Selected Publications

    P. Sen, S. Lamichhane, V. B. Mathema, A. McGlinchey, A. M. Dickens, S. Khoomrung, M. Orešič. Deep learning meets metabolomics: A methodological perspective. Brief Bioinformatics (2020, accepted). [REVIEW]

    M. Dickens, F. Borgan, H. Laurikainen, S. Lamichhane, T. Marques, T. Rönkkö, M. Veronese, T. Lindeman, METSY Investigators, T. Hyötyläinen, O. Howes, J. Hietala, M. Orešič. Links between central CB1-receptor availability and peripheral endocannabinoids in patients with first episode psychosis. npj Schizophr (2020, accepted). doi: 10.1038/s41537-020-00110-7

    M. Dickens, P. Sen, M. J. Kempton, N. Barrantes-Vidal, C. Iyegbe, M. Nordentoft, T. Pollak, A. Riecher-Rössler, S. Ruhrmann, G. Sachs, R. Bressan, M.-O. Krebs, G. P. Amminger, L. de Haan, M. van der Gaag, L. Valmaggia, T. Hyötyläinen, the EU-GEI High Risk Study, M. Orešič, P. McGuire. Dysregulated lipid metabolism precedes onset of psychosis. Biol Psych (2020). doi: 10.1016/j.biopsych.2020.07.012

    S. Lamichhane, A. M. Dickens, P. Sen, H. Laurikainen, F. Borgan, J. Suvisaari, T. Hyötyläinen, O. Howes, J. Hietala, M. Orešič. Circulating lipids associate with future weight gain in individuals with an at-risk mental state and in first-episode psychosis. Schizophr Bull (2020). doi: 10.1093/schbul/sbaa087

    McGlinchey, T. Sinioja, S. Lamichhane, P. Sen, J. Bodin, H. Siljander, Alex M. Dickens, D. Geng, C. Carlsson, D. Duberg, J. Ilonen, S. M. Virtanen, H. Dirven, H. Friis Berntsen, K. Zimmer, U. C. Nygaard, M. Orešič, M. Knip, T. Hyötyläinen. Prenatal exposure to perfluoroalkyl substances modulates neonatal serum phospholipids, increasing risk of type 1 diabetes. Environ Int (2020). doi: 10.1016/j.envint.2020.105935

    Sinisalu, P. Sen, S. Salihović, S. Virtanen, H. Hyöty, J. Ilonen, J. Toppari, R. Veijola, M. Orešič, M. Knip, T. Hyötyläinen. Early-life exposure to perfluorinated alkyl substances modulates lipid metabolism in progression to celiac disease. Environ Res (2020). doi: 10.1016/j.envres.2020.109864 Shared senior and corresponding author

    E. Segal, F. Zhang, X. Lin, G. King, O. Shalem, S. Shilo, W. E. Allen, F. Alquaddoomi, H. Altae-Tran, S. Anders, R. Balicer, T. Bauman, X. Bonilla, G. Booman, A. T. Chan, O. O. Cohen, S. Coletti, N. Davidson, Y. Dor, D. A. Drew, O. Elemento, G. Evans, P. Ewels, J. Gale, A. Gavrieli, B. Geiger, Y. H. Grad, C. S. Greene, I. Hajirasouliha, R. Jerala, A. Kahles, O. Kallioniemi, A. Keshet, L. Kocarev, G. Landua, T. Meir, A. Muller, Long H. Nguyen, M. Orešič, S. Ovchinnikova, H. Peterson, J. Prodanova, J. Rajagopal, G. Ratsch, H. Rossman, J. Rung, A. Sboner, A. Sigaras, T. Spector, R. Steinherz, I. Stevens, J. Vilo, P. Wilmes, CCC (Coronavirus Census Collective). Building an International Consortium for Tracking Coronavirus Health Status. Nature Medicine (2020). doi: 10.1038/s41591-020-0929-x

    Xu, B. Wu, M. Orešič, Y. Xie, P. Yao, Z.-y. Wu, X. Lv, H. Chen, F. Wei. Double Derivatization Strategy for High-Sensitivity and High-Coverage Localization of Double Bonds in Free Fatty Acids by Mass Spectrometry. Anal Chem (2020). doi: 10.1021/acs.analchem.9b05588

    K. Luukkonen, T. Tukiainen, A. Juuti, H. Sammalkorpi, P.A. N. Haridas, O. Niemelä, J. Arola, M. Orho-Melander, A. Hakkarainen, P. T. Kovanen, O. Dwivedi, L. Groop, L. Hodson, A. Gastaldelli, T. Hyötyläinen, M. Orešič, H. Yki-Järvinen. Hydroxysteroid 17-β Dehydrogenase 13 Variant Increases Phospholipids and Protects Against Fibrosis in Nonalcoholic Fatty Liver Disease. JCI Insight 5(5), 132158 (2020).

    Thomas, A. M. Dickens, J. P. Posti, M. Mohammadian, C. Ledig, R. S. K. Takala, T. Hyötyläinen, O. Tenovuo, M. Orešič. Integrative analysis of circulating metabolite profiles and magnetic resonance imaging metrics in patients with traumatic brain injury. Int J Mol Sci 21(4), 1395 (2020).

    Sen, A. M. Dickens, M. A. López-Bascón, T. Lindeman, E. Kemppainen, S. Lamichhane, T. Rönkkö, J. Ilonen, J. Toppari, R. Veijola, H. Hyöty, T. Hyötyläinen, M. Knip, M. Orešič. Metabolic Alterations in Human Peripheral Blood Mononuclear Cells Associate with Progression to Type 1 Diabetes. Diabetologia 63(5), 1017-1031 (2020). doi: 10.1007/s00125-020-05107-6

    Salihović, A. M. Dickens, I. Schoultz, F. Fart, L. Sinisalu, T. Lindeman, J. Halfvarson, M. Orešič, T. Hyötyläinen. Simultaneous determination of per- and polyfluoroalkyl substances and bile acids in human serum using ultra-high-performance liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 412(10), 2251-2259 (2020).

    Ahonen, S. Jäntti, T. Suvitaival, S. Theilade, C. Risz, R. Kostiainen, P. Rossing, M. Orešič, T. Hyötyläinen. Targeted clinical metabolite profling platform for the stratification of diabetic patients. Metabolites 9, 184 (2019).

    F. Wei, S. Lamichhane, M. Orešič, T. Hyötyläinen. Lipidomes in health and disease: analytical startegies and considerations. Trends Anal Chem 120, e115664 (2019). doi: 10.1016/j.trac.2019.115664 [REVIEW]

    Lamichhane, E. Kemppainen, K. Trost, H. Siljander, H. Hyoty, J. Ilonen, J. Toppari, R. Veijola, T. Hyotylainen, M. Knip, M. Orešič. Circulating Metabolites in Progression to Islet Autoimmunity and Type 1 Diabetes. Diabetologia 62(12), 2287-2297 (2019).

    P. Sen, C. Carlsson, S. M. Virtanen, S. Simell, H. Hyöty, J. Ilonen, J. Toppari, R. Veijola, T. Hyötyläinen, M. Knip, M. Orešič. Persistent alterations in plasma lipid profiles prior to introduction of gluten in the diet associate with progression to celiac disease. Clin Transl Gastroenterol 10, 1-10 (2019).

    Lamichhane, L. Ahonen, T. S. Dyrlund, A. M. Dickens, H. Siljander, H. Hyöty, J. Ilonen, J. Toppari, R. Veijola, T. Hyötyläinen, M. Knip, M. Orešič. Cord-Blood Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes. Biomolecules 9, 33 (2019).

    Sen, M. Orešič. Modeling of human Gut Microbiota on a Genome-Scale: An Overview. Metabolites 9, 22 (2019). [REVIEW]

    K. Pedersen, S. K. Forslund, V. Gudmundsdottir, A. Østergaard Petersen, F. Hildebrand, T. Hyötyläinen, T. Nielsen, T. Hansen, P. Bork, S. D. Ehrlich, S. Brunak, M. Orešič, O. Pedersen, H. B. Nielsen. A computational framework for conducting a three-pronged association study to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links. Nature Prot 13, 2781-2800 (2018).

    Lamichhane, L. Ahonen, T. S. Dyrlund, H. Siljander, H. Hyöty, J. Ilonen, J. Toppari, R. Veijola, T. Hyötyläinen, M. Knip, M. Orešič. A longitudinal plasma lipidomics dataset from children who developed islet autoimmunity and type 1 diabetes. Sci Data 5, 180250 (2018).

    Burla, M. Arita, M. Arita, A. K. Bendt, A. Cazenave-Gassiot, E. A. Dennis, K. Ekroos, X. Han, K. Ikeda, G. Liebisch, M. K. Lin, T. P. Loh, P. J. Meikle, M. Orešič, O. Quehenberger, A. Shevchenko, F. Torta, M. J. O. Wakelam, C. E. Wheelock, M. R. Wenk. MS-based lipidomics of human blood plasma – a community-initiated position paper to develop accepted guidelines. J Lipid Res 59, 2001-2017 (2018).

    M. Dickens, J. P. Posti, R. S. Takala, H. M. Ala-Seppälä, I. Mattila, J. C. Coles, J. Frantzén, P. J. Hutchinson, A. J. Katila, A. Kyllönen, H. R. Maanpää, V. Newcombe, J. Outtrim, J. Tallus, K. Carpenter, D. Menon, T. Hyotylainen, O. Tenovuo, M. Orešič. Serum metabolites associate with CT findings following TBI. J Neurotrauma 35, 2673-2683 (2018).

    Lamichhane, L. Ahonen, T. S. Dyrlund, E. Kemppainen, H. Siljander, H. Hyöty, J. Ilonen, J. Toppari, R. Veijola, T. Hyötyläinen, M. Knip, M. Orešič. Dynamics of Plasma Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes – Type 1 Diabetes Prediction and Prevention Study (DIPP). Sci Rep 8, 10635 (2018).

    T. Suvitaival, I. Bondia-Pons, L. Yetukuri, P. Pöhö, J. J. Nolan, T. Hyötyläinen, J. Kuusisto, M. Orešič. Lipidome as a predictive tool in progression to type 2 diabetes in Finnish men. Metabolism 78, 1-12 (2018).

    M. Orešič, G. Anderson, I. Mattila, M. Manoucheri, H. Soininen, T. Hyötyläinen, C. Basignani. Targeted Serum Metabolite Profiling Identifies Metabolic Signatures in Patients with Alzheimer’s Disease, Normal Pressure Hydrocephalus and Brain Tumor. Front Neurosci 11, 747 (2018).

    Frank, D. Maier, J. Pajula, T. Suvitaival, F. Borgan, M. Butz-Ostendorf, A. Fischer, J. Hietala, O. Howes, T. Hyötyläinen, J. Janssen, H. Laurikainen, C. Moreno, J. Suvisaari, M. Van Gils, M. Orešič. Platform for systems medicine research and diagnostic applications in psychotic disorders – the METSY project. Eur Psych 50, 40-46 (2018).

    Suvitaival T, Mantere O, Kieseppä T, Mattila I, Pöhö P, Hyötyläinen T, Suvisaari J, Orešič M. Serum metabolite profile associates with the development of metabolic co-morbidities in first-episode psychosis. Transl Psychiatry. 2016 Nov 15;6(11):e951. doi: 10.1038/tp.2016.222

    Orešič M, Posti JP, Kamstrup-Nielsen MH, Takala RS, Lingsma HF, Mattila I, Jäntti S, Katila AJ, Carpenter KL, Ala-Seppälä H, Kyllönen A, Maanpää HR, Tallus  J, Coles JP, Heino I, Frantzén J, Hutchinson PJ, Menon DK, Tenovuo O, Hyötyläinen T. Human Serum Metabolites Associate With Severity and Patient Outcomes in Traumatic Brain Injury. EBioMedicine. 2016 Jul 15. doi: 10.1016/j.ebiom.2016.07.015

    Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. 2016; 535:376-81.

    Hyötyläinen T, Jerby L, Petäjä EM, Mattila I, Jäntti S, Auvinen P, Gastaldelli A, Yki-Järvinen H, Ruppin E, Orešič M.Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nat Commun. 2016 Feb 3;7:8994. doi: 10.1038/ncomms9994

    Luukkonen PK, Zhou Y, Sädevirta S, Leivonen M, Arola J, Orešič M, Hyötyläinen T, Yki-Järvinen H. Hepatic ceramides dissociate steatosis and insulin resistance in patients with non-alcoholic fatty liver disease. J Hepatol. 2016; 64(5):1167-75

    A. D. Kostic, D. Gevers, H. Siljander, T. Vatanen, T. Hyötyläinen, A.-M. Hämäläinen, A. Peet, V. Tillmann, P. Pöho, I. Mattila, H. Lähdesmäki, E. A. Franzosa, O. Vaarala, M. de Goffau, H. Harmsen, J. Ilonen, S. M. Virtanen, C. B. Clish, M. Orešič, C. Huttenhower, M. Knip, R. J. Xavier. The Dynamics of the Human Infant Gut Microbiome in Development and in Progression towards Type 1 Diabetes. Cell Host Microbe 17(2): 260-273 (2015).

    B. Jørgenrud, S. Jäntti, I. Mattila, P. Pöhö, K. S. Rønningen, H. Yki-Järvinen, M. Orešič, T. Hyötyläinen. The influence of sample collection methodology and sample preprocessing on the blood metabolic profile. Bioanalysis 7(8): 991-1006 (2015).

    T. U. Greiner, T. Hyötyläinen, M. Knip, F. Bäckhed, M. Orešič. The gut microbiota modulates glycaemic control and serum metabolite profile in Non-Obese Diabetic mice. PLoS ONE 9(11): e110359 (2014).

    S. E. Jäntti, M. Kivilompolo, L. Öhrnberg, K. H. Pietiläinen, H. Nygren, M. Orešič, T. Hyötyläinen. Quantitative profiling of bile acids in blood, adipose tissue, intestine, and gall bladder samples using ultra high performance liquid chromatography-tandem mass spectrometry. Anal. Bioanal. Chem. 406: 7799-7815 (2014).

    Hyötyläinen T, Orešič M. Systems biology strategies to study lipidomes in health and disease. Prog Lipid Res. 55:43-60 (2014).

    Bondia-Pons I, Maukonen J, Mattila I, Rissanen A, Saarela M, Kaprio J, Hakkarainen A, Lundbom J, Lundbom N, Hyötyläinen T, Pietiläinen KH, Orešič M. Metabolome and fecal microbiota in monozygotic twin pairs discordant for weight: a Big Mac challenge. FASEB J. 28:4169-79 (2014).

    D. La Torre, T. Seppänen-Laakso, H. E. Larsson, T. Hyötyläinen, S. A. Ivarsson, Å. Lernmark, M. Orešič, the DiPiS study group, Decreased cord-blood phospholipids in young age at onset type 1 diabetes. Diabetes 62: 3951-3956 (2013).

    M. Orešič, T. Hyötyläinen, A. Kotronen, P. Gopalacharyulu, H. Nygren, J. Arola, S. Castillo, I. Mattila, A. Hakkarainen, R. J.H. Borra, M.-J. Honka, A. Verrijken, S. Francque, P. Iozzo, M. Leivonen, N. Jaser, A. Juuti, T. I. A. Sørensen, P. Nuutila, L. Van Gaal, H. Yki-Järvinen, Prediction of non-alcoholic fatty liver disease and liver fat content by serum molecular lipids. Diabetologia 56: 2266-2274 (2013).

    M. Orešič, P. Gopalacharyulu, J. Mykkänen, N. Lietzen, M. Mäkinen, H. Nygren, S. Simell, V. Simell, H. Hyöty, R. Veijola, J. Ilonen, M. Sysi-Aho, M. Knip, T. Hyötyläinen, O. Simell, Cord serum lipidome in prediction of islet autoimmunity and type 1 diabetes. Diabetes 62: 3268-3274 (2013). (Faculty of 1000 recommendation)

    S. I. Sayin, A. Wahlström, J. Felin, S. Jäntti, H.-U. Marschall, K. Bamberg, B. Angelin, T. Hyötyläinen, M. Orešič, F. Bäckhed, Gut microbiota regulates bile acid metabolism by reducing the levels of taurobetamuricholic acid, a naturally occurring FXR antagonist. Cell Metab. 17, 225–235 (2013).

    T. Hyötyläinen, I. Mattila, S. Wiedmer, A. Koivuniemi, M.-R. Taskinen, H. Yki-Järvinen, M. Orešič, Metabolomic analysis of polar metabolites in lipoprotein fractions identifies lipoprotein-specific metabolic profiles and their association with insulin resistance. Mol. Biosyst. 8: 2559-2565 (2012).

    M. Orešič, T. Seppänen-Laakso, D. Sun, J. Tang, S. Therman, R. Viehman, U. Mustonen, T. G. M. van Erp, T. Hyötyläinen, P. Thompson, A. W. Toga, M. O. Huttunen, J. Suvisaari, J. Kaprio, J. Lönnqvist, T. D. Cannon, Phospholipids and insulin resistance in psychosis: a lipidomics study of twin pairs discordant for schizophrenia. Genome Med. 4: e1 (2012).

    M. Orešič, T. Hyötyläinen, S.-K. Herukka, M. Sysi-Aho, I. Mattila, T. Seppänan-Laakso, V. Julkunen, P. V. Gopalacharyulu, M. Hallikainen, J. Koikkalainen, M. Kivipelto, S. Helisalmi, J. Lötjönen, H. Soininen, Metabolome in progression to Alzheimer’s disease. Transl. Psychiatry 1: e57 (2011). (Commentary in Alzheimer Research Forum) (Commentary in Neurology Today)

    M. Sysi-Aho, A. Ermolov, P. V. Gopalacharyulu, A. Tripathi, T. Seppänen-Laakso, J. Maukonen, I. Mattila, S. T. Ruohonen, L. Vähätalo, L. Yetukuri, T. Härkönen, E. Lindfors, J. Nikkilä, J. Ilonen, O. Simell, M. Saarela, M. Knip, S. Kaski, E. Savontaus, M. Orešič, Metabolic regulation in progression to autoimmune diabetes. PLoS Comp. Biol. 7 (10): e1002257 (2011).

    K. Pietiläinen, T. Róg, T. Seppänen-Laakso, S. Virtue, P. Gopalacharyulu, J. Tang, S. Rodriguez-Cuenca, A. Maciejewski, J. Naukkarinen, A. Rissanen, A.-L. Ruskeepää, P. Niemelä, V. Velagapudi, S. Castillo, H. Nygren, T. Hyötyläinen, J. Kaprio, H. Yki-Järvinen, I. Vattulainen, A. Vidal-Puig, M. Orešič, Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans. PLoS Biol. 9(6): e1000623 (2011). (commentary)

    M. Orešič, J. Tang, T. Seppänen-Laakso, I. Mattila, S. E. Saarni, S. I. Saarni, J. Lönnqvist, M. Sysi-Aho, T. Hyötyläinen, J. Perälä, J. Suvisaari, Metabolome in schizophrenia and other psychotic disorders: a general population-based study. Genome Med. 3: e19 (2011).

    M. Hilvo, C. Denkert, L. Lehtinen, B. Müller, S. Brockmöller, T. Seppänen-Laakso, J. Budczies, E. Bucher, L. Yetukuri, S. Castillo, E. Berg, H. Nygren, M. Sysi-Aho, J. L. Griffin, O. Fiehn, S. Loibl, C. Richter-Ehrenstein, C. Radke, T. Hyötyläinen, O. Kallioniemi, K. Iljin, M. Orešič, Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression.Cancer Res. 71: 3236-3245 (2011).

    T. Pluskal, S. Castillo, A. Villar-Briones, M. Orešič, MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11: 395 (2010).

    J. Westerbacka, A. Kotronen, B. A. Fielding, J. Wahren, L. Hodson, J. Perttilä, T. Seppänen-Laakso, T. Suortti, J. Arola, R. Hultcrantz, S. Castillo, V. M. Olkkonen, K. N. Frayn, M. Orešič, H. Yki-Järvinen, Splanchnic balance of free fatty acids, endocannabinoids and lipids in subjects with NAFLD. Gastroenterology 139: 1961-1971 (2010).

    L. Yetukuri, S. Söderlund, A. Koivuniemi, T. Seppänen-Laakso, P. S. Niemelä, M. Hyvönen, M.-R. Taskinen, I. Vattulainen, M. Jauhiainen, M. Orešič. Composition and lipid spatial distribution of High Density Lipoprotein particles in subjects with low and high HDL-cholesterol, J. Lipid Res. 51: 2341-2351 (2010).

    V. R. Velagapudi, R. Hezaveh, C. S. Reigstad, P. V. Gopalacharyulu, L. Yetukuri, S. Islam, J. Felin, R. Perkins, J. Borén, M. Orešič, and Fredrik Backhed, The gut microbiota modulates host energy and lipid metabolism in mice. J. Lipid Res. 51: 1101-1112 (2010).

    M. Orešič, T. Seppänen-Laakso, L. Yetukuri, F. Bäckhed, V. Hänninen, Gut microbiota affects lens and retinal lipid composition, Exp. Eye Res. 89, 604-607 (2009).

    A. Kotronen, V. R. Velagapudi, L. Yetukuri, J. Westerbacka, R. Bergholm, K. Ekroos, J. Makkonen, M.-R. Taskinen, M. Orešič, H. Yki-Järvinen, Saturated fatty acids containing triacylglycerols are better markers of insulin resistance than total serum triacylglycerol concentrations, Diabetologia 52(4), 684-690 (2009).

    P. V. Gopalacharyulu, V. R. Velagapudi, E. Lindfors, Eran Halperin, M. Orešič, Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast, Mol. BioSyst. 5, 276-287 (2009).

    M. Orešič, S. Simell, M. Sysi-Aho, K. Näntö-Salonen, T. Seppänen-Laakso, V. Parikka, M. Katajamaa, A. Hekkala, I. Mattila, P. Keskinen, L. Yetukuri, A. Reinikainen, J. Lähde, T. Suortti, J. Hakalax, T. Simell, H. Hyöty, R. Veijola, J. Ilonen, R. Lahesmaa, M. Knip, O. Simell, Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes, J. Exp. Med. 205(13), 2975-2984 (2008). (commentary) (Faculty of 1000 Biology evaluation)

    J. Nikkilä, M. Sysi-Aho, A. Ermolov, T. Seppänen-Laakso, O. Simell, S. Kaski, M. Orešič, Gender dependent progression of systemic metabolic states in early childhood, Mol. Syst. Biol. 4, e197 (2008).

    M. Katajamaa and M. Orešič, Processing methods for differential analysis of LC/MS profile data, BMC Bioinformatics 6:179 (2005).

    M. Orešič and D. Shalloway, Specific Correlations between Relative Synonymous Codon Usage and Protein Secondary Structure, J. Mol. Biol. 281, 31-48 (1998).

    M. Orešič and D. Shalloway, Hierarchical characterization of energy landscapes using Gaussian packet states, J. Chem. Phys. 101, 9844-9856 (1994).