Matej Oresic

Articles in journals

• Isokääntä, H. , Pinto da Silva, L. , Karu, N. , Kallonen, T. , Aatsinki, A. , Hankemeier, T. , Schimmel, L. , Diaz, E. & et al. (2024). Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization.  Analytical Chemistry, 96 (22), 8893-9304. [BibTeX]
• Torta, F. , Oresic, M. , Ekroos, K. , Ahrends, R. & Wenk, M. R. (2024). Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards.  Nature Communications, 15 (1). [BibTeX]
• Chester, L. A. , Englund, A. , Chesney, E. , Oliver, D. , Wilson, J. , Sovi, S. , Dickens, A. M. , Oresic, M. & et al. (2024). Effects of Cannabidiol and Delta-9-Tetrahydrocannabinol on Plasma Endocannabinoid Levels in Healthy Volunteers: A Randomized Double-Blind Four-Arm Crossover Study.  Cannabis and cannabinoid research, 9 (1), 188-198. [BibTeX]
• Sen, P. , Fan, Y. , Schlezinger, J. J. , Ehrlich, S. D. , Webster, T. F. , Hyötyläinen, T. , Pedersen, O. & Oresic, M. (2024). Exposure to environmental toxicants is associated with gut microbiome dysbiosis, insulin resistance and obesity.  Environment International, 186. [BibTeX]
• Salihovic, S. , Nyström, N. , Mathisen, C. B. , Kruse, R. , Olbjørn, C. , Andersen, S. , Noble, A. J. , Dorn-Rasmussen, M. & et al. (2024). Identification and validation of a blood- based diagnostic lipidomic signature of pediatric inflammatory bowel disease.  Nature Communications, 15 (1). [BibTeX]
• Hyötyläinen, T. , Ghaffarzadegan, T. , Karthikeyan, B. S. , Triplett, E. , Oresic, M. & Ludvigsson, J. (2024). Impact of Environmental Exposures on Human Breast Milk Lipidome in Future Immune-Mediated Diseases.  Environmental Science and Technology, 58 (5), 2214-2223. [BibTeX]
• Hyötyläinen, T. , McGlinchey, A. J. , Salihovic, S. , Schubert, A. , Douglas, A. , Hay, D. C. , O'Shaughnessy, P. J. , Iredale, J. P. & et al. (2024). In utero exposures to perfluoroalkyl substances and the human fetal liver metabolome in Scotland: a cross-sectional study.  The Lancet Planetary Health, 8 (1), e5-e17. [BibTeX]
• Ahrens, A. P. , Hyötyläinen, T. , Petrone, J. R. , Igelström, K. , George, C. D. , Garrett, T. J. , Oresic, M. , Triplett, E. W. & et al. (2024). Infant microbes and metabolites point to childhood neurodevelopmental disorders.  Cell, 187 (8), 1853-1873.e15. [BibTeX]
• Andrabi, S. B. A. , Kalim, U. U. , Palani, S. , Khan, M. M. , Khan, M. H. , Fagersund, J. , Orpana, J. , Paulin, N. & et al. (2024). Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4+ regulatory T cells by regulating IL2RA.  Proceedings of the National Academy of Sciences of the United States of America, 121 (23). [BibTeX]
• Alijagic, A. , Sinisalu, L. , Duberg, D. , Kotlyar, O. , Scherbak, N. , Engwall, M. , Oresic, M. & Hyötyläinen, T. (2024). Metabolic and phenotypic changes induced by PFAS exposure in two human hepatocyte cell models.  Environment International, 190. [BibTeX]
• Cruz, A. K. , Oresic, M. & Da Silva, S. (2024). Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors.  Metabolomics, 20 (6). [BibTeX]
• Van Deynse, H. , Cools, W. , De Deken, V. , Depreitere, B. , Hubloue, I. , Tisseghem, E. , Putman, K. & Oresic, M. (2024). One-year employment outcome prediction after traumatic brain injury: A CENTER-TBI study.  Disability and Health Journal. [BibTeX]
• Bagavathy Shanmugam, K. , Hyötyläinen, T. , Ghaffarzadegan, T. , Triplett, E. , Oresic, M. & Ludvigsson, J. (2024). Prenatal exposure to environmental contaminants and cord serum metabolite profiles in future immune-mediated diseases.  Journal of Exposure Science and Environmental Epidemiology, 34 (4), 647-658. [BibTeX]
• Thomas, I. , Newcombe, V. F. J. , Dickens, A. M. , Richter, S. , Posti, J. P. , Maas, A. I. R. , Tenovuo, O. , Hyötyläinen, T. & et al. (2024). Serum lipidome associates with neuroimaging features in patients with traumatic brain injury.  iScience, 27 (9). [BibTeX]
• Laudette, M. , Lindbom, M. , Arif, M. , Cinato, M. , Ruiz, M. , Doran, S. , Miljanovic, A. , Rutberg, M. & et al. (2023). Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function.  Cardiovascular Research, 119 (7), 1537-1552. [BibTeX]
• Aye, C. , Hammond, D. E. , Rodriguez-Cuenca, S. , Doherty, M. K. , Whitfield, P. D. , Phelan, M. M. , Yang, C. , Perez-Perez, R. & et al. (2023). CBL/CAP Is Essential for Mitochondria Respiration Complex I Assembly and Bioenergetics Efficiency in Muscle Cells.  International Journal of Molecular Sciences, 24 (4). [BibTeX]
• Lamichhane, S. , Sen, P. , Dickens, A. M. , Kråkström, M. , Ilonen, J. , Lempainen, J. , Hyöty, H. , Lahesmaa, R. & et al. (2023). Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children.  Frontiers in Endocrinology, 14. [BibTeX]
• Monfort-Pires, M. , Lamichhane, S. , Alonso, C. , Egelandsdal, B. , Oresic, M. , Jordahl, V. O. , Skjølsvold, O. , Pérez-Ruiz, I. & et al. (2023). Classification of Common Food Lipid Sources Regarding Healthiness Using Advanced Lipidomics: A Four-Arm Crossover Study.  International Journal of Molecular Sciences, 24 (5). [BibTeX]
• Hyötyläinen, T. , Bagavathy Shanmugam, K. , Ghaffarzadegan, T. , Triplett, E. W. , Oresic, M. & Ludvigsson, J. (2023). Cord serum metabolic signatures of future progression to immune-mediated diseases.  iScience, 26 (3). [BibTeX]
• Kråkström, M. , Dickens, A. M. , Alves, M. A. , Forssten, S. D. , Ouwehand, A. C. , Hyötyläinen, T. , Oresic, M. & Lamichhane, S. (2023). Dynamics of the Lipidome in a Colon Simulator.  Metabolites, 13 (3). [BibTeX]
• Lamichhane, S. , Härkönen, T. , Vatanen, T. , Hyötyläinen, T. , Knip, M. & Oresic, M. (2023). Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.  Environment International, 176. [BibTeX]
• Schmid, R. , Heuckeroth, S. , Korf, A. , Smirnov, A. , Myers, O. , Dyrlund, T. S. , Bushuiev, R. , Murray, K. J. & et al. (2023). Integrative analysis of multimodal mass spectrometry data in MZmine 3.  Nature Biotechnology, 41 (4), 447-449. [BibTeX]
• Hirvonen, M. K. , Lietzén, N. , Moulder, R. , Bhosale, S. D. , Koskenniemi, J. , Vähä-Mäkilä, M. , Nurmio, M. , Oresic, M. & et al. (2023). Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetes.  Scientific Reports, 13 (1). [BibTeX]
• Fan, Y. , Støving, R. K. , Berreira Ibraim, S. , Hyötyläinen, T. , Thirion, F. , Arora, T. , Lyu, L. , Stankevic, E. & et al. (2023). The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.  Nature Microbiology, 8 (5), 787-802. [BibTeX]
• Mózes, F. E. , Pavlides, M. & Oresic, M. (2022). Diagnostic accuracy of non-invasive tests for advanced fibrosis in patients with NAFLD: an individual patient data meta-analysis.  Gut, 71 (5), 1006-1019. [BibTeX]
• Lamichhane, S. , Sen, P. , Dickens, A. M. , Alves, M. A. , Härkönen, T. , Honkanen, J. , Vatanen, T. , Xavier, R. J. & et al. (2022). Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes.  Cell Reports Medicine, 3 (10). [BibTeX]
• Sussulini, A. , Xia, J. & Oresic, M. (2022). Editorial: Multi-omics: Trends and applications in clinical research.  Frontiers in Molecular Biosciences, 9. [BibTeX]
• Galimberti, S. , Graziano, F. , Maas, A. I. R. , Isernia, G. , Lecky, F. , Jain, S. , Sun, X. , Gardner, R. C. & et al. (2022). Effect of frailty on 6-month outcome after traumatic brain injury: a multicentre cohort study with external validation.  Lancet Neurology, 21 (2), 153-162. [BibTeX]
• Sen, P. , Qadri, S. , Luukkonen, P. K. , Ragnarsdottir, O. , McGlinchey, A. J. , Jäntti, S. , Juuti, A. , Arola, J. & et al. (2022). Exposure to environmental contaminants is associated with altered hepatic lipid metabolism in non-alcoholic fatty liver disease.  Journal of Hepatology, 76 (2), 283-293. [BibTeX]
• Sinioja, T. , Bodin, J. , Duberg, D. , Dirven, H. , Berntsen, H. F. , Zimmer, K. , Nygaard, U. C. , Oresic, M. & et al. (2022). Exposure to persistent organic pollutants alters the serum metabolome in non-obese diabetic mice.  Metabolomics, 18 (11). [BibTeX]
• van der Vlegel, M. , Oresic, M. & Ylén, P. (2022). Health care utilization and outcomes in older adults after Traumatic Brain Injury: A CENTER-TBI study.  Injury, 53 (8), 2774-2782. [BibTeX]
• Lamichhane, S. , Siljander, H. , Salonen, M. , Ruohtula, T. , Virtanen, S. M. , Ilonen, J. , Hyötyläinen, T. , Knip, M. & et al. (2022). Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life.  Frontiers in Nutrition, 9. [BibTeX]
• Johnson, K. , Leary, P. J. , Govaere, O. , Barter, M. J. , Charlton, S. H. , Cockell, S. J. , Tiniakos, D. , Zatorska, M. & et al. (2022). Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance.  JHEP Reports, 4 (2). [BibTeX]
• McGlinchey, A. J. , Govaere, O. , Geng, D. , Ratziu, V. , Allison, M. , Bousier, J. , Petta, S. , de Oliviera, C. & et al. (2022). Metabolic signatures across the full spectrum of non-alcoholic fatty liver disease.  JHEP Reports, 4 (5). [BibTeX]
• Ribeiro, H. C. , Sen, P. , Dickens, A. , Santa Cruz, E. C. , Oresic, M. & Sussulini, A. (2022). Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis.  Metabolomics, 18 (8). [BibTeX]
• Van Praag, D. L. G. , Wouters, K. , Van Den Eede, F. , Wilson, L. , Maas, A. I. R. & Oresic, M. (2022). Neurocognitive correlates of probable posttraumatic stress disorder following traumatic brain injury..  Brain & spine, 2. [BibTeX]
• Laajala, E. , Halla-Aho, V. , Grönroos, T. , Kalim, U. U. , Vähä-Mäkilä, M. , Nurmio, M. , Kallionpää, H. , Lietzén, N. & et al. (2022). Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples.  Epigenetics, 17 (12), 1608-1627. [BibTeX]
• Yin, X. , Mongan, D. , Cannon, M. , Zammit, S. , Hyötyläinen, T. , Oresic, M. , Brennan, L. & Cotter, D. R. (2022). Plasma lipid alterations in young adults with psychotic experiences: A study from the Avon Longitudinal Study of Parents and Children cohort.  Schizophrenia Research, 243, 78-85. [BibTeX]
• Sen, P. , Govaere, O. , Sinioja, T. , McGlinchey, A. J. , Geng, D. , Ratziu, V. , Bugianesi, E. , Schattenberg, J. M. & et al. (2022). Quantitative modeling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease.  iScience, 25 (9). [BibTeX]
• Thomas, I. , Dickens, A. M. , Posti, J. P. , Czeiter, E. , Duberg, D. , Sinioja, T. , Kråkström, M. , Retel Helmrich, I. R. A. & et al. (2022). Serum metabolome associated with severity of acute traumatic brain injury.  Nature Communications, 13 (1). [BibTeX]
• Lahelma, M. , Qadri, S. , Ahlholm, N. , Porthan, K. , Ruuth, M. , Juuti, A. , Oresic, M. , Hyötyläinen, T. & et al. (2022). The human liver lipidome is significantly related to the lipid composition and aggregation susceptibility of low-density lipoprotein (LDL) particles.  Atherosclerosis, 363, 22-29. [BibTeX]
• Laajala, E. , Kalim, U. U. , Grönroos, T. , Rasool, O. , Halla-Aho, V. , Konki, M. , Kattelus, R. , Mykkänen, J. & et al. (2022). Umbilical cord blood DNA methylation in children who later develop type 1 diabetes.  Diabetologia, 65 (9), 1534-1540. [BibTeX]
• Sen, P. , Hyötyläinen, T. & Oresic, M. (2021). 1-Deoxyceramides: key players in lipotoxicity and progression to type 2 diabetes?.  Acta Physiologica, 232 (1). [BibTeX]
• Karpale, M. , Käräjämäki, A. J. , Kummu, O. , Gylling, H. , Hyötyläinen, T. , Oresic, M. , Tolonen, A. , Hautajärvi, H. & et al. (2021). Activation of nuclear receptor PXR induces atherogenic lipids and PCSK9 through SREBP2-mediated mechanism.  British Journal of Pharmacology, 178 (12), 2461-2481. [BibTeX]
• Rodriguez-Cuenca, S. , Lelliot, C. J. , Campbell, M. , Peddinti, G. , Martinez-Uña, M. , Ingvorsen, C. , Dias, A. R. , Relat, J. & et al. (2021). Allostatic hypermetabolic response in PGC1α/β heterozygote mouse despite mitochondrial defects.  The FASEB Journal, 35 (9). [BibTeX]
• Gürdeniz, G. , Uusitupa, M. , Hermansen, K. , Savolainen, M. J. , Schwab, U. , Kolehmainen, M. , Brader, L. , Cloetens, L. & et al. (2021). Analysis of the SYSDIET Healthy Nordic Diet randomized trial based on metabolic profiling reveal beneficial effects on glucose metabolism and blood lipids.  Clinical Nutrition, 41 (2), 441-451. [BibTeX]
• Lamichhane, S. , Dickens, A. M. , Sen, P. , Laurikainen, H. , Borgan, F. , Suvisaari, J. , Hyötyläinen, T. , Howes, O. & et al. (2021). Association Between Circulating Lipids and Future Weight Gain in Individuals With an At-Risk Mental State and in First-Episode Psychosis.  Schizophrenia Bulletin, 47 (1), 160-169. [BibTeX]
• Huie, J. R. , Mondello, S. , Lindsell, C. J. , Antiga, L. , Yuh, E. L. , Zanier, E. R. , Masson, S. , Rosario, B. L. & et al. (2021). Biomarkers for Traumatic Brain Injury: Data Standards and Statistical Considerations.  Journal of Neurotrauma, 38 (18), 2514-2529. [BibTeX]
• Petersen, A. Ø. , Julienne, H. , Hyötyläinen, T. , Sen, P. , Fan, Y. , Pedersen, H. K. , Jäntti, S. , Hansen, T. H. & et al. (2021). Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species.  Scientific Reports, 11 (1). [BibTeX]
• Selvaraj, E. A. , Mózes, F. E. , Ajmer Jayaswal, A. N. , Zafarmand, M. H. , Vali, Y. , Lee, J. A. , Levick, C. K. , Joseph Young, L. A. & et al. (2021). Diagnostic accuracy of elastography and magnetic resonance imaging in patients with NAFLD: a systematic review and meta-analysis.  Journal of Hepatology, 75 (4), 770-785. [BibTeX]
• Mikolić, A. , van Klaveren, D. , Oude Groeniger, J. , Wiegers, E. J. A. , Lingsma, H. F. , Zeldovich, M. , von Steinbüchel, N. , Roeters van Lennep, J. E. & et al. (2021). Differences between Men and Women in Treatment and Outcome after Traumatic Brain Injury.  Journal of Neurotrauma, 38 (2), 235-251. [BibTeX]
• Dickens, A. M. , Sen, P. , Kempton, M. J. , Barrantes-Vidal, N. , Iyegbe, C. , Nordentoft, M. , Pollak, T. , Riecher-Rössler, A. & et al. (2021). Dysregulated Lipid Metabolism Precedes Onset of Psychosis.  Biological Psychiatry, 89 (3), 288-297. [BibTeX]
• Lamichhane, S. , Siljander, H. , Duberg, D. , Honkanen, J. , Virtanen, S. M. , Oresic, M. , Knip, M. & Hyötyläinen, T. (2021). Exposure to per- and polyfluoroalkyl substances associates with an altered lipid composition of breast milk.  Environment International, 157. [BibTeX]
• Wiegers, E. J. A. , Lingsma, H. F. , Huijben, J. A. , Cooper, D. J. , Citerio, G. , Frisvold, S. , Helbok, R. , Maas, A. I. R. & et al. (2021). Fluid balance and outcome in critically ill patients with traumatic brain injury (CENTER-TBI and OzENTER-TBI): a prospective, multicentre, comparative effectiveness study.  Lancet Neurology, 20 (8), 627-638. [BibTeX]
• Andelic, N. , Røe, C. , Brunborg, C. , Zeldovich, M. , Løvstad, M. , Løke, D. , Borgen, I. M. , Voormolen, D. C. & et al. (2021). Frequency of fatigue and its changes in the first 6 months after traumatic brain injury: results from the CENTER-TBI study.  Journal of Neurology, 268 (1), 61-73. [BibTeX]
• Böhm, J. K. , Güting, H. , Thorn, S. , Schäfer, N. , Rambach, V. , Schöchl, H. , Grottke, O. , Rossaint, R. & et al. (2021). Global Characterisation of Coagulopathy in Isolated Traumatic Brain Injury (iTBI): A CENTER-TBI Analysis.  Neurocritical Care, 35 (1), 184-196. [BibTeX]
• Andersson, L. , Cinato, M. , Mardani, I. , Miljanovic, A. , Arif, M. , Koh, A. , Lindbom, M. , Laudette, M. & et al. (2021). Glucosylceramide synthase deficiency in the heart compromises β1-adrenergic receptor trafficking.  European Heart Journal, 42 (43), 4481-4492. [BibTeX]
• Brial, F. , Chilloux, J. , Nielsen, T. , Vieira-Silva, S. , Falony, G. , Andrikopoulos, P. , Olanipekun, M. , Hoyles, L. & et al. (2021). Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.  Gut, 70 (11), 2105-2114. [BibTeX]
• Lamichhane, S. , Sen, P. , Alves, M. A. , Ribeiro, H. C. , Raunioniemi, P. , Hyötyläinen, T. & Oresic, M. (2021). Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations.  Metabolites, 11 (1). [BibTeX]
• Hyötyläinen, T. , Bodin, J. , Duberg, D. , Dirven, H. , Nygaard, U. C. & Oresic, M. (2021). Lipidomic Analyses Reveal Modulation of Lipid Metabolism by the PFAS Perfluoroundecanoic Acid (PFUnDA) in Non-Obese Diabetic Mice.  Frontiers in Genetics, 12. [BibTeX]
• Lanzon, B. , Martin-Taboada, M. , Castro Alves, V. , Vila-Bedmar, R. , González de Pablos, I. , Duberg, D. , Gomez, P. , Rodriguez, E. & et al. (2021). Lipidomic and Metabolomic Signature of Progression of Chronic Kidney Disease in Patients with Severe Obesity.  Metabolites, 11 (12). [BibTeX]
• Citerio, G. , Robba, C. , Rebora, P. , Petrosino, M. , Rossi, E. , Malgeri, L. , Stocchetti, N. , Galimberti, S. & et al. (2021). Management of arterial partial pressure of carbon dioxide in the first week after traumatic brain injury: results from the CENTER-TBI study.  Intensive Care Medicine, 47 (9), 961-973. [BibTeX]
• Gravesteijn, B. Y. , Sewalt, C. A. , Venema, E. , Nieboer, D. , Steyerberg, E. W. & Oresic, M. (2021). Missing Data in Prediction Research: A Five-Step Approach for Multiple Imputation, Illustrated in the CENTER-TBI Study.  Journal of Neurotrauma, 38 (13), 1842-1857. [BibTeX]
• van Veen, E. , van der Jagt, M. , Citerio, G. , Stocchetti, N. , Gommers, D. , Burdorf, A. , Menon, D. K. , Maas, A. I. R. & et al. (2021). Occurrence and timing of withdrawal of life-sustaining measures in traumatic brain injury patients: a CENTER-TBI study.  Intensive Care Medicine, 47 (10), 1115-1129. [BibTeX]
• Dijkland, S. A. , Helmrich, I. R. A. R. , Nieboer, D. , van der Jagt, M. , Dippel, D. W. J. , Menon, D. K. , Stocchetti, N. , Maas, A. I. R. & et al. (2021). Outcome Prediction after Moderate and Severe Traumatic Brain Injury: External Validation of Two Established Prognostic Models in 1742 European Patients.  Journal of Neurotrauma, 38 (10), 1377-1388. [BibTeX]
• Yuh, E. L. , Zafonte, R. & Oresic, M. (2021). Pathological Computed Tomography Features Associated With Adverse Outcomes After Mild Traumatic Brain Injury: A TRACK-TBI Study With External Validation in CENTER-TBI.  JAMA Neurology, 78 (9), 1137-1148. [BibTeX]
• Fart, F. , Salihovic, S. , McGlinchey, A. J. , Gareau, M. G. , Oresic, M. , Halfvarson, J. , Hyötyläinen, T. & Schoultz, I. (2021). Perfluoroalkyl substances are increased in patients with late-onset ulcerative colitis and induce intestinal barrier defects ex vivo in murine intestinal tissue.  Scandinavian Journal of Gastroenterology, 56 (11), 1286-1295. [BibTeX]
• Riemann, L. , Voormolen, D. C. , Rauen, K. , Zweckberger, K. , Unterberg, A. , Younsi, A. & Oresic, M. (2021). Persistent postconcussive symptoms in children and adolescents with mild traumatic brain injury receiving initial head computed tomography.  Journal of Neurosurgery: Pediatrics, 27 (5), 538-547. [BibTeX]
• Jendle, J. , Hyötyläinen, T. , Oresic, M. & Nyström, T. (2021). Pharmacometabolomic profiles in type 2 diabetic subjects treated with liraglutide or glimepiride.  Cardiovascular Diabetology, 20 (1). [BibTeX]
• Hylén, U. , McGlinchey, A. J. , Oresic, M. , Bejerot, S. , Humble, M. B. , Särndahl, E. , Hyötyläinen, T. & Eklund, D. (2021). Potential Transdiagnostic Lipid Mediators of Inflammatory Activity in Individuals With Serious Mental Illness.  Frontiers in Psychiatry, 12. [BibTeX]
• Mikolić, A. , Polinder, S. , Steyerberg, E. W. , Retel Helmrich, I. R. A. , Giacino, J. T. , Maas, A. I. R. , van der Naalt, J. , Voormolen, D. C. & et al. (2021). Prediction of Global Functional Outcome and Post-Concussive Symptoms after Mild Traumatic Brain Injury: External Validation of Prognostic Models in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) Study.  Journal of Neurotrauma, 38 (2), 196-209. [BibTeX]
• Sewalt, C. A. , Gravesteijn, B. Y. , Menon, D. , Lingsma, H. F. , Maas, A. I. R. , Stocchetti, N. , Venema, E. , Lecky, F. E. & et al. (2021). Primary versus early secondary referral to a specialized neurotrauma center in patients with moderate/severe traumatic brain injury: a CENTER TBI study.  Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine, 29 (1). [BibTeX]
• Sen, P. , Andrabi, S. B. A. , Buchacher, T. , Khan, M. M. , Kalim, U. U. , Lindeman, T. M. , Alves, M. A. , Hinkkanen, V. & et al. (2021). Quantitative genome-scale metabolic modeling of human CD4⁺ T cell differentiation reveals subset-specific regulation of glycosphingolipid pathways.  Cell Reports, 37 (6). [BibTeX]
• Wilson, L. , Horton, L. , Kunzmann, K. , Sahakian, B. J. , Newcombe, V. F. , Stamatakis, E. A. , von Steinbuechel, N. , Cunitz, K. & et al. (2021). Understanding the relationship between cognitive performance and function in daily life after traumatic brain injury..  Journal of Neurology, Neurosurgery and Psychiatry, 92, 407-417. [BibTeX]
• Salonurmi, T. , Nabil, H. , Ronkainen, J. , Hyötyläinen, T. , Hautajärvi, H. , Savolainen, M. J. , Tolonen, A. , Oresic, M. & et al. (2020). 4β-Hydroxycholesterol Signals From the Liver to Regulate Peripheral Cholesterol Transporters..  Frontiers in Pharmacology, 11. [BibTeX]
• Segal, E. , Oresic, M. & Vilmes, P. (2020). Building an international consortium for tracking coronavirus health status.  Nature Medicine, 26 (8), 1161-1165. [BibTeX]
• Feng, J. , van Veen, E. , Yang, C. , Huijben, J. A. , Lingsma, H. F. , Gao, G. , Jiang, J. , Maas, A. I. R. & et al. (2020). Comparison of Care System and Treatment Approaches for Patients with Traumatic Brain Injury in China versus Europe: A CENTER-TBI Survey Study.  Journal of Neurotrauma, 37 (16), 1806-1817. [BibTeX]
• Xu, S. , Wu, B. , Oresic, M. , Xie, Y. , Yao, P. , Wu, Z. , Lv, X. , Chen, H. & et al. (2020). Double Derivatization Strategy for High-Sensitivity and High-Coverage Localization of Double Bonds in Free Fatty Acids by Mass Spectrometry.  Analytical Chemistry, 92 (9), 6446-6455. [BibTeX]
• Sinisalu, L. , Sen, P. , Salihovic, S. , Virtanen, S. M. , Hyöty, H. , Ilonen, J. , Toppari, J. , Veijola, R. & et al. (2020). Early-life exposure to perfluorinated alkyl substances modulates lipid metabolism in progression to celiac disease.  Environmental Research, 188. [BibTeX]
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• 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. [BibTeX]
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• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• Lindfors, E. , Jouhten, P. , Oja, M. , Rintala, E. , Oresic, M. & Penttilä, M. (2014). Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae.  BMC Systems Biology, 8. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Greiner, T. U. , Hyötyläinen, T. , Knip, M. , Bäckhed, F. & Oresic, M. (2014). The gut microbiota modulates glycaemic control and serum metabolite profiles in non-obese diabetic mice.  PLOS ONE, 9 (11). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Suvisaari, J. & Oresic, M. (2013). Metabolomiikka psyko o situtkimuksessa [Metabolomics in psychosis research].  Duodecim, 129 (21), 2237-2244. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• Marinković, T. , Sysi-Aho, M. & Oresic, M. (2012). Integrated model of metabolism and autoimmune response in β-cell death and progression to type 1 diabetes.  PLOS ONE, 7 (12). [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Oresic, M. (2012). Metabolomics in the studies of islet autoimmunity and type 1 diabetes.  The review of diabetic studies : RDS, 9 (4), 236-247. [BibTeX]
• 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. [BibTeX]
• Oresic, M. (2012). Obesity and psychotic disorders: uncovering common mechanisms through metabolomics.  Disease Models and Mechanisms, 5 (5), 614-620. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• Kankainen, M. , Gopalacharyulu, P. , Holm, L. & Oresic, M. (2011). MPEA--metabolite pathway enrichment analysis.  Bioinformatics, 27 (13), 1878-1879. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• Elo, L. L. , Järvenpää, H. , Tuomela, S. , Raghav, S. , Ahlfors, H. , Laurila, K. , Gupta, B. , Lund, R. J. & et al. (2010). Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming.  Immunity, 32 (6), 852-862. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Huopaniemi, I. , Suvitaival, T. , Nikkilä, J. , Oresic, M. & Kaski, S. (2010). Multivariate multi-way analysis of multi-source data.  Bioinformatics, 26 (12), i391-i398. [BibTeX]
• Pluskal, T. , Castillo, S. , Villar-Briones, A. & Oresic, M. (2010). MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.  BMC Bioinformatics, 11. [BibTeX]
• 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. [BibTeX]
• Moulder, R. , Lönnberg, T. , Elo, L. L. , Filén, J. , Rainio, E. , Corthals, G. , Oresic, M. , Nyman, T. A. & et al. (2010). Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation.  Molecular & Cellular Proteomics, 9 (9), 1937-1953. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Oresic, M. (2010). Systems biology strategy to study lipotoxicity and the metabolic syndrome.  Biochimica et Biophysica Acta, 1801 (3), 235-239. [BibTeX]
• Oresic, M. , Lötjönen, J. & Soininen, H. (2010). Systems medicine and the integration of bioinformatic tools for the diagnosis of Alzheimer's disease.  Genome Medicine, 2 (11). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Lindfors, E. , Gopalacharyulu, P. V. , Halperin, E. & Oresic, M. (2009). Detection of molecular paths associated with insulitis and type 1 diabetes in non-obese diabetic mouse.  PLOS ONE, 4 (10). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Sirén, H. , Seppänen-Laakso, T. & Oresic, M. (2008). Capillary electrophoresis with UV detection and mass spectrometry in method development for profiling metabolites of steroid hormone metabolism.  Journal of chromatography. B, 871 (2), 375-382. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• Oresic, M. , Hänninen, V. A. & Vidal-Puig, A. (2008). Lipidomics: a new window to biomedical frontiers.  Trends in Biotechnology, 26 (12), 647-652. [BibTeX]
• Laaksonen, R. , Jänis, M. T. & Oresic, M. (2008). Lipidomics-based safety biomarkers for lipid-lowering treatments.  Angiology, 59 (2 Suppl), 65S-68S. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Sysi-Aho, M. , Katajamaa, M. , Yetukuri, L. & Oresic, M. (2007). Normalization method for metabolomics data using optimal selection of multiple internal standards.  BMC Bioinformatics, 8. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Katajamaa, M. , Miettinen, J. & Oresic, M. (2006). MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data.  Bioinformatics, 22 (5), 634-636. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Katajamaa, M. & Oresic, M. (2005). Processing methods for differential analysis of LC/MS profile data.  BMC Bioinformatics, 6. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Oresic, M. & Shalloway, D. (1998). Specific correlations between relative synonymous codon usage and protein secondary structure.  Journal of Molecular Biology, 281 (1), 31-48. [BibTeX]
• Oresic, M. & Pirc, R. (1993). Model of a quasi-one-dimensional spin glass.  Physical Review B Condensed Matter, 47 (5), 2655-2660. [BibTeX]

Articles, reviews/surveys

• Heuckeroth, S. , Damiani, T. , Smirnov, A. , Mokshyna, O. , Brungs, C. , Korf, A. , Smith, J. D. , Stincone, P. & et al. (2024). Reproducible mass spectrometry data processing and compound annotation in MZmine 3.  Nature Protocols, 19 (9), 2597-2641. [BibTeX]
• Mathema, V. B. , Sen, P. , Lamichhane, S. , Oresic, M. & Khoomrung, S. (2023). Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine.  Computational and Structural Biotechnology Journal, 21, 1372-1382. [BibTeX]
• Sen, P. & Oresic, M. (2023). Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine.  Metabolites, 13 (7). [BibTeX]
• Salihovic, S. , Lamichane, S. , Hyötyläinen, T. & Oresic, M. (2023). Recent advances towards mass spectrometry-based clinical lipidomics.  Current opinion in chemical biology, 76. [BibTeX]
• Kobeissy, F. , Kobaisi, A. , Peng, W. , Barsa, C. , Goli, M. , Sibahi, A. , El Hayek, S. , Abdelhady, S. & et al. (2022). Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers.  Cells, 11 (3). [BibTeX]
• Castro Alves, V. , Oresic, M. & Hyötyläinen, T. (2022). Lipidomics in nutrition research.  Current opinion in clinical nutrition and metabolic care, 25 (5), 311-318. [BibTeX]
• Maas, A. I. R. , Menon, D. K. , Büki, A. , Oresic, M. , Thomas, I. & Zemek, R. (2022). Traumatic brain injury: progress and challenges in prevention, clinical care, and research.  Lancet Neurology, 21 (1), 1004-1060. [BibTeX]
• Sen, P. , Lamichhane, S. , Mathema, V. B. , McGlinchey, A. J. , Dickens, A. M. , Khoomrung, S. & Oresic, M. (2021). Deep learning meets metabolomics: a methodological perspective.  Briefings in Bioinformatics, 22 (2), 1531-1542. [BibTeX]
• Kyle, J. E. , Aimo, L. , Bridge, A. J. , Clair, G. , Fedorova, M. , Helms, J. B. , Molenaar, M. R. , Ni, Z. & et al. (2021). Interpreting the lipidome: bioinformatic approaches to embrace the complexity.  Metabolomics, 17 (6). [BibTeX]
• Masoodi, M. , Gastaldelli, A. , Hyötyläinen, T. , Arretxe, E. , Alonso, C. , Gaggini, M. , Brosnan, J. , Anstee, Q. M. & et al. (2021). Metabolomics and lipidomics in NAFLD: biomarkers and non-invasive diagnostic tests.  Nature Reviews. Gastroenterology & Hepatology, 18 (12), 835-856. [BibTeX]
• Alves, M. A. , Lamichhane, S. , Dickens, A. , McGlinchey, A. J. , Ribeiro, H. C. , Sen, P. , Wei, F. , Hyötyläinen, T. & et al. (2021). Systems biology approaches to study lipidomes in health and disease.  Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, 1866 (2). [BibTeX]
• Franks, P. W. , Melén, E. , Friedman, M. , Sundström, J. , Kockum, I. , Klareskog, L. , Almqvist, C. , Bergen, S. E. & et al. (2021). Technological readiness and implementation of genomic-driven precision medicine for complex diseases.  Journal of Internal Medicine, 290 (3), 602-620. [BibTeX]
• Vali, Y. , Lee, J. , Boursier, J. , Spijker, R. , Löffler, J. , Verheij, J. , Brosnan, M. J. , Böcskei, Z. & et al. (2020). Enhanced liver fibrosis test for the non-invasive diagnosis of fibrosis in patients with NAFLD: A systematic review and meta-analysis.  Journal of Hepatology, 73 (2), 252-262. [BibTeX]
• Oresic, M. , McGlinchey, A. J. , Wheelock, C. E. & Hyötyläinen, T. (2020). Metabolic Signatures of the Exposome-Quantifying the Impact of Exposure to Environmental Chemicals on Human Health.  Metabolites, 10 (11). [BibTeX]
• Fang, W. , Santosh, L. , Oresic, M. & Hyötyläinen, T. (2019). Lipidomes in health and disease: Analytical strategies and considerations.  TrAC. Trends in analytical chemistry, 120. [BibTeX]
• Sen, P. & Oresic, M. (2019). Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview.  Metabolites, 9 (2). [BibTeX]
• 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. [BibTeX]
• Sen, P. , Kempainen, E. & Oresic, M. (2018). Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells.  Frontiers in Molecular Biosciences, 4. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Hyötyläinen, T. & Oresic, M. (2015). Optimizing the lipidomics workflow for clinical studies: practical considerations.  Analytical and Bioanalytical Chemistry, 407 (17), 4973-4993. [BibTeX]
• Hyötyläinen, T. & Oresic, M. (2014). Systems biology strategies to study lipidomes in health and disease.  Progress in lipid research, 55 (1), 43-60. [BibTeX]
• Hyötyläinen, T. , Bondia-Pons, I. & Oresic, M. (2013). Lipidomics in nutrition and food research.  Molecular Nutrition & Food Research, 57 (8), 1306-1318. [BibTeX]
• 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). [BibTeX]
• Oresic, M. (2011). Informatics and computational strategies for the study of lipids.  Biochimica et Biophysica Acta, 1811 (11), 991-999. [BibTeX]
• Seppänen-Laakso, T. & Oresic, M. (2009). How to study lipidomes.  Journal of Molecular Endocrinology, 42 (3), 185-190. [BibTeX]
• Tang, J. , Tan, C. Y. , Oresic, M. & Vidal-Puig, A. (2009). Integrating post-genomic approaches as a strategy to advance our understanding of health and disease.  Genome Medicine, 1 (3). [BibTeX]
• 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. [BibTeX]
• 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. [BibTeX]
• Katajamaa, M. & Oresic, M. (2007). Data processing for mass spectrometry-based metabolomics.  Journal of Chromatography A, 1158 (1-2), 318-328. [BibTeX]
• Curtis, R. K. , Oresic, M. & Vidal-Puig, A. (2005). Pathways to the analysis of microarray data.  Trends in Biotechnology, 23 (8), 429-435. [BibTeX]

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. [BibTeX]

Conference papers

• Salihovic, S. , Nyström, N. , Mathisen, C. B. , Andersen, S. , Olbjørn, C. , Perminow, G. , Opheim, R. , Detlie, T. E. & et al. (2023). Identification and validation of a lipidomic signature as a novel diagnostic biomarker of paediatric Inflammatory Bowel Disease. In:  Journal of Crohn's & Colitis. Oxford University Press. [BibTeX]
• Büki, A. , Tsitsopoulos, P. , Oresic, M. & Mondello, S. (2022). BIOMARKERS OF TRAUMATIC BRAIN- AND SPINAL CORD INJURY. In:  Journal of Neurotrauma. Paper presented at 15th International Neurotrauma Symposium, Berlin, Germany, July 17-20, 2022. (pp. A7-A7). Mary Ann Liebert. [BibTeX]
• Qadri, S. , Vartiainen, E. , Ahlholm, N. , Porthan, K. , Juuti, A. , Sammalkorpi, H. , Penttilä, A. , Arola, J. & et al. (2022). Hepatic insulin resistance is the basis of bile acid dysmetabolism in non-alcoholic fatty liver disease. In:  Journal of Hepatology. Paper presented at The International Liver Congress 2022, London, UK, June 22-26, 2022. (pp. S694-S695). Elsevier. [BibTeX]
• Qadri, S. , Blom, S. , Pitkänen, K. , Ahlholm, N. , Porthan, K. , Luukkonen, P. K. , Juuti, A. , Sammalkorpi, H. & et al. (2022). Heterogeneity of phosphatidylcholine metabolism in nonalcoholic fatty liver disease. In:  Journal of Hepatology. Paper presented at The International Liver Congress 2022, London, UK, June 22-26, 2022. (pp. S111-S111). Elsevier. [BibTeX]
• Oresic, M. , Sen, P. , Quadri, S. , Luukkonen, P. , Ragnarsdottir, O. , Jäntti, S. , Juuti, A. , Arola, J. & et al. (2021). Exposure to environmental contaminants is associated with sex-specific disturbances of hepatic lipid metabolism in non-alcoholic fatty liver disease. In:  Journal of Hepatology. Paper presented at The International Liver Congress, (Digital congress), June 23–26, 2021. (pp. S605-S606). Elsevier. [BibTeX]
• Sen, P. , Govaere, O. , Sinioja, T. , McGlinchey, A. J. , Geng, D. , Ratziu, V. , Bugianesi, E. , Schattenberg, J. & et al. (2021). Genome-scale metabolic modeling of human hepatocytes reveals dysregulation of glycosphingolipid pathways in progressive non-alcoholic fatty liver disease. In:  Journal of Hepatology. Paper presented at The International Liver Congress, (Digital congress), June 23–26, 2021. (pp. S256-S256). Elsevier. [BibTeX]
• Oresic, M. (2021). Molecular lipids in prediction of psychosis and the associated cardiometabolic co-morbidities. In:  European psychiatry. Paper presented at 29th European Congress of Psychiatry (EPA Virtual 2021), April 10-13, 2021. (pp. S16-S16). Cambridge University Press. [BibTeX]
• Sen, P. , Andrabi, S. B. A. , Buchacher, T. , Khan, M. M. , Ullah, U. , Lindeman, T. M. , Alves, M. A. , Hinkkanen, V. & et al. (2021). Quantitative analysis of human CD4+T-cell differentiation reveals subset-specific regulation of glycosphingolipid pathways. In:  European Journal of Immunology. Paper presented at 6th European Congress of Immunology, (Virtual meeting), September 1–4, 2021. (pp. 237-237). John Wiley & Sons. [BibTeX]
• McGlinchey, A. J. , Geng, D. , Govaere, O. , Ratziu, V. , Bugianesi, E. , Schattenberg, J. M. , Daley, A. , Hyötyläinen, T. & et al. (2021). The Metabolomics of Non-Alcoholic Fatty Liver Disease: Of Networks and Biomarkers. In:  Journal of Hepatology. Paper presented at The International Liver Congress, (Digital congress), June 23–26, 2021. (pp. S579-S580). Elsevier. [BibTeX]
• Laajala, E. , Ullah, U. , Grönroos, T. , Rasool, O. , Aho, V. H. , Konki, M. , Kattelus, R. , Mykkänen, J. & et al. (2021). Umbilical cord blood DNA methylation in children who later develop type 1 diabetes. In:  European Journal of Immunology. Paper presented at 6th European Congress of Immunology, (Virtual meeting), September 1–4, 2021. (pp. 291-291). John Wiley & Sons. [BibTeX]
• Sen, P. , Govaere, O. , McGlinchey, A. J. , Ratziu, V. , Bugianesi, E. , Schattenberg, J. M. , Allison, M. , Cockell, S. & et al. (2020). Metabolism of human liver on a genome scale in non-alcoholic fatty liver disease. In:  Journal of Hepatology. Paper presented at The Digital International Liver Congress (EASL 2020), August 27-29, 2020. (pp. S671-S672). Elsevier. [BibTeX]
• McGlinchey, A. J. , Geng, D. , Govaere, O. , Ratziu, V. , Bugianesi, E. , Schattenberg, J. M. , Daly, A. K. , Hyötyläinen, T. & et al. (2020). Metabolomics approaches to identify biomarkers of nonalcoholic fatty liver disease. In:  Journal of Hepatology. Paper presented at The Digital International Liver Congress (EASL 2020), August 27-29, 2020. (pp. S438-S438). Elsevier. [BibTeX]
• Fart, F. , Salihovic, S. , McGlinchey, A. J. , Oresic, M. , Halfvarson, J. , Hyötyläinen, T. & Schoultz, I. (2020). Per- and polyfluoroalkyl substances (PFAS) are significantly increased in patients with late-onset of ulcerative colitis. In:  Journal of Crohn's & Colitis. Oxford University Press. [BibTeX]