Research paper

  • Adiels M, Matikainen N, Westerbacka J, Söderlund S, Larsson T, Olofsson SO, Jan Borén, Taskinen MR. 2012. Postprandial accumulation of chylomicron and chylomicron remnants is determined by the clearance capacity. Atherosclerosis, 222, 1, 222-228.

  • Adiels M, Larsson T, Sutton P, Taskinen MR, Boren J, Fielding BA. 2010. Optimization of N-methyl-N-[tert-butyldimethylsilyl]trifluoroacetamide as a derivatization agent for determining isotopic enrichment of glycerol in very-low density lipoproteins. Rapid Communications in Mass Spectrometry 24, 586-592.

  • Alcarraz-Vizán G, Boren J, Lee VN, Cascante, M. 2010. Histone deacetylase inhibition results in a common metabolic profile associated with HT29 differentiation. Metabolomics. 6, 2, 229-237. DOI 10.1007/s11306-009-0192-0

  • Annuzzi G, Bozzetto L, Costabile G, Giacco R, Mangione A., Anniballi G, Vitalena M, Vetrani C, Cipriano P, Della Corte G, Pasanisi F, Riccardi G, Rivellese AA. 2014. Diets naturally rich in polyphenols improve fasting and postprandial dyslipidemia and reduce oxidative stress: a randomized controlled trial. Am. J. Clin. Nutr. 99, 463-471. DOI: 10.3945/ajcn.113.073445.

  • Aura A-M, Mattila I, Hyötyläinen T, Gopalacharyulu P, Cheynier V, Souquet J-M, Bes M, Le Bourvellec C, Guyot S, Orešič M. 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, 833-846. DOI: 10.1007/s00394-012-0391-8

  • Aura, A.-M. 2013. In vitro colon model to study metabolic syndrome. In Systems Biology Approach to Study Metabolic Syndrome (Eds. M. Oresic and A. Vidal Puig). Springer Verlag, pp. 251-278.

  • Berglund M, Sunnåker M, Adiels M, Jirstrand M, Wennberg B. 2011. Investigations of a compartmental model for leucine kinetics using non-linear mixed effects models with ordinary and stochastic differential equations. Math Med Biol. September issue.

  • Cascante M, Benito A, Marin de Mas I, Centelles JJ, Miranda A, de Atauri P. Fluxomics. 2013. In Systems Biology Approaches to Study Metabolic Syndrome (Ed.: Oresic M.) Springer Verlag. In press

  • Castillo S, Gopalacharyulu P, Yetukuri L, Orešič M. 2011. Algorithms and tools for the preprocessing of LC-MS metabolomics data, Chemometr. Intell. Lab. Syst. 108, 1, 23-32.

  • Castillo S, Mattila I, Miettinen J, Orešič M, Hyötyläinen T. 2011. Data analysis tool for comprehensive two-dimensional gas chromatography-time of flight mass spectrometry, Anal. Chem. 83, 8, 3058-3067.

  • Diaz-Moralli S, Ramos-Montoya A, Marin S, Fernandez-Alvarez A, Casado M, Cascante M. 2012. Target metabolomics revealed complementary roles of hexose- and pentose-phosphates in the regulation of carbohydrate-dependent gene expression. Am J Physiol Endocrinol Metab. 303, E234-42.

  • Gizzatkulov NM, Goryanin I.I, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV. 2010. DBSolve Otimum: a software package for kinetic modelling which allows dynamic visualization of simulation results. BMC Systems Biology, 4, 109-119. Open access.

  • Hiukka M, Ståhlman C, Pettersson M, Levin M, Adiels M, Teneberg, S, Leinonen, ES, Hultén L-M, Wiklund, O, Orešič M, Olofsson S-O, Taskinen M-R, Ekroos K, Borén J. 2009. ApoCIII-enriched LDL in type 2 diabetes displays altered lipid composition, increased susceptibility for sphingomyelinase, and increased binding to biglycan. Diabetes 58, 2018-26.

  • Hyötyläinen T, Bondia-Pons I, Orešič M. 2013. Lipidomics in nutrition and food research. Mol Nutr Food Res. DOI: 10.1002/mnfr.201200759.

  • Hyötyläinen T. 2010. Editorial article. Bioanalysis 2, 919-923.

  • Kankainen M, Gopalacharyulu P, Holm L, Orešič M. 2011. MPEA – metabolite pathway enrichment analysis, Bioinformatics 27, 1878-1879. DOI:10.1093/bioinformatics/btr278

  • Karelina T, Ma H, Goryanin I, Demin OV. 2011. EI of Phosphotransferase System of Escherichia coli: Mathematical modelling approach to analysis of its kinetic properties. J. Biophysics. DOI: 10.1155/2011/579402, Open access trade journal.

  • Kivilompolo M, Öhrnberg L, Hyötyläinen T, Orešič M. 2013. Rapid quantitative analysis of carnitine and acylcarnitines by ultra-high performance–hydrophilic interaction liquid chromatography-tandem mass spectrometry, J. Chromatogr. A 1292, 189-194.

  • Larsson E, Tremaroli V, Lee YS, Koren O, Fricker A, Nookaew I, Nielsen J, Ley RE., Bäckhed, F. 2012. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut 61,1124-1131.

  • Lizarraga D, Vinardell MP, Noé V, van Delft JH, Alcarraz-Vizán G, van Breda SG, Staal Y, Günther UL, Carrigan JB, Reed MA, Ciudad CJ, Torres JL, Cascante M. 2011. A lyophilized red grape pomace containing proanthocyanidin-rich dietary fiber induces genetic and metabolic alterations in colon mucosa of female C57BL/6J mice. J Nutr. 141, 1597-604.

  • Marin de Mas I, Selivanov VA, Marin S, Roca J, Orešič M, Agius L, Cascante M. 2011. Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions, BMC Syst. Biol. 5, e175.

  • Marín S, Miranda A, Selivanov V, Cascante M. 2010. Analysis of the control exerted by glucokinase and glucose-6-phosphatase on glycerol metabolism of liver cells using different systems biology frameworks. Diabetologia 53, [Suppl1] S273.

  • Maukonen J, Simões C, Saarela M. 2011. The currently used commercial DNA extraction methods give different results of clostridial populations derived from human fecal samples. Current Challenges in Gastrointestinal Health Research, The first Workshop of the European Network for Gastrointestinal Health Research (ENGIHR). Braga, Portugal, 15-16.2.2011, P 26.

  • Maukonen J, Simões C, Saarela M. 2012. The currently used commercial DNA extraction methods give different results of clostridial and Actinobacterial populations derived from human fecal samples. FEMS Microbiology Ecology, 79, 697-708.

  • Maukonen J. 2012. Characterization of the human predominant fecal microbiota. With special focus on the Clostridial clusters IV and XIVa. VTT, Espoo. 161 p. + app. 62 p. VTT Science: 26

  • Metelkin E, Demin O, Kovacs Z, Chinopoulos C. 2009. Modelling of ATP-ADP steady-state exchange rate mediated by the adenine nucleotide translocase in isolated mitochondria. FEBS Journal 276, 6942-6955. DOI: 10.1111/j.1742-4658.2009.07394.x

  • Miranda A, Marín S, Selivanov V, Cascante M, Rodriguez-Cuenca S. 2011. Characterisation of the metabolic fluxes in the adipocyte differentiation process using bioinformatics tools. Diabetologia 54, [Suppl1] S294.

  • Mogilevskaya E, Bagrova N, Plyusnina T, Gizzatkulov N, Metelkin E, Goryacheva E, Smirnov S, Kosinsky Y, Dorodnov A, Peskov K, Karelina T, Goryanin I, Demin O. 2009. Kinetic modeling as a tool to integrate multilevel dynamic experimental data. Methods Mol Biol. 563, 197-218.

  • Niemelä PS, Castillo S, Sysi-Aho M, Orešič, M. 2009. Bioinformatics and computational strategies for lipidomics, J. Chromatogr. B B 877, 2855-2862.

  • Nygren H, Pöhö P, Seppänen-Laakso T, Lahtinen U, Orešič M, Hyötyläinen T. 2013. Ultra high performance liquid chromatography- mass spectrometry in lipidomics. LCGC Europe (03/2013). Open access trade journal.

  • Nygren H, Seppänen-Laakso T, Castillo S, Hyötyläinen T, Orešič M. 2010. Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics for studies of body fluids and tissues, Methods Mol. Biol. in press.

  • Nygren H, Seppänen-Laakso T, Castillo S, Hyötyläinen T, Orešič M. 2011. Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics for studies of body fluids and tissues, Methods Mol. Biol. 708, 247-257.

  • Orešič M. 2010. Systems biology strategy to study lipotoxicity and the metabolic syndrome, Biochim. Biophys. Acta 1801, 235-239.

  • Peskov K, Mogilevskaya E, Demin O. 2012. Kinetic modelling of central carbon metabolim in Escherichia coli. FEBS Journal 279: 3374-3385. DOI: 10.111/j.1742-4658.2012.08719x. Open access

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

  • Pluskal T, Castillo S, Villar-Briones A, Orešič M. 2010. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics 11, 395-405.

  • Rodríguez-Prados J-C, Través PG, Cuenca J, Rico D, Aragonés J, Martín-Sanz P, Cascante M, Boscá L. 2010. Substrate Fate in Activated Macrophages: A Comparison between Innate, Classic, and Alternative Activation J. Immunol. 185, 605-614. DOI:10.4049/jimmunol.0901698.

  • Sánchez-Tena S, Alcarraz-Vizán G, Marín S, Torres JL, Cascante M. 2013. Epicatechin gallate impairs colon cancer cell metabolic productivity. J Agric Food Chem. 61, 4310-7.

  • Sayin SI, Wahlström A, Felin J, Jäntti S, Marschall HU, Bamberg K, Angelin B, Hyötyläinen T, Orešič M, Bäckhed F. 2013. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab. 17, 225-235.

  • Selivanov VA, Cascante M, Friedman M, Schumaker MF, Trucco M, Votyakova TV. 2012. Multistationary and oscillatory modes of free radicals generation by the mitochondrial respiratory chain revealed by a bifurcation analysis. PLoS Comput Biol. 8, e1002700.

  • Selivanov VA, Votyakova TV, Zeak JA, Trucco M, Roca J, Cascante M. 2009. Bistability of mitochondrial respiration underlies paradoxical reactive oxygen species generation induced by anoxia. PLoS Comput. Biol. 5, 12, e1000619. DOI:10.1371/journal.pcbi.1000619.

  • Smirnov S, Metelkin E, Gizzatkulov N, Stepanov O, Demin O. 2013. Towards modeling of metabolic syndrome: Tissue crosstalk in lipid spillover. In Systems Biology Approach to Study Metabolic Syndrome (Eds. M. Oresic and A. Vidal Puig). Springer Verlag, In press.

  • Taskinen MR, Adiels M, Westerbacka J, Söderlund S, Kahri J, Lundbom N, Lundbom J, Hakkarainen A, Olofsson SO, Orho-Melander M, Borén J. 2011. Dual metabolic defects are required to produce hypertriglyceridemia in obese subjects. Arterioscler Thromb Vasc Biol. 31, 9, 2144-50.

  • Touriño S, Fuguet E, Vinardell MP, Cascante M, Torres JL. 2009. Phenolic metabolites of grape antioxidant dietary fiber in rat urine. Agric. Food Chem. 57, 23, 11418-26.

  • Velagapudi VR, Hezaveh R, Reigstad CS, Gopalacharyulu P, Yetukuri L, Islam S, Felin J, Perkins R, Borén J, Orešič M, Bäckhed F. 2010. The gut microbiota modulates host energy and lipid metabolism in mice. J. Lipid Res. 51, 1101-12.

  • Vetrani C, Rivellese AR, Annuzzi G, Mattila I, Meudec E, Hyötyläinen T, Orešič M, Aura A-M. 2014. Phenolic metabolites as compliance biomarker for polyphenol intake in a randomized controlled human intervention. Food Research International. 63 Pat B: 233-238. DOIi: 10.1016/j.foodres.2014.01.018

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

Review paper