre of Finland
Tietotie 2
P.O. Box 1000
FIN-02044 VTT, Espoo

Education

Ph.D. in biophysics (1999), Cornell University, Ithaca, NY, USA
Diploma in physics (1992), University of Ljubljana, Slovenia

Other affiliations

Institute for Molecular Medicine Finland FIMM (Associate Group Leader)
Turku Centre for Biotechnology (Group Leader)

Other current advisory roles and positions of trust

Metabolomics Society (Member, Board of Directors)
Zora Biosciences, Ltd. (Co-founder, Chief scientific advisor, Member of the board)
Metabolomics Journal (Member, Editorial Board)
PLoS ONE journal (Member, Editorial Board)
Molecular BioSystems journal (Member, Scientific Advisory Board)
ERASysBio (Member, Scientific Advisory Board)
Skolkovo Foundation (Expert Panel Member, Bio-Medical Cluster)

Hobbies

Argentine tango (former www), sailing.

Publications

Link to Google Schoolar profile (citations)

Highlights  Research publications  Reviews and commentaries  

Proceedings & Edited volumes Patents  Monographs  Conference & workshop talks

Highlights

Research publications (for reviews see below)

2013 and beyond

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

Before 2000

Reviews and commentaries in refereed journals

Scientific edited volumes and conference proceedings

  • T. Hyötyläinen, S. Castillo, M. Sysi-Aho, M. Orešič, Data (pre-) processing: when a peak is a metabolite? In Microbial metabolomics (S. Villas-Boas and K. Ruggiero, Eds.), CAB International (accepted).
  • M. Orešič, Systems biology in food and nutrition research, In Foodomics: advanced mass spectrometry in modern food science and nutrition (A. Cifuentes, Ed.), John Wiley & Sons (accepted).
  • K. Ketola, A. Vuoristo, M. Orešič, O. Kallioniemi, K. Iljin, Monensin induced oxidative stress reduces prostate cancer cell migration and cancer stem cell population, In Oxidative Stress and Diseases (V. Lushchak, Ed.), INTECH, pp. 521-540 (2012). doi: 10.5772/34713
  • M. Orešič, T. Hyötyläinen, S.-K. Herukka, M. Sysi-Aho, I. Mattila, T. Seppänan-Laakso, V. Julkunen, M. Hallikainen, J. Koikkalainen, M. Kivipelto, S. Helisalmi, J. Lötjönen, H. Soininen, Metaboliikka mahdollistaa Alzheimerin taudin toteamisen jo varhaisvaiheessa, Duodecim 128, 318 (2012). In Finnish
  • K. Pietiläinen, T. Róg, T. Seppänen-Laakso, S. Virtue, P. Gopalacharyulu, J. Tang, S. Rodriguez-Cuenca, A. Maciejewski, J. Naukkarinen, A. Rissanen, A.-L. Ruskeepää, P. Niemelä, V. Velagapudi, S. Castillo, M. Sysi-Aho, T. Hyötyläinen, J. Kaprio, H. Yki-Järvinen, I. Vattulainen, A. Vidal-Puig, M. Orešič, Rasvasolujen solukalvo mukautuu ylimääräiseen rasvaan, Duodecim 127, 1493 (2011). In Finnish
  • M. Orešič, Metabolic biomarker and target discovery in obesity-associated comorbidities, Pharma Focus Asia Issue 15, 6-8 (2011).
  • T. Suvitaival, I. Huopaniemi, M. Orešič, S. Kaski, Cross-species translation of multi-way biomarkers, ICANN 2011, Part I, LNCS 6791, pp. 209–216 (2011). doi: 10.1007/978-3-642-21735-7_26
  • M. Sysi-Aho, J. Koikkalainen, J. Lötjönen, T. Seppänen-Laakso, H. Söderlund, T. Heliö, M. Orešič, Searching for linear dependencies between heart magnetic resonance images and lipid profiles, In Ukkonen Festschrift (T. Elomaa et al., Eds.), LNCS 6060, Springer Verlag, Berlin Heidelberg, pp. 232–243 (2010).
  • C. J. Lelliott, M. Orešič, A. Vidal-Puig, Obesity and diabetes: lipotoxicity, In Adipose Tissue in Health and Disease (T. A. Leff, J. Granneman, Eds.), Wiley-VCH, Weinheim, pp. 347-368 (2010).
  • M. Orešič, A. Vidal-Puig, Handbook of Research on Systems Biology Applications in Medicine. Daskalaki, A. (ed.). Volume I. Medical Information Science Reference. Hershey, PA, USA (2009), pp. 354 - 360.
  • M. Orešič, S. Simell, M. Sysi-Aho, K. Näntö-Salonen, T. Seppänen-Laakso, V. Parikka, M. Katajamaa, A. Hekkala, I. Mattila, P. Keskinen, L. Yetukuri, A. Reinikainen, J. Lähde, T. Suortti, J. Hakalax, T. Simell, H. Hyöty, R. Veijola, J. Ilonen, R. Lahesmaa, M. Knip, O. Simell, Aineenvaihdunnan säätelyhäiriöt edeltävät tyypin 1 diabetesta, Duodecim 125, 84 (2009). In Finnish
  • J. R. Koikkalainen, M. Antila, J. M. P. Lötjönen, T. Heliö, K. Lauerma, S. M. Kivistö, P. Sipola, M. A. Kaartinen, S. T. J. Kärkkäinen, E. Reissell, J. Kuusisto, M. Laakso, M. Orešič, M. S. Nieminen, K. J. Peuhkurinen, Sydänsairauksien varhainen tunnistaminen magneettikuvauksella, Duodecim 124, 90-91 (2008).
  • C. Gatu, M. Sysi-Aho, M. Orešič, A regression subset-selection strategy for fat-structure data, Proc. International Conference on Computational Statistics, COMPSTAT´08, 349-358 (2008).
  • M. Orešič, J. Koikkalainen, E. Lindfors, J. Mattila, T. Heliö, J. Lötjönen, Data integration and visualization of highly complex biological and medical data: application to Lamin A/C mutation, VTT Symposium on Service Science, Technology and Business (2008).
  • M. Orešič, V. Hänninen, K. Pietiläinen, Metabolomiikka on diabetestutkimuksen uusi työkalu, Diabetes ja Lääkäri 36, 20-23 (2007). In Finnish
  • R. Laaksonen, T. Lehtimäki, H. Päiva, M. Orešič, Statiinien aiheuttama myopatia: yleinen vai harvinainen haitta?, TABU 15(3), 13-15 (2007).
  • K. Curtis, M. Orešič, A. Vidal-Puig, A systems biology approach to identify novel mechanisms of obesity and associated complications, In Obesity: Genomics and Post-Genomics (K. Clement and T. Sörensen, Eds.), Informa Healthcare, 1st Ed. (2007).
  • M. Orešič, Metabolomics strategy: Identifying tissue-specific drug effects, Pharma Focus Asia 2008, Issue 6, 64-65.
  • M. Orešič, J. Lötjönen, C. Bounsaythip, megNet®: visualization and modeling environment for translational medicine, ERCIM News 69, 32-34 (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, Systeemibiologia paljastaa statiinien aiheuttamien lihastoksisten muutosten aineenvaihduntateitä ja plasman biomerkkiaineita, Duodecim 123, 261-262 (2007).
  • M. Orešič, Data integration and visualization system: Enabling conceptual biology, CSC News 18(3), 14-16 (2006).
  • M. Orešič, Normalization of metabolomics data using multiple internal standards, Proceedings of Probabilistic Modelling and Machine Learning in Structural and Systems Biology Workshop (Rousu, J., Kaski, S., and Ukkonen, E. eds.), Tuusula, Finland, June 17-18, 2006, pp. 147-152.
  • P. V. Gopalacharyulu, E. Lindfors, C. Bounsaythip, and M. Orešič, Context dependent visualization of protein function, Proceedings of Probabilistic Modelling and Machine Learning in Structural and Systems Biology Workshop (Rousu, J., Kaski, S., and Ukkonen, E. eds.), Tuusula, Finland, June 17-18, 2006, pp. 26-31.
  • M. Orešič, Role of metabolomics in pharmaceutical research and nutrition, Dosis 22, 13-19 (2006).
  • M. Orešič, H. Rischer, and K.-M. Oksman-Caldentey, Metabolomics of plant secondary compounds: Profiling of Catharanthus cell cultures (2006). In Plant Metabolomics. Biotechnology in Agriculture and Forestry Vol. 57 (Saito, K., Willmitzer, L. and Dixon, D. eds.), Springer Verlag, Heidelberg, pp. 277-289.
  • M. Orešič and M. Sysi-Aho, Exploratory multivariate analyses of cross-sectional and longitudinal molecular profile data. 2005 Proceedings of the American Statistical Association, Biopharmaceutical Section [CD-ROM], American Statistical Association, Alexandria, VA, pp. 660-665.
  • H. Söderlund, M. Orešič, K. Kataja, R. Satokari, T. Pulli, K. Takkinen, S. Home, Biomarkers, a new tool for process control in malting and brewing. Proceedings of the 30th European Brewery Convention Congress. Prague, 14-19 May 2005. CD. Fachverlag Hans Carl . Nürnberg (2005), paper 134: 1109 ?1114.
  • M. Orešič, M. Katajamaa, and T. Seppänen-Laakso, Lipidomics as a tool for characterizing biological systems, Lipid Technology 17, 59-63 (2005).
  • M. Orešič, P. V. Gopalacharyulu, E. Lindfors, C. Bounsaythip, I. Karanta, M. Hiirsalmi, L. Seitsonen and P. Silvonen, Towards an integrative and context sensitive approach to in silico disease modelling, ERCIM News 60, 25-26 (2005).
  • C. Bounsaythip, E. Lindfors, P. Gopalacharyulu, J. Hollmén, and M. Orešič, Network-based representation of biological data for enabling context-based mining, In Proc. KRBIO'05, 1-6 (2005).
  • P. V. Gopalacharyulu, E. Lindfors, C. Bounsaythip, W. Wefelmeyer & M. Orešič, Ontology based data integration and context-based mining for life sciences, Position paper: W3C Workshop on Semantic Web for Life Sciences, Cambridge, MA, USA (2004).
  • M. Orešič, Computational tools for analyses of metabolic and proteomic profile data, in Proceedings of the Nordic MATLAB Conference 2003, 148-153 (2003).
  • J. v.-d. Greef, E. Davidov, E. Verheij, J. Vogels, R. v.-d. Heiden, A. S. Adourian, M. Orešič, E. W. Marple, S. Naylor, The role of metabolomics in systems biology: A new vision for drug discovery and development. In “Metabolic Profiling: Its role in biomarker discovery and gene function analysis”, eds. G. G. Harrigan and R. Goodacre (Kluwer Academic Publishers, Boston), 171-198 (2003).
  • B. Church, M. Orešič, and D. Shalloway, Tracking metastable states to free-energy global minima, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 23, 41-64 (1996).

Published patents and patent applications

  • Biofluid metabolite profiling as a tool for early prediction of autoimmunity and type 1 diabetes risk (WO/2008/031917, pub. date 20.03.2008).
  • Normalizing spectroscopy data with multiple internal standards (WO/2007/147938, pub. date 27.12.2007).
  • Diagnostic method for myopathy (WO/2007/144467, pub. date 21.12.2007).
  • Information management techniques for metabolism-related data (WO/2007/128882, pub. date 15.11.2007).
  • Correlation analysis of biological systems (WO/2007/035613 , pub. date 29.03.2007).
  • Means and methods to enhance the production of vinblastine and vincristine in Catharanthus roseus (WO/2007/031556 , pub. date 22.03.2007).
  • Analysis techniques for liquid chromatography mass spectrometry (WO/2006/125865, pub. date 30.11.2006).
  • Analysis techniques for liquid chromatography mass spectrometry (WO/2006/125864, pub. date 30.11.2006).
  • Analysis techniques for liquid chromatography mass spectrometry (WO/2006/125863, pub. date 30.11.2006).
  • Visualization technique for biological information (WO/2006/114479, pub. date 02.11.2006).
  • Methods and systems for profiling biological systems (WO/2005/020125, pub. date 03.03.2005).

Scientific monographs

  • M. Orešič, Studies of specific correlations between synonymous codon usage and protein secondary structure (Ph.D. Thesis, Cornell University, Ithaca, NY, USA, 1999).

Conference & workshop talks

June 25 - July 2, 2012 Society for Experimental Biology Annual Main Meeting, Salzburg, Austria
June 25-28, 2012 Metabolomics 2012, Washington, DC, USA
June 14-16, 2012 6th Kuopio Alzheimer Symposium , Kuopio, Finland
May 27-June 1, 2012 36th International Symposium on Capillary Chromatography (ISCC) and 9th GCxGC Symposium, Riva del Garda, Italy
May 9-12, 2012 19th European Congress of Obesity (ECO2012), Lyon, France
April 2-4, 2012 Inserm workshop 214 “Metabolomics for biomedical research: where do we stand?”, Bordeaux, France.
October 27-28, 2011 64th Annual Meeting of the Finnish Endocrine Society, Helsinki, Finland
October 21-26, 2011 The obese species, Erice, Sicily, Italy
September 25-28, 2011 Metabomeeting 2011, Helsinki, Finland [MZmine developer's workshop on 28.9.2011]
August 29 - 31, 2011 Adipose tissue: A Key Target for Prevention of Metabolic Syndrome, Kuopio, Finland
August 23-26, 2011 2nd International Symposium on: Mass Spectrometry in Life Sciences, Bangalore, India
June 19-22, 2011 Translational and Systems Medicine, Stockholm, Sweden
June 15, 2011 PredictAD Workshop: From Patient Data to Personalised Healthcare in Alzheimer’s Disease, Kuopio, Finland
May 23-25, 2011 5e Journées Scientifiques du Réseau Francais Métabolomique et Fluxomique, Paris, France
May 15-20, 2011 Lipid biology and lipotoxicity (Keystone Symposia), Killarney, Co. Kerry, Ireland
March 14, 2011 MASS SPECTROMETRY and METABOLOMICS, Stockholm, Sweden
December 6-10, 2010 British Society for Immunology Congress 2010, Liverpool, UK
October 10-15, 2010 The 11th International Conference on Systems Biology, Edinburgh, UK
July 11-15, 2010 11th International Congress on Obesity, Stockholm, Sweden
June 27 - July 1, 2010 2010 Metabolomics Society Conference, Amsterdam, The Netherlands
June 26 - July 1, 2010 35th FEBS Congress, Gothenburg, Sweden