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Matej Oresic

Title: Senior Lecturer School/office: School of Medical Sciences

Email:

Phone: +46 19 302137

Room: C2201

Matej Oresic

About Matej Oresic

Matej Orešič holds a PhD in biophysics from Cornell University. He is a visiting senior lecturer at Örebro Universitry, group leader in systems medicine at the Turku Centre for Biotechnology, University of Turku, and guest professor at the Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (Wuhan, Hubei, P. R. China). His main research areas are metabolomics applications in biomedical research and integrative bioinformatics. He is particularly interested in the identification of disease vulnerabilities associated with different metabolic phenotypes and the underlying mechanisms linking these vulnerabilities with the development of specific disorders or their co-morbidities, with specific focus on obesity and diabetes and their co-morbidities.

Dr. Orešič has also initiated the popular MZmine open source project, leading to popular software for metabolomics data processing. Previosuly, Dr. Orešič was principal investigator at Steno Diabetes Center (Gentofte, Denmark), research professor at VTT Technical Research Centre of Finland (Espoo, Finland), head of computational biology and modeling at Beyond Genomics, Inc. (Waltham/MA) and bioinformatician at LION Bioscience Research in Cambridge/MA. In 2016, Dr. Oresic received the Lifetime Honorary Fellow award from the Metabolomics Society. He is co-founder and currently chair of the board of the Nordic Metabolomics Society.

Dr. Oresic recently chaired two international metabolomics meetings:

1st Nordic Metabolomics Conference (Örebro, Sweden, August 26-28, 2018)

Gordon Research Conference - Metabolomics and Human Health (Ventura, CA, USA, February 3-8, 2019)

Research Projects

Research Teams

Research Teams

Publications

Publications

Articles in journals |  Articles, reviews/surveys |  Chapters in books | 

Articles in journals

Vande Vyvere, T. , Wilms, G. , Claes, L. , Martin Leon, F. , Nieboer, D. , Verheyden, J. , van den Hauwe, L. , Pullens, P. & et al. (2019). Central versus Local Radiological Reading of Acute Computed Tomography Characteristics in Multi-Center Traumatic Brain Injury Research.. Journal of Neurotrauma, 36 (7), 1080-1092.
Lamichhane, S. , Kemppainen, E. , Trošt, K. , Siljander, H. , Hyöty, H. , Ilonen, J. , Toppari, J. , Veijola, R. & et al. (2019). Circulating metabolites in progression to islet autoimmunity and type 1 diabetes. Diabetologia.
Lamichhane, S. , Ahonen, L. , Dyrlund, T. S. , Dickens, A. M. , Siljander, H. , Hyöty, H. , Ilonen, J. , Toppari, J. & et al. (2019). Cord-Blood Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes. Biomolecules, 9 (1).
van Essen, T. A. , den Boogert, H. F. , Cnossen, M. C. , de Ruiter, G. C. W. , Haitsma, I. , Polinder, S. , Steyerberg, E. W. , Menon, D. & et al. (2019). Correction to: Variation in neurosurgical management of traumatic brain injury. Acta Neurochirurgica, 161 (3), 451-455.
Hernández-Alvarez, M. I. , Sebastián, D. , Vives, S. , Ivanova, S. , Bartoccioni, P. , Kakimoto, P. , Plana, N. , Veiga, S. R. & et al. (2019). Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease. Cell, 177 (4), 881-895.e17.
Geng, D. , Musse, A. A. , Wigh, V. , Carlsson, C. , Engwall, M. , Oresic, M. , Scherbak, N. & Hyötyläinen, T. (2019). Effect of perfluorooctanesulfonic acid (PFOS) on the liver lipid metabolism of the developing chicken embryo. Ecotoxicology and Environmental Safety, 170, 691-698.
Luukkonen, P. K. , Nick, A. , Hölttä-Vuori, M. , Thiele, C. , Isokuortti, E. , Lallukka-Brück, S. , Zhou, Y. , Hakkarainen, A. & et al. (2019). Human PNPLA3-I148M variant increases hepatic retention of polyunsaturated fatty acids. JCI Insight, 4 (16).
Madrid-Gambin, F. , Focking, M. , Sabherwal, S. , Heurich, M. , English, J. A. , O'Gorman, A. , Suvitaival, T. , Ahonen, L. & et al. (2019). Integrated Lipidomics and Proteomics Point to Early Blood-Based Changes in Childhood Preceding Later Development of Psychotic Experiences: Evidence From the Avon Longitudinal Study of Parents and Children. Biological Psychiatry, 86 (1), 25-34.
Playdon, M. C. , Joshi, A. D. , Tabung, F. K. , Cheng, S. , Henglin, M. , Kim, A. , Lin, T. , van Roekel, E. H. & et al. (2019). Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS). Metabolites, 9 (7).
Sen, P. , Carlsson, C. , Virtanen, S. M. , Simell, S. , Hyöty, H. , Ilonen, J. , Toppari, J. , Veijola, R. & et al. (2019). Persistent Alterations in Plasma Lipid Profiles Before Introduction of Gluten in the Diet Associated With Progression to Celiac Disease. Clinical and Translational Gastroenterology, 10.
Pedersen, H. K. , Forslund, S. K. , Gudmundsdottir, V. , Østergaard Petersen, A. , Hildebrand, F. , Hyötyläinen, T. , Nielsen, T. , Hansen, T. & et al. (2018). A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links. Nature Protocols, 13 (12), 2781-2800.
Lamichhane, S. , Ahonen, L. , Dyrlund, T. S. , Siljander, H. , Hyöty, H. , Ilonen, J. , Toppari, J. , Veijola, R. & et al. (2018). A longitudinal plasma lipidomics dataset from children who developed islet autoimmunity and type 1 diabetes. Scientific Data, 5.
Schwarz, E. , Maukonen, J. , Hyytiäinen, T. , Kieseppä, T. , Oresic, M. , Sabunciyan, S. , Mantere, O. , Saarela, M. & et al. (2018). Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response. Schizophrenia Research, 192, 398-403.
Lamichhane, S. , Ahonen, L. , Dyrlund, T. S. , Kemppainen, E. , Siljander, H. , Hyöty, H. , Ilonen, J. , Toppari, J. & et al. (2018). Dynamics of Plasma Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes - Type 1 Diabetes Prediction and Prevention Study (DIPP). Scientific Reports, 8.
Lamichhane, S. , Sen, P. , Dickens, A. M. , Oresic, M. & Bertram, H. C. (2018). Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods, 149, 3-12.
Suvitaival, T. , Bondia-Pons, I. , Yetukuri, L. , Pöhö, P. , Nolan, J. J. , Hyötyläinen, T. , Kuusisto, J. & Orešič, M. (2018). Lipidome as a predictive tool in progression to type 2 diabetes in Finnish men. Metabolism: Clinical and Experimental, 78 (January), 1-12.
Burla, B. , Arita, M. , Arita, M. , Bendt, A. K. , Cazenave-Gassiot, A. , Dennis, E. A. , Ekroos, K. , Han, X. & et al. (2018). MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. Journal of Lipid Research, 59 (10), 2001-2017.
Frank, E. , Maier, D. , Pajula, J. , Suvitaival, T. , Borgan, F. , Butz-Ostendorf, M. , Fischer, A. , Hietala, J. & et al. (2018). Platform for systems medicine research and diagnostic applications in psychotic disorders - The METSY project. European psychiatry, 50, 40-46.
Luukkonen, P. K. , Sädevirta, S. , Zhou, Y. , Kayser, B. , Ali, A. , Ahonen, L. , Lallukka, S. , Pelloux, V. & et al. (2018). Saturated Fat Is More Metabolically Harmful for the Human Liver Than Unsaturated Fat or Simple Sugars. Diabetes Care, 41 (8), 1732-1739.
Dickens, A. M. , Posti, J. P. , Takala, R. S. , Ala-Seppälä, H. M. , Mattila, I. , Coles, J. C. , Frantzén, J. , Hutchinson, P. J. & et al. (2018). Serum Metabolites Associated with Computed TomographyFindings after Traumatic Brain Injury. Journal of Neurotrauma, 35 (22), 2673-2683.
Grip, T. , Dyrlund, T. S. , Ahonen, L. , Domellöf, M. , Hernell, O. , Hyötyläinen, T. , Knip, M. , Lönnerdal, B. & et al. (2018). Serum, plasma and erythrocyte membrane lipidomes in infants fed formula supplemented with bovine milk fat globule membranes. Pediatric Research, 84 (5), 726-732.
Oresic, M. , Anderson, G. , Mattila, I. , Manoucheri, M. , Soininen, H. , Hyötyläinen, T. & Basignani, C. (2018). Targeted Serum Metabolite Profiling Identifies Metabolic Signatures in Patients with Alzheimer's Disease, Normal Pressure Hydrocephalus and Brain Tumor. Frontiers in Neuroscience, 11.
OʼConnell, B. , Kelly, Á. M. , Mockler, D. , Oresic, M. , Denvir, K. , Farrell, G. , Janigro, D. & Wilson, F. (2018). Use of Blood Biomarkers in the Assessment of Sports-Related Concussion-A Systematic Review in the Context of Their Biological Significance. Clinical Journal of Sports Medicine, 28 (6), 561-571.
Bowden, J. A. , Hyötyläinen, T. , Oresic, M. & Zhou, S. (2017). Harmonizing Lipidomics: NIST Interlaboratory Comparison Exercise for Lipidomics using Standard Reference Material 1950 Metabolites in Frozen Human Plasma. Journal of Lipid Research, 58 (12), 2275-2288.
Martínez-Sánchez, N. , Seoane-Collazo, P. , Contreras, C. , Varela, L. , Villarroya, J. , Rial-Pensado, E. , Buqué, X. , Aurrekoetxea, I. & et al. (2017). Hypothalamic AMPK-ER Stress-JNK1 Axis Mediates the Central Actions of Thyroid Hormones on Energy Balance. Cell Metabolism, 26 (1), 212-229.e12.
O'Gorman, A. , Suvitaival, T. , Ahonen, L. , Cannon, M. , Zammit, S. , Lewis, G. , Roche, H. M. , Mattila, I. & et al. (2017). Identification of a plasma signature of psychotic disorder in children and adolescents from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Translational Psychiatry, 7.
Luukkonen, P. K. , Zhou, Y. , Haridas, N. P. A. , Dwivedi, O. P. , Hyötyläinen, T. , Ali, A. , Juuti, A. , Leivonen, M. & et al. (2017). Impaired hepatic lipid synthesis from polyunsaturated fatty acids in TM6SF2 E167K variant carriers with NAFLD. Journal of Hepatology, 67 (1), 128-136.
Hyötyläinen, T. , Ahonen, L. , Pöhö, P. & Oresic, M. (2017). Lipidomics in biomedical research-practical considerations. Biochimica et Biophysica Acta, 1862 (8), 800-803.
Jørgenrud, B. , Stene, L. C. , Tapia, G. , Bøås, H. , Pepaj, M. , Berg, J. P. , Thorsby, P. M. , Orešič, M. & et al. (2017). Longitudinal plasma metabolic profiles, infant feeding, and islet autoimmunity in the MIDIA study. Pediatric Diabetes, 18 (2), 111-119.
Duszka, K. , Oresic, M. , Le May, C. , König, J. & Wahli, W. (2017). PPARγ Modulates Long Chain Fatty Acid Processing in the Intestinal Epithelium. International Journal of Molecular Sciences, 18 (12).
Lankinen, M. , Schwab, U. , Kolehmainen, M. , Paananen, J. , Nygren, H. , Seppänen-Laakso, T. , Poutanen, K. , Hyötyläinen, T. & et al. (2016). A Healthy Nordic Diet Alters the Plasma Lipidomic Profile in Adults with Features of Metabolic Syndrome in a Multicenter Randomized Dietary Intervention. Journal of Nutrition, 146 (4), 662-672.
Hyötyläinen, T. & Orešič, M. (2016). Bioanalytical techniques in nontargeted clinical lipidomics. Bioanalysis, 8 (4), 351-364.
Rocca-Serra, P. , Salek, R. M. , Arita, M. , Correa, E. , Dayalan, S. , Gonzalez-Beltran, A. , Ebbels, T. , Goodacre, R. & et al. (2016). Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics, 12.
Hyötyläinen, T. , Jerby, L. , Petäjä, E. M. , Mattila, I. , Jäntti, S. , Auvinen, P. , Gastaldelli, A. , Yki-Järvinen, H. & et al. (2016). Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature Communications, 7.
Luukkonen, P. K. , Zhou, Y. , Sädevirta, S. , Leivonen, M. , Arola, J. , Oresic, M. , Hyötyläinen, T. & Yki-Järvinen, H. (2016). Hepatic ceramides dissociate steatosis and insulin resistance in patients with non-alcoholic fatty liver disease. Journal of Hepatology, 64 (5), 1167-1175.
Pedersen, H. K. , Gudmundsdottir, V. , Nielsen, H. B. , Hyötyläinen, T. , Nielsen, T. , Jensen, B. A. H. , Forslund, K. , Hildebrand, F. & et al. (2016). Human gut microbes impact host serum metabolome and insulin sensitivity. Nature, 535 (7612), 376-381.
Oresic, M. , Posti, J. P. , Kamstrup-Nielsen, M. H. , Takala, R. S. K. , Lingsma, H. F. , Mattila, I. , Jäntti, S. , Katila, A. J. & et al. (2016). Human Serum Metabolites Associate With Severity and Patient Outcomes in Traumatic Brain Injury. EBioMedicine, 12, 118-126.
Kurko, J. , Tringham, M. , Tanner, L. , Näntö-Salonen, K. , Vähä-Mäkilä, M. , Nygren, H. , Pöhö, P. , Lietzen, N. & et al. (2016). Imbalance of plasma amino acids, metabolites and lipids in patients with lysinuric protein intolerance (LPI). Metabolism: Clinical and Experimental, 65 (9), 1361-1375.
Caesar, R. , Nygren, H. , Orešič, M. & Bäckhed, F. (2016). Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism. Journal of Lipid Research, 57 (3), 474-481.
Vetrani, C. , Rivellese, A. A. , Annuzzi, G. , Adiels, M. , Borén, J. , Mattila, I. , Oresic, M. & Aura, A. (2016). Metabolic transformations of dietary polyphenols: comparison between in vitro colonic and hepatic models and in vivo urinary metabolites. Journal of Nutritional Biochemistry, 33, 111-118.
Beger, R. D. , Dunn, W. , Schmidt, M. A. , Gross, S. S. , Kirwan, J. A. , Cascante, M. , Brennan, L. , Wishart, D. S. & et al. (2016). Metabolomics enables precision medicine: "A White Paper, Community Perspective". Metabolomics, 12 (10).
Zhou, Y. , Oresic, M. , Leivonen, M. , Gopalacharyulu, P. , Hyysalo, J. , Arola, J. , Verrijken, A. , Francque, S. & et al. (2016). Noninvasive Detection of Nonalcoholic Steatohepatitis Using Clinical Markers and Circulating Levels of Lipids and Metabolites. Clinical Gastroenterology and Hepatology, 14 (10), 1463-1472.e6.
Aho, V. , Ollila, H. M. , Kronholm, E. , Bondia-Pons, I. , Soininen, P. , Kangas, A. J. , Hilvo, M. , Seppälä, I. & et al. (2016). Prolonged sleep restriction induces changes in pathways involved in cholesterol metabolism and inflammatory responses. Scientific Reports, 6.
Luukkonen, P. K. , Zhou, Y. , Hyötyläinen, T. , Leivonen, M. , Arola, J. , Orho-Melander, M. , Oresic, M. & Yki-Järvinen, H. (2016). The MBOAT7 variant rs641738 alters hepatic phosphatidylinositols and increases severity of non-alcoholic fatty liver disease in humans. Journal of Hepatology, 65 (6), 1263-1265.
Hyötyläinen, T. & Orešič, M. (2015). Analytical Lipidomics in Metabolic and Clinical Research. Trends in endocrinology and metabolism, 26 (12), 671-673.
Zhou, Y. , Llauradó, G. , Oresic, M. , Hyötyläinen, T. , Orho-Melander, M. & Yki-Järvinen, H. (2015). Circulating triacylglycerol signatures and insulin sensitivity in NAFLD associated with the E167K variant in TM6SF2. Journal of Hepatology, 62 (3), 657-663.
Salek, R. M. , Neumann, S. , Schober, D. , Hummel, J. , Billiau, K. , Kopka, J. , Correa, E. , Reijmers, T. & et al. (2015). COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics, 11 (6), 1587-1597.
Barbarroja, N. , Rodriguez-Cuenca, S. , Nygren, H. , Camargo, A. , Pirraco, A. , Relat, J. , Cuadrado, I. , Pellegrinelli, V. & et al. (2015). Increased dihydroceramide/ceramide ratio mediated by defective expression of degs1 impairs adipocyte differentiation and function. Diabetes, 64 (4), 1180-1192.
Arora, T. , Velagapudi, V. , Pournaras, D. J. , Welbourn, R. , le Roux, C. W. , Oresic, M. & Bäckhed, F. (2015). Roux-en-Y Gastric Bypass Surgery Induces Early Plasma Metabolomic and Lipidomic Alterations in Humans Associated with Diabetes Remission. PLoS ONE, 10 (5).
Foerster, J. , Hyötyläinen, T. , Oresic, M. , Nygren, H. & Boeing, H. (2015). Serum Lipid and Serum Metabolite Components in relation to anthropometric parameters in EPIC-Potsdam participants. Metabolism: Clinical and Experimental, 64 (10), 1348-58.
Kostic, A. D. , Gevers, D. , Siljander, H. , Vatanen, T. , Hyötyläinen, T. , Hämäläinen, A. , Peet, A. , Tillmann, V. & et al. (2015). The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host and Microbe, 17 (2), 260-273.
Hukkanen, J. , Puurunen, J. , Hyötyläinen, T. , Savolainen, M. J. , Ruokonen, A. , Morin-Papunen, L. , Oresic, M. , Piltonen, T. & et al. (2015). The effect of atorvastatin treatment on serum oxysterol concentrations and cytochrome P450 3A4 activity. British Journal of Clinical Pharmacology, 80 (3), 473-479.
Jørgenrud, B. , Jäntti, S. , Mattila, I. , Pöhö, P. , Rønningen, K. S. , Yki-Järvinen, H. , Oresic, M. & Hyötyläinen, T. (2015). The influence of sample collection methodology and sample preprocessing on the blood metabolic profile.. Bioanalysis, 7 (8), 991-1006.
Jørgenrud, B. , Jalanko, M. , Heliö, T. , Jääskeläinen, P. , Laine, M. , Hilvo, M. , Nieminen, M. S. , Laakso, M. & et al. (2015). The Metabolome in Finnish Carriers of the MYBPC3-Q1061X Mutation for Hypertrophic Cardiomyopathy. PLoS ONE, 10 (8).
Naukkarinen, J. , Heinonen, S. , Hakkarainen, A. , Lundbom, J. , Vuolteenaho, K. , Saarinen, L. , Hautaniemi, S. , Rodriguez, A. & et al. (2014). Characterising metabolically healthy obesity in weight-discordant monozygotic twins. Diabetologia, 57 (1), 167-176.
Hyysalo, J. , Gopalacharyulu, P. , Bian, H. , Hyötyläinen, T. , Leivonen, M. , Jaser, N. , Juuti, A. , Honka, M. & et al. (2014). Circulating triacylglycerol signatures in nonalcoholic fatty liver disease associated with the I148M variant in PNPLA3 and with obesity. Diabetes, 63 (1), 312-322.
Lankinen, M. , Kolehmainen, M. , Jääskeläinen, T. , Paananen, J. , Joukamo, L. , Kangas, A. J. , Soininen, P. , Poutanen, K. & et al. (2014). Effects of whole grain, fish and bilberries on serum metabolic profile and lipid transfer protein activities: a randomized trial (Sysdimet). PLoS ONE, 9 (2).
Snowden, S. G. , Grapov, D. , Settergren, M. , D'Alexandri, F. L. , Haeggström, J. Z. , Fiehn, O. , Hyötyläinen, T. , Pedersen, T. L. & et al. (2014). High-dose simvastatin exhibits enhanced lipid-lowering effects relative to simvastatin/ezetimibe combination therapy. Circulation: Cardiovascular Genetics, 7 (6), 955-964.
Bondia-Pons, I. , Pöhö, P. , Bozzetto, L. , Vetrani, C. , Patti, L. , Aura, A. , Annuzzi, G. , Hyötyläinen, T. & et al. (2014). Isoenergetic diets differing in their n-3 fatty acid and polyphenol content reflect different plasma and HDL-fraction lipidomic profiles in subjects at high cardiovascular risk. Molecular Nutrition & Food Research, 58 (9), 1873-1882.
Hohl, M. , Ardehali, H. , Azuaje, F. J. , Breckenridge, R. A. , Doehner, W. , Eaton, P. , Ehret, G. B. , Fujita, T. & et al. (2014). Meeting highlights from the 2013 European Society of Cardiology Heart Failure Association Winter Meeting on Translational Heart Failure Research. European Journal of Heart Failure, 16 (1), 6-14.
Bondia-Pons, I. , Maukonen, J. , Mattila, I. , Rissanen, A. , Saarela, M. , Kaprio, J. , Hakkarainen, A. , Lundbom, J. & et al. (2014). Metabolome and fecal microbiota in monozygotic twin pairs discordant for weight: a Big Mac challenge. The FASEB Journal, 28 (9), 4169-4179.
Hilvo, M. , Gade, S. , Hyötyläinen, T. , Nekljudova, V. , Seppänen-Laakso, T. , Sysi-Aho, M. , Untch, M. , Huober, J. & et al. (2014). Monounsaturated fatty acids in serum triacylglycerols are associated with response to neoadjuvant chemotherapy in breast cancer patients. International Journal of Cancer, 134 (7), 1725-1733.
Hogh, K. N. , Craig, M. N. , Uy, C. E. , Nygren, H. , Asadi, A. , Speck, M. , Fraser, J. D. , Rudecki, A. P. & et al. (2014). Overexpression of PPARγ specifically in pancreatic β-cells exacerbates obesity-induced glucose intolerance, reduces β-cell mass, and alters islet lipid metabolism in male mice. Endocrinology, 155 (10), 3843-3852.
Vetrani, C. , Rivellese, A. A. , Annuzzi, G. , Mattila, I. , Meudec, E. , Hyötyläinen, T. , Oresic, M. & Aura, A. -. (2014). Phenolic metabolites as compliance biomarker for polyphenol intake in a randomized controlled human intervention. Food Research International, 63 (B), 233-238.
Jäntti, S. E. , Kivilompolo, M. , Öhrnberg, L. , Pietiläinen, K. H. , Nygren, H. , Oresic, M. & Hyötyläinen, T. (2014). Quantitative profiling of bile acids in blood, adipose tissue, intestine, and gall bladder samples using ultra high performance liquid chromatography-tandem mass spectrometry. Analytical and Bioanalytical Chemistry, 406 (30), 7799-7815.
Andersen, G. S. T. , Thybo, T. , Cederberg, H. , Oresic, M. , Esteller, M. B. , Zorzano, A. , Carr, B. M. , Walker, M. G. & et al. (2014). The DEXLIFE study methods: identifying novel candidate biomarkers that predict progression to type 2 diabetes in high risk individuals. Diabetes Research and Clinical Practice, 106 (2), 383-389.
Nygren, H. , Pöhö, P. , Seppänen-Laakso, T. , Lahtinen, U. , Oresic, M. & Hyötyläinen, T. (2014). Ultrahigh-performance liquid chromatography-mass spectrometry in Lipidomics. LC GC North America, 32 (4), 286-293.
Carobbio, S. , Hagen, R. M. , Lelliott, C. J. , Slawik, M. , Medina-Gomez, G. , Tan, C. , Sicard, A. , Atherton, H. J. & et al. (2013). Adaptive changes of the Insig1/SREBP1/SCD1 set point help adipose tissue to cope with increased storage demands of obesity. Diabetes, 62 (11), 3697-3708.
Lahti, L. , Salonen, A. , Kekkonen, R. A. , Salojärvi, J. , Jalanka-Tuovinen, J. , Palva, A. , Oresic, M. & de Vos, W. M. (2013). Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data. PeerJ, 1.
Hartonen, M. , Mattila, I. , Ruskeepää, A. , Oresic, M. & Hyötyläinen, T. (2013). Characterization of cerebrospinal fluid by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry. Journal of Chromatography A, 1293, 142-149.
Aura, A. , Mattila, I. , Hyötyläinen, T. , Gopalacharyulu, P. , Cheynier, V. , Souquet, J. , Bes, M. , Le Bourvellec, C. & et al. (2013). Characterization of microbial metabolism of Syrah grape products in an in vitro colon model using targeted and non-targeted analytical approaches. European Journal of Nutrition, 52 (2), 833-846.
Budczies, J. , Brockmöller, S. F. , Müller, B. M. , Barupal, D. K. , Richter-Ehrenstein, C. , Kleine-Tebbe, A. , Griffin, J. L. , Oresic, M. & et al. (2013). Comparative metabolomics of estrogen receptor positive and estrogen receptor negative breast cancer: alterations in glutamine and beta-alanine metabolism. Journal of Proteomics, 94, 279-288.
Oresic, M. , Gopalacharyulu, P. , Mykkänen, J. , Lietzen, N. , Mäkinen, M. , Nygren, H. , Simell, S. , Simell, V. & et al. (2013). Cord serum lipidome in prediction of islet autoimmunity and type 1 diabetes. Diabetes, 62 (9), 3268-3274.
La Torre, D. , Seppänen-Laakso, T. , Larsson, H. E. , Hyötyläinen, T. , Ivarsson, S. A. , Lernmark, Å. & Oresic, M. (2013). Decreased cord-blood phospholipids in young age-at-onset type 1 diabetes. Diabetes, 62 (11), 3951-3956.
Uusitupa, M. U. , Hermansen, K. , Savolainen, M. J. , Schwab, U. S. , Kolehmainen, M. , Brader, L. J. , Mortensen, L. S. , Cloetens, L. & et al. (2013). Effects of an isocaloric healthy Nordic diet on insulin sensitivity, lipid profile and inflammation markers in metabolic syndrome: a randomized study (SYSDIET). Journal of Internal Medicine, 274 (1), 52-66.
Laurila, P. , Surakka, I. , Sarin, A. , Yetukuri, L. , Hyötyläinen, T. , Söderlund, S. , Naukkarinen, J. , Tang, J. & et al. (2013). Genomic, transcriptomic, and lipidomic profiling highlights the role of inflammation in individuals with low high-density lipoprotein cholesterol. Arteriosclerosis, Thrombosis and Vascular Biology, 33 (4), 847-857.
Sayin, S. I. , Wahlström, A. , Felin, J. , Jäntti, S. , Marschall, H. , Bamberg, K. , Angelin, B. , Hyötyläinen, T. & et al. (2013). Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metabolism, 17 (2), 225-235.
Koivuniemi, A. , Sysi-Aho, M. , Oresic, M. & Ollila, S. (2013). Interfacial properties of high-density lipoprotein-like lipid droplets with different lipid and apolipoprotein A-I compositions. Biophysical Journal, 104 (10), 2193-2201.
Suvisaari, J. & Oresic, M. (2013). Metabolomiikka psyko o situtkimuksessa [Metabolomics in psychosis research]. Duodecim, 129 (21), 2237-2244.
Havula, E. , Teesalu, M. , Hyötyläinen, T. , Seppälä, H. , Hasygar, K. , Auvinen, P. , Oresic, M. , Sandmann, T. & et al. (2013). Mondo/ChREBP-Mlx-regulated transcriptional network is essential for dietary sugar tolerance in Drosophila. PLoS Genetics, 9 (4).
Orešič, M. , Hyötyläinen, T. , Kotronen, A. , Gopalacharyulu, P. , Nygren, H. , Arola, J. , Castillo, S. , Mattila, I. & et al. (2013). Prediction of non-alcoholic fatty-liver disease and liver fat content by serum molecular lipids. Diabetologia, 56 (10), 2266-2274.
Kivilompolo, M. , Öhrnberg, L. , Oresic, M. & Hyötyläinen, T. (2013). Rapid quantitative analysis of carnitine and acylcarnitines by ultra-high performance-hydrophilic interaction liquid chromatography-tandem mass spectrometry. Journal of Chromatography A, 1292, 189-194.
Joukamo, L. , Lankinen, M. , Schwab, U. , Soininen, P. , Kangas, A. J. , Kolehmainen, M. , Paananen, J. , Poutanen, K. & et al. (2013). Rasvainen kala muokkaa HDL-hiukkaskokoa ja lipidipitoisuuksia [Fatty fish modifies HDL particle size and lipid concentrations]. Duodecim, 129 (24), 2661-2670.
Lonnberg, T. , Yetukuri, L. , Seppanen-Laakso, T. , Lahesmaa, R. & Oresic, M. (2013). T-cell activation induces selective changes of cellular lipidome. Frontiers in Bioscience (Elite Edition), 5, 558-573.
Antila, K. , Lötjönen, J. , Thurfjell, L. , Laine, J. , Massimini, M. , Rueckert, D. , Zubarev, R. A. , Oresic, M. & et al. (2013). The PredictAD project: development of novel biomarkers and analysis software for early diagnosis of the Alzheimer's disease. Interface Focus, 3 (2).
Nygren, H. , Pöhö, P. , Seppänen-Laakso, T. , Lahtinen, U. , Oresic, M. & Hyötyläinen, T. (2013). Ultrahigh-performance liquid chromatography-mass spectrometry in lipidomics. LC GC Europe, 26 (3), 142-148.
Lehtinen, L. , Vainio, P. , Wikman, H. , Reemts, J. , Hilvo, M. , Issa, R. , Pollari, S. , Brandt, B. & et al. (2012). 15-Hydroxyprostaglandin dehydrogenase associates with poor prognosis in breast cancer, induces epithelial-mesenchymal transition, and promotes cell migration in cultured breast cancer cells. Journal of Pathology, 226 (4), 674-686.
Martínez-García, C. , Izquierdo, A. , Velagapudi, V. , Vivas, Y. , Velasco, I. , Campbell, M. , Burling, K. , Cava, F. & et al. (2012). Accelerated renal disease is associated with the development of metabolic syndrome in a glucolipotoxic mouse model. Disease Models and Mechanisms, 5 (5), 636-48.
Finckenberg, P. , Eriksson, O. , Baumann, M. , Merasto, S. , Lalowski, M. M. , Levijoki, J. , Haasio, K. , Kytö, V. & et al. (2012). Caloric restriction ameliorates angiotensin II-induced mitochondrial remodeling and cardiac hypertrophy. Hypertension, 59 (1), 76-84.
Jauhiainen, T. A. , Niittynen, L. H. , Oresic, M. , Järvenpää, S. K. , Hiltunen, T. P. , Rönnback, M. , Vapaatalo, H. I. & Korpela, R. A. (2012). Effects of long-term intake of lactotripeptides on cardiovascular risk factors in hypertensive subjects. European Journal of Clinical Nutrition, 66 (7), 843-849.
Ylipaasto, P. , Smura, T. , Gopalacharyulu, P. , Paananen, A. , Seppänen-Laakso, T. , Kaijalainen, S. , Ahlfors, H. , Korsgren, O. & et al. (2012). Enterovirus-induced gene expression profile is critical for human pancreatic islet destruction. Diabetologia, 55 (12), 3273-3283.
Kolak, M. , Gertow, J. , Westerbacka, J. , Summers, S. A. , Liska, J. , Franco-Cereceda, A. , Oresic, M. , Yki-Järvinen, H. & et al. (2012). Expression of ceramide-metabolising enzymes in subcutaneous and intra-abdominal human adipose tissue. Lipids in Health and Disease, 11.
Ottestad, I. , Hassani, S. , Borge, G. I. , Kohler, A. , Vogt, G. , Hyötyläinen, T. , Oresic, M. , Brønner, K. W. & et al. (2012). Fish oil supplementation alters the plasma lipidomic profile and increases long-chain PUFAs of phospholipids and triglycerides in healthy subjects. PLoS ONE, 7 (8).
Lindfors, E. , Mattila, J. , Gopalacharyulu, P. V. , Pesonen, A. , Lötjönen, J. & Oresic, M. (2012). Heterogeneous biological network visualization system: case study in context of medical image data. Advances in Experimental Medicine and Biology, 736, 95-118.
Xu, X. , Gopalacharyulu, P. , Seppänen-Laakso, T. , Ruskeepää, A. , Aye, C. C. , Carson, B. P. , Mora, S. , Oresic, M. & et al. (2012). Insulin signaling regulates fatty acid catabolism at the level of CoA activation. PLoS Genetics, 8 (1).
Brockmöller, S. F. , Bucher, E. , Müller, B. M. , Budczies, J. , Hilvo, M. , Griffin, J. L. , Oresic, M. , Kallioniemi, O. & et al. (2012). Integration of metabolomics and expression of glycerol-3-phosphate acyltransferase (GPAM) in breast cancer-link to patient survival, hormone receptor status, and metabolic profiling. Journal of Proteome Research, 11 (2), 850-60.
Virtue, S. , Masoodi, M. , Velagapudi, V. , Tan, C. Y. , Dale, M. , Suorti, T. , Slawik, M. , Blount, M. & et al. (2012). Lipocalin prostaglandin D synthase and PPARγ2 coordinate to regulate carbohydrate and lipid metabolism in vivo. PLoS ONE, 7 (7).
Jerby, L. , Wolf, L. , Denkert, C. , Stein, G. Y. , Hilvo, M. , Oresic, M. , Geiger, T. & Ruppin, E. (2012). Metabolic associations of reduced proliferation and oxidative stress in advanced breast cancer. Cancer Research, 72 (22), 5712-5720.
Hyötyläinen, T. , Mattila, I. , Wiedmer, S. K. , Koivuniemi, A. , Taskinen, M. , Yki-Järvinen, H. & Oresic, M. (2012). Metabolomic analysis of polar metabolites in lipoprotein fractions identifies lipoprotein-specific metabolic profiles and their association with insulin resistance. Molecular Biosystems, 8 (10), 2559-2565.
Sebastián, D. , Hernández-Alvarez, M. I. , Segalés, J. , Sorianello, E. , Muñoz, J. P. , Sala, D. , Waget, A. , Liesa, M. & et al. (2012). Mitofusin 2 (Mfn2) links mitochondrial and endoplasmic reticulum function with insulin signaling and is essential for normal glucose homeostasis. Proceedings of the National Academy of Sciences of the United States of America, 109 (14), 5523-5528.
Rodriguez-Cuenca, S. , Carobbio, S. , Velagapudi, V. R. , Barbarroja, N. , Moreno-Navarrete, J. M. , Tinahones, F. J. , Fernandez-Real, J. M. , Oresic, M. & et al. (2012). Peroxisome proliferator-activated receptor γ-dependent regulation of lipolytic nodes and metabolic flexibility. Molecular and Cellular Biology, 32 (8), 1555-1565.
Oresic, M. , Seppänen-Laakso, T. , Sun, D. , Tang, J. , Therman, S. , Viehman, R. , Mustonen, U. , van Erp, T. G. & et al. (2012). Phospholipids and insulin resistance in psychosis: A lipidomics study of twin pairs discordant for schizophrenia. Genome Medicine, 4 (1).
Budczies, J. , Denkert, C. , Müller, B. M. , Brockmöller, S. F. , Klauschen, F. , Györffy, B. , Dietel, M. , Richter-Ehrenstein, C. & et al. (2012). Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study. BMC Genomics, 13 (1).
Ketola, K. , Hilvo, M. , Hyötyläinen, T. , Vuoristo, A. , Ruskeepää, A. L. , Oresic, M. , Kallioniemi, O. P. & Iljin, K. (2012). Salinomycin inhibits prostate cancer growth and migration via induction of oxidative stress. British Journal of Cancer, 106 (1), 99-106.
Pflueger, M. , Seppänen-Laakso, T. , Suortti, T. , Hyötyläinen, T. , Achenbach, P. , Bonifacio, E. , Oresic, M. & Ziegler, A. (2011). Age- and islet autoimmunity-associated differences in amino acid and lipid metabolites in children at risk for type 1 diabetes. Diabetes, 60 (11), 2740-2747.
Pietiläinen, K. H. , Róg, T. , Seppänen-Laakso, T. , Virtue, S. , Gopalacharyulu, P. , Tang, J. , Rodriguez-Cuenca, S. , Maciejewski, A. & et al. (2011). Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans. PLoS biology, 9 (6).
de Mas, I. M. , Selivanov, V. A. , Marin, S. , Roca, J. , Oresic, M. , Agius, L. & Cascante, M. (2011). Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions. BMC Systems Biology, 5.
Castillo, S. , Mattila, I. , Miettinen, J. , Oresic, M. & Hyötyläinen, T. (2011). Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry. Analytical Chemistry, 83 (8), 3058-3067.
Gurung, I. S. , Medina-Gomez, G. , Kis, A. , Baker, M. , Velagapudi, V. , Neogi, S. G. , Campbell, M. , Rodriguez-Cuenca, S. & et al. (2011). Deletion of the metabolic transcriptional coactivator PGC1β induces cardiac arrhythmia. Cardiovascular Research, 92 (1), 29-38.
Prieur, X. , Mok, C. Y. L. , Velagapudi, V. R. , Núñez, V. , Fuentes, L. , Montaner, D. , Ishikawa, K. , Camacho, A. & et al. (2011). Differential lipid partitioning between adipocytes and tissue macrophages modulates macrophage lipotoxicity and M2/M1 polarization in obese mice. Diabetes, 60 (3), 797-809.
Aura, A. , Mattila, I. , Hyötyläinen, T. , Gopalacharyulu, P. , Bounsaythip, C. , Oresic, M. & Oksman-Caldentey, K. (2011). Drug metabolome of the simvastatin formed by human intestinal microbiota in vitro. Molecular Biosystems, 7 (2), 437-446.
Götz, A. , Tyynismaa, H. , Euro, L. , Ellonen, P. , Hyötyläinen, T. , Ojala, T. , Hämäläinen, R. H. , Tommiska, J. & et al. (2011). Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. American Journal of Human Genetics, 88 (5), 635-642.
Prawitt, J. , Abdelkarim, M. , Stroeve, J. H. M. , Popescu, I. , Duez, H. , Velagapudi, V. R. , Dumont, J. , Bouchaert, E. & et al. (2011). Farnesoid X receptor deficiency improves glucose homeostasis in mouse models of obesity. Diabetes, 60 (7), 1861-1871.
Yetukuri, L. , Huopaniemi, I. , Koivuniemi, A. , Maranghi, M. , Hiukka, A. , Nygren, H. , Kaski, S. , Taskinen, M. & et al. (2011). High density lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy. PLoS ONE, 6 (8).
Rantamäki, A. H. , Seppänen-Laakso, T. , Oresic, M. , Jauhiainen, M. & Holopainen, J. M. (2011). Human tear fluid lipidome: from composition to function. PLoS ONE, 6 (5).
Oresic, M. (2011). Informatics and computational strategies for the study of lipids. Biochimica et Biophysica Acta, 1811 (11), 991-999.
Nygren, H. , Seppänen-Laakso, T. , Castillo, S. , Hyötyläinen, T. & Oresic, M. (2011). Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics for studies of body fluids and tissues. Methods in Molecular Biology, 708, 247-257.
Sysi-Aho, M. , Ermolov, A. , Gopalacharyulu, P. V. , Tripathi, A. , Seppänen-Laakso, T. , Maukonen, J. , Mattila, I. , Ruohonen, S. T. & et al. (2011). Metabolic regulation in progression to autoimmune diabetes. PloS Computational Biology, 7 (10).
Orešič, M. , Hyötyläinen, T. , Herukka, S. , Sysi-Aho, M. , Mattila, I. , Seppänan-Laakso, T. , Julkunen, V. , Gopalacharyulu, P. V. & et al. (2011). Metabolome in progression to Alzheimer's disease. Translational Psychiatry, 1.
Oresic, M. , Tang, J. , Seppänen-Laakso, T. , Mattila, I. , Saarni, S. E. , Saarni, S. I. , Lönnqvist, J. , Sysi-Aho, M. & et al. (2011). Metabolome in schizophrenia and other psychotic disorders: a general population-based study. Genome Medicine, 3 (3).
Lankinen, M. , Schwab, U. , Seppänen-Laakso, T. , Mattila, I. , Juntunen, K. , Mykkänen, H. , Poutanen, K. , Gylling, H. & et al. (2011). Metabolomic analysis of plasma metabolites that may mediate effects of rye bread on satiety and weight maintenance in postmenopausal women. Journal of Nutrition, 141 (1), 31-36.
Kankainen, M. , Gopalacharyulu, P. , Holm, L. & Oresic, M. (2011). MPEA--metabolite pathway enrichment analysis. Bioinformatics, 27 (13), 1878-1879.
Hilvo, M. , Denkert, C. , Lehtinen, L. , Müller, B. , Brockmöller, S. , Seppänen-Laakso, T. , Budczies, J. , Bucher, E. & et al. (2011). Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression. Cancer Research, 71 (9), 3236-45.
Vainio, P. , Lehtinen, L. , Mirtti, T. , Hilvo, M. , Seppänen-Laakso, T. , Virtanen, J. , Sankila, A. , Nordling, S. & et al. (2011). Phospholipase PLA2G7, associated with aggressive prostate cancer, promotes prostate cancer cell migration and invasion and is inhibited by statins. OncoTarget, 2 (12), 1176-1190.
Bondia-Pons, I. , Nordlund, E. , Mattila, I. , Katina, K. , Aura, A. , Kolehmainen, M. , Oresic, M. , Mykkänen, H. & et al. (2011). Postprandial differences in the plasma metabolome of healthy Finnish subjects after intake of a sourdough fermented endosperm rye bread versus white wheat bread. Nutrition Journal, 10.
Sysi-Aho, M. , Koikkalainen, J. , Seppänen-Laakso, T. , Kaartinen, M. , Kuusisto, J. , Peuhkurinen, K. , Kärkkäinen, S. , Antila, M. & et al. (2011). Serum lipidomics meets cardiac magnetic resonance imaging: profiling of subjects at risk of dilated cardiomyopathy. PLoS ONE, 6 (1).
Lankinen, M. , Schwab, U. , Kolehmainen, M. , Paananen, J. , Poutanen, K. , Mykkänen, H. , Seppänen-Laakso, T. , Gylling, H. & et al. (2011). Whole grain products, fish and bilberries alter glucose and lipid metabolism in a randomized, controlled trial: the Sysdimet study. PLoS ONE, 6 (8).
Kotronen, A. , Seppänen-Laakso, T. , Westerbacka, J. , Kiviluoto, T. , Arola, J. , Ruskeepää, A. , Yki-Järvinen, H. & Oresic, M. (2010). Comparison of lipid and fatty acid composition of the liver, subcutaneous and intra-abdominal adipose tissue, and serum. Obesity, 18 (5), 937-944.
Yetukuri, L. , Söderlund, S. , Koivuniemi, A. , Seppänen-Laakso, T. , Niemelä, P. S. , Hyvönen, M. , Taskinen, M. , Vattulainen, I. & et al. (2010). Composition and lipid spatial distribution of HDL particles in subjects with low and high HDL-cholesterol. Journal of Lipid Research, 51 (8), 2341-2351.
Lankinen, M. A. , Schwab, U. S. , Gopalacharyulu, P. , Seppänen-Laakso, T. E. V. T. R. C. o. F. E. F. A. I. 5. F. t. A. , Yetukuri, L. , Sysi-Aho, M. , Kallio, P. , Suortti, T. M. & et al. (2010). Dietary carbohydrate modification alters serum metabolic profiles in individuals with the metabolic syndrome. NMCD. Nutrition Metabolism and Cardiovascular Diseases, 20 (4), 249-57.
Leskinen, T. , Rinnankoski-Tuikka, R. , Rintala, M. , Seppänen-Laakso, T. , Pöllänen, E. , Alen, M. , Sipilä, S. , Kaprio, J. & et al. (2010). Differences in muscle and adipose tissue gene expression and cardio-metabolic risk factors in the members of physical activity discordant twin pairs. PLoS ONE, 5 (9).
López, M. , Varela, L. , Vázquez, M. J. , Rodríguez-Cuenca, S. , González, C. R. , Velagapudi, V. R. , Morgan, D. A. , Schoenmakers, E. & et al. (2010). Hypothalamic AMPK and fatty acid metabolism mediate thyroid regulation of energy balance. Nature Medicine, 16 (9), 1001-1008.
Ahola-Erkkilä, S. , Carroll, C. J. , Peltola-Mjösund, K. , Tulkki, V. , Mattila, I. , Seppänen-Laakso, T. , Oresic, M. , Tyynismaa, H. & et al. (2010). Ketogenic diet slows down mitochondrial myopathy progression in mice. Human Molecular Genetics, 19 (10), 1974-1984.
Mervaala, E. , Biala, A. , Merasto, S. , Lempiäinen, J. , Mattila, I. , Martonen, E. , Eriksson, O. , Louhelainen, M. & et al. (2010). Metabolomics in angiotensin II-induced cardiac hypertrophy. Hypertension, 55 (2), 508-515.
Tyynismaa, H. , Carroll, C. J. , Raimundo, N. , Ahola-Erkkilä, S. , Wenz, T. , Ruhanen, H. , Guse, K. , Hemminki, A. & et al. (2010). Mitochondrial myopathy induces a starvation-like response. Human Molecular Genetics, 19 (20), 3948-3958.
Huopaniemi, I. , Suvitaival, T. , Nikkilä, J. , Oresic, M. & Kaski, S. (2010). Multivariate multi-way analysis of multi-source data. Bioinformatics, 26 (12), i391-i398.
Hall, D. , Poussin, C. , Velagapudi, V. R. , Empsen, C. , Joffraud, M. , Beckmann, J. S. , Geerts, A. E. , Ravussin, Y. & et al. (2010). Peroxisomal and microsomal lipid pathways associated with resistance to hepatic steatosis and reduced pro-inflammatory state. Journal of Biological Chemistry, 285 (40), 31011-31023.
Lagathu, C. , Christodoulides, C. , Tan, C. Y. , Virtue, S. , Laudes, M. , Campbell, M. , Ishikawa, K. , Ortega, F. & et al. (2010). Secreted frizzled-related protein 1 regulates adipose tissue expansion and is dysregulated in severe obesity.. International Journal of Obesity, 34 (12), 1695-1705.
Westerbacka, J. , Kotronen, A. , Fielding, B. A. , Wahren, J. , Hodson, L. , Perttilä, J. , Seppänen-Laakso, T. , Suortti, T. & et al. (2010). Splanchnic balance of free fatty acids, endocannabinoids, and lipids in subjects with nonalcoholic fatty liver disease. Gastroenterology, 139 (6), 1961-1971.e1.
Oresic, M. (2010). Systems biology strategy to study lipotoxicity and the metabolic syndrome. Biochimica et Biophysica Acta, 1801 (3), 235-239.
Velagapudi, V. R. , Hezaveh, R. , Reigstad, C. S. , Gopalacharyulu, P. , Yetukuri, L. , Islam, S. , Felin, J. , Perkins, R. & et al. (2010). The gut microbiota modulates host energy and lipid metabolism in mice. Journal of Lipid Research, 51 (5), 1101-1112.
Medina-Gomez, G. , Yetukuri, L. , Velagapudi, V. , Campbell, M. , Blount, M. , Jimenez-Linan, M. , Ros, M. , Oresic, M. & et al. (2009). Adaptation and failure of pancreatic beta cells in murine models with different degrees of metabolic syndrome. Disease Models and Mechanisms, 2 (11-12), 582-592.
Hiukka, A. , Ståhlman, M. , Pettersson, C. , Levin, M. , Adiels, M. , Teneberg, S. , Leinonen, E. S. , Hultén, L. M. & et al. (2009). ApoCIII-enriched LDL in type 2 diabetes displays altered lipid composition, increased susceptibility for sphingomyelinase, and increased binding to biglycan. Diabetes, 58 (9), 2018-2026.
Niemelä, P. S. , Castillo, S. , Sysi-Aho, M. & Oresic, M. (2009). Bioinformatics and computational methods for lipidomics. Journal of chromatography. B, 877 (26), 2855-2862.
Wheelock, C. E. , Goto, S. , Yetukuri, L. , D'Alexandri, F. L. , Klukas, C. , Schreiber, F. & Oresic, M. (2009). Bioinformatics strategies for the analysis of lipids. Methods in Molecular Biology, 580, 339-368.
Gopalacharyulu, P. V. , Velagapudi, V. R. , Lindfors, E. , Halperin, E. & Oresic, M. (2009). Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. Molecular Biosystems, 5 (3), 276-287.
Kajander, K. , Myllyluoma, E. , Kyrönpalo, S. , Rasmussen, M. , Sipponen, P. , Mattila, I. , Seppänen-Laakso, T. , Vapaatalo, H. & et al. (2009). Elevated pro-inflammatory and lipotoxic mucosal lipids characterise irritable bowel syndrome. World Journal of Gastroenterology, 15 (48), 6068-6074.
Lankinen, M. , Schwab, U. , Erkkilä, A. , Seppänen-Laakso, T. , Hannila, M. , Mussalo, H. , Lehto, S. , Uusitupa, M. & et al. (2009). Fatty fish intake decreases lipids related to inflammation and insulin signaling: a lipidomics approach. PLoS ONE, 4 (4).
Oresic, M. , Seppänen-Laakso, T. , Yetukuri, L. , Bäckhed, F. & Hänninen, V. (2009). Gut microbiota affects lens and retinal lipid composition. Experimental Eye Research, 89 (5), 604-607.
Kotronen, A. , Seppänen-Laakso, T. , Westerbacka, J. , Kiviluoto, T. , Arola, J. , Ruskeepää, A. , Oresic, M. & Yki-Järvinen, H. (2009). Hepatic stearoyl-CoA desaturase (SCD)-1 activity and diacylglycerol but not ceramide concentrations are increased in the nonalcoholic human fatty liver. Diabetes, 58 (1), 203-208.
Gatfield, D. , Le Martelot, G. , Vejnar, C. E. , Gerlach, D. , Schaad, O. , Fleury-Olela, F. , Ruskeepää, A. , Oresic, M. & et al. (2009). Integration of microRNA miR-122 in hepatic circadian gene expression. Genes & Development, 23 (11), 1313-26.
de Mello, V. D. F. , Lankinen, M. , Schwab, U. , Kolehmainen, M. , Lehto, S. , Seppänen-Laakso, T. , Oresic, M. , Pulkkinen, L. & et al. (2009). Link between plasma ceramides, inflammation and insulin resistance: association with serum IL-6 concentration in patients with coronary heart disease. Diabetologia, 52 (12), 2612-2615.
Oresic, M. (2009). Metabolomics, a novel tool for studies of nutrition, metabolism and lipid dysfunction. NMCD. Nutrition Metabolism and Cardiovascular Diseases, 19 (11), 816-824.
Nath, A. K. , Krauthammer, M. , Li, P. , Davidov, E. , Butler, L. C. , Copel, J. , Katajamaa, M. , Oresic, M. & et al. (2009). Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. PLoS ONE, 4 (1).
Róg, T. , Martinez-Seara, H. , Munck, N. , Oresic, M. , Karttunen, M. & Vattulainen, I. (2009). Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations. Journal of Physical Chemistry B, 113 (11), 3413-3422.
Kotronen, A. , Velagapudi, V. R. , Yetukuri, L. , Westerbacka, J. , Bergholm, R. , Ekroos, K. , Makkonen, J. , Taskinen, M. & et al. (2009). Serum saturated fatty acids containing triacylglycerols are better markers of insulin resistance than total serum triacylglycerol concentrations. Diabetologia, 52 (4), 684-690.
de Mello, V. D. F. , Erkkilä, A. T. , Schwab, U. S. , Pulkkinen, L. , Kolehmainen, M. , Atalay, M. , Mussalo, H. , Lankinen, M. & et al. (2009). The effect of fatty or lean fish intake on inflammatory gene expression in peripheral blood mononuclear cells of patients with coronary heart disease. European Journal of Nutrition, 48 (8), 447-455.
Gopalacharyulu, P. V. , Lindfors, E. , Miettinen, J. , Bounsaythip, C. K. & Oresic, M. (2008). An integrative approach for biological data mining and visualisation. International Journal of Data Mining and Bioinformatics, 2 (1), 54-77.
Mattila, I. , Seppänen-Laakso, T. , Suortti, T. & Oresic, M. (2008). Application of lipidomics and metabolomics to the study of adipose tissue. Methods in Molecular Biology, 456, 123-130.
Minehira, K. , Young, S. G. , Villanueva, C. J. , Yetukuri, L. , Oresic, M. , Hellerstein, M. K. , Farese, R. V. , Horton, J. D. & et al. (2008). Blocking VLDL secretion causes hepatic steatosis but does not affect peripheral lipid stores or insulin sensitivity in mice. Journal of Lipid Research, 49 (9), 2038-2044.
Oresic, M. , Simell, S. , Sysi-Aho, M. , Näntö-Salonen, K. , Seppänen-Laakso, T. , Parikka, V. , Katajamaa, M. , Hekkala, A. & et al. (2008). Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes. Journal of Experimental Medicine, 205 (13), 2975-2984.
Koikkalainen, J. R. , Antila, M. , Lötjönen, J. M. P. , Heliö, T. , Lauerma, K. , Kivistö, S. M. , Sipola, P. , Kaartinen, M. A. & et al. (2008). Early familial dilated cardiomyopathy: identification with determination of disease state parameter from cine MR image data. Radiology, 249 (1), 88-96.
Kekkonen, R. , Sysi-Aho, M. , Seppanen-Laakso, T. , Julkunen, I. , Vapaatalo, H. , Oresic, M. & Korpela, R. (2008). Effect of probiotic Lactobacillus rhamnosus GG intervention on global serum lipidomic profiles in healthy adults. World Journal of Gastroenterology, 14 (20), 3188-3194.
Nikkilä, J. , Sysi-Aho, M. , Ermolov, A. , Seppänen-Laakso, T. , Simell, O. , Kaski, S. & Oresic, M. (2008). Gender-dependent progression of systemic metabolic states in early childhood. Molecular Systems Biology, 4.
Pietiläinen, K. H. , Naukkarinen, J. , Rissanen, A. , Saharinen, J. , Ellonen, P. , Keränen, H. , Suomalainen, A. , Götz, A. & et al. (2008). Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Medicine, 5 (3).
Yetukuri, L. , Ekroos, K. , Vidal-Puig, A. & Oresic, M. (2008). Informatics and computational strategies for the study of lipids. Molecular Biosystems, 4 (2), 121-127.
Oresic, M. , Hänninen, V. A. & Vidal-Puig, A. (2008). Lipidomics: a new window to biomedical frontiers. Trends in Biotechnology, 26 (12), 647-652.
Laaksonen, R. , Jänis, M. T. & Oresic, M. (2008). Lipidomics-based safety biomarkers for lipid-lowering treatments. Angiology, 59 (2 Suppl), 65S-68S.
Pilvi, T. , Seppanen-Laakso, T. , Simolin, H. , Finckenberg, P. , Huotari, A. , Herzig, K. , Korpela, R. , Oresic, M. & et al. (2008). Metabolomic changes in fatty liver can be modified by dietary protein and calcium during energy restriction. World Journal of Gastroenterology, 14 (28), 4462-4472.
Karpanen, T. , Bry, M. , Ollila, H. M. , Seppänen-Laakso, T. , Liimatta, E. , Leskinen, H. , Kivelä, R. , Helkamaa, T. & et al. (2008). Overexpression of vascular endothelial growth factor-B in mouse heart alters cardiac lipid metabolism and induces myocardial hypertrophy. Circulation Research, 103 (9), 1018-1026.
Schwab, U. , Seppänen-Laakso, T. , Yetukuri, L. , Ågren, J. , Kolehmainen, M. , Laaksonen, D. E. , Ruskeepää, A. , Gylling, H. & et al. (2008). Triacylglycerol fatty acid composition in diet-induced weight loss in subjects with abnormal glucose metabolism: the GENOBIN study. PLoS ONE, 3 (7).
Pietiläinen, K. H. , Sysi-Aho, M. , Rissanen, A. , Seppänen-Laakso, T. , Yki-Järvinen, H. , Kaprio, J. & Oresic, M. (2007). Acquired obesity is associated with changes in the serum lipidomic profile independent of genetic effects: a monozygotic twin study. PLoS ONE, 2 (2).
Kolak, M. , Westerbacka, J. , Velagapudi, V. R. , Wågsäter, D. , Yetukuri, L. , Makkonen, J. , Rissanen, A. , Häkkinen, A. & et al. (2007). Adipose tissue inflammation and increased ceramide content characterize subjects with high liver fat content independent of obesity. Diabetes, 56 (8), 1960-1968.
Yetukuri, L. , Katajamaa, M. , Medina-Gomez, G. , Seppänen-Laakso, T. , Vidal-Puig, A. & Oresic, M. (2007). Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. BMC Systems Biology, 1.
Sysi-Aho, M. , Vehtari, A. , Velagapudi, V. R. , Westerbacka, J. , Yetukuri, L. , Bergholm, R. , Taskinen, M. , Yki-Järvinen, H. & et al. (2007). Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles. Bioinformatics, 23 (13), i519-i528.
Medina-Gomez, G. , Gray, S. L. , Yetukuri, L. , Shimomura, K. , Virtue, S. , Campbell, M. , Curtis, R. K. , Jimenez-Linan, M. & et al. (2007). PPAR gamma 2 prevents lipotoxicity by controlling adipose tissue expandability and peripheral lipid metabolism. PLoS Genetics, 3 (4).
Elo, L. L. , Järvenpää, H. , Oresic, M. , Lahesmaa, R. & Aittokallio, T. (2007). Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics, 23 (16), 2096-2103.
Laaksonen, R. , Katajamaa, M. , Päivä, H. , Sysi-Aho, M. , Saarinen, L. , Junni, P. , Lütjohann, D. , Smet, J. & et al. (2006). A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS ONE, 1.
Lelliott, C. J. , Medina-Gomez, G. , Petrovic, N. , Kis, A. , Feldmann, H. M. , Bjursell, M. , Parker, N. , Curtis, K. & et al. (2006). Ablation of PGC-1beta results in defective mitochondrial activity, thermogenesis, hepatic function, and cardiac performance. PLoS biology, 4 (11).
Rischer, H. , Oresic, M. , Seppänen-Laakso, T. , Katajamaa, M. , Lammertyn, F. , Ardiles-Diaz, W. , Van Montagu, M. C. E. , Inzé, D. & et al. (2006). Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells. Proceedings of the National Academy of Sciences of the United States of America, 103 (14), 5614-5619.
Elo, L. L. , Katajamaa, M. , Lund, R. , Oresic, M. , Lahesmaa, R. & Aittokallio, T. (2006). Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays. Omics, 10 (3), 369-380.
Oresic, M. , Vidal-Puig, A. & Hänninen, V. (2006). Metabolomic approaches to phenotype characterization and applications to complex diseases. Expert Review of Molecular Diagnostics, 6 (4), 575-585.
Moulder, R. , Filén, J. , Salmi, J. , Katajamaa, M. , Nevalainen, O. S. , Oresic, M. , Aittokallio, T. , Lahesmaa, R. & et al. (2005). A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. Proteomics, 5 (11), 2748-2760.
Gopalacharyulu, P. V. , Lindfors, E. , Bounsaythip, C. , Kivioja, T. , Yetukuri, L. , Hollmén, J. & Oresic, M. (2005). Data integration and visualization system for enabling conceptual biology. Bioinformatics, 21 Suppl 1, i177-i185.
Medina-Gomez, G. , Virtue, S. , Lelliott, C. , Boiani, R. , Campbell, M. , Christodoulides, C. , Perrin, C. , Jimenez-Linan, M. & et al. (2005). The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific peroxisome proliferator-activated receptor-gamma2 isoform. Diabetes, 54 (6), 1706-1716.
Oksman-Caldentey, K. , Inzé, D. & Oresic, M. (2004). Connecting genes to metabolites by a systems biology approach. Proceedings of the National Academy of Sciences of the United States of America, 101 (27), 9949-9950.
Clish, C. B. , Davidov, E. , Oresic, M. , Plasterer, T. N. , Lavine, G. , Londo, T. , Meys, M. , Snell, P. & et al. (2004). Integrative biological analysis of the APOE*3-leiden transgenic mouse. Omics, 8 (1), 3-13.
Davidov, E. , Clish, C. B. , Oresic, M. , Meys, M. , Stochaj, W. , Snell, P. , Lavine, G. , Londo, T. R. & et al. (2004). Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model. Omics, 8 (4), 267-288.
Oresic, M. , Clish, C. B. , Davidov, E. J. , Verheij, E. , Vogels, J. , Havekes, L. M. , Neumann, E. , Adourian, A. & et al. (2004). Phenotype characterisation using integrated gene transcript, protein and metabolite profiling. Applied bioinformatics, 3 (4), 205-217.
Oresic, M. , Dehn, M. , Korenblum, D. & Shalloway, D. (2003). Tracing specific synonymous codon-secondary structure correlations through evolution. Journal of Molecular Evolution, 56 (4), 473-484.
Oresic, M. & Shalloway, D. (1998). Specific correlations between relative synonymous codon usage and protein secondary structure. Journal of Molecular Biology, 281 (1), 31-48.
Oresic, M. & Pirc, R. (1993). Model of a quasi-one-dimensional spin glass. Physical Review B Condensed Matter, 47 (5), 2655-2660.

Articles, reviews/surveys

Sen, P. , Kempainen, E. & Oresic, M. (2018). Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells. Frontiers in Molecular Biosciences, 4.
Posti, J. P. , Dickens, A. M. , Orešič, M. , Hyötyläinen, T. & Tenovuo, O. (2017). Metabolomics Profiling As a Diagnostic Tool in Severe Traumatic Brain injury. Frontiers in Neurology, 8.
Rodriguez-Cuenca, S. , Pellegrinelli, V. , Campbell, M. , Oresic, M. & Vidal-Puig, A. (2017). Sphingolipids and glycerophospholipids.: The "ying and yang" of lipotoxicity in metabolic diseases. Progress in lipid research, 66, 14-29.
Marinković, T. & Oresic, M. (2016). Modeling strategies to study metabolic pathways in progression to type 1 diabetes: Challenges and opportunities. Archives of Biochemistry and Biophysics, 589, 131-7.
Hyötyläinen, T. & Oresic, M. (2015). Optimizing the lipidomics workflow for clinical studies: practical considerations. Analytical and Bioanalytical Chemistry, 407 (17), 4973-4993.
Hyötyläinen, T. & Oresic, M. (2014). Systems biology strategies to study lipidomes in health and disease. Progress in lipid research, 55 (1), 43-60.
Hyötyläinen, T. , Bondia-Pons, I. & Oresic, M. (2013). Lipidomics in nutrition and food research. Molecular Nutrition & Food Research, 57 (8), 1306-1318.
Denkert, C. , Bucher, E. , Hilvo, M. , Salek, R. , Oresic, M. , Griffin, J. , Brockmöller, S. , Klauschen, F. & et al. (2012). Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery. Genome Medicine, 4 (4).
Seppänen-Laakso, T. & Oresic, M. (2009). How to study lipidomes. Journal of Molecular Endocrinology, 42 (3), 185-190.
Jänis, M. T. , Laaksonen, R. & Oresic, M. (2008). Metabolomic strategies to identify tissue-specific effects of cardiovascular drugs. Expert Opinion on Drug Metabolism & Toxicology, 4 (6), 665-680.
Katajamaa, M. & Oresic, M. (2007). Data processing for mass spectrometry-based metabolomics. Journal of Chromatography A, 1158 (1-2), 318-328.
Curtis, R. K. , Oresic, M. & Vidal-Puig, A. (2005). Pathways to the analysis of microarray data. Trends in Biotechnology, 23 (8), 429-435.

Chapters in books

Lamichhane, S. , Sen, P. , Dickens, A. M. , Hyötyläinen, T. & Orešič, M. (2018). An Overview of Metabolomics Data Analysis: Current Tools and Future Perspectives. In: Joaquim Jaumot; Carmen Bedia; Romà Tauler, Data Analysis for Omic Sciences: Methods and Applications (pp. 387-413). . Elsevier.