Research papers and literature reviews
Our research in spotlight
In this page, we introduce some of our key publications. A complete list of publications is available here. If you cannot access a publication, we are happy to send a PDF on request.
Latest papers
Plasma metabolites related to diet and microbiota may be future targets in the management of AUD
Leclercq, S., Ahmed, H., Amadieu, C., Petit, G., Koistinen, V., Leyrolle, Q., ... & Delzenne, N. (2024). Blood metabolomic profiling reveals new targets in the management of psychological symptoms associated with severe alcohol use disorder. eLife Nov 29:13:RP96937. Open-access paper.
The PANIC study on the metabolic impact of diet and physical activity in adolescents
Zarei, I., Eloranta, A. M., Klåvus, A., Väistö, J., Lehtonen, M., Mikkonen, S., ... & Lakka, T. A. (2024). Eight-year Diet and Physical Activity Intervention Affects Serum Metabolites during Childhood & Adolescence: A Nonrandomized Controlled Trial. iScience, 27(7), 110295. Open-access paper.
The GrainMark study: the impact of varying levels of whole-grain intake on the blood metabolome
Koistinen, V. M., Haldar, S., Tuomainen, M., Lehtonen, M., Klåvus, A., Draper, J., ... & Hanhineva, K. (2024). Metabolic changes in response to varying whole-grain wheat and rye intake. npj Science of Food, 8(1), 8. Open-access paper.
Metabolic changes in serum after a cold stimulation of brown adipose tissue
Mueez, U. D., de Mello, V. D., Tuomainen, M., Raiko, J., Niemi, T., Fromme, T., ... & Virtanen, K. A. (2023). Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans. Cell Reports, 42(9). Open-access paper.
Advances in nutritional metabolomics related to clinical studies, microbiota and precision nutrition
Kortesniemi, M., Noerman, S., Kårlund, A., Raita, J., Meuronen, T., Koistinen, V., ... & Hanhineva, K. (2023). Nutritional metabolomics: Recent developments and future needs. Current Opinion in Chemical Biology, 77, 102400. Open-access paper.
Review: the role of indolepropionic acid in metabolic diseases
Tuomainen, M., Uusitupa, M., Männistö, V., Lindström, J., Tuomilehto, J., & Hanhineva, K. (2024). Suolistomikrobiston syntetisoima indolipropionihappo metabolisissa sairauksissa. Duodecim, 140(18), 1506-1514. Open-access paper in Finnish.
Comment: Towards a harmonized metabolite nomenclature
Koistinen, V., Kärkkäinen, O., Keski-Rahkonen, P., Tsugawa, H., Scalbert, A., Arita, M., Wishart, D., & Hanhineva, K. (2023). Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature. Nature Metabolism, 1-4. PDF available on request from the corresponding author.
2019–2022
The complex roles of microbial metabolites in the gut–brain axis
Ahmed, H., Leyrolle, Q., Koistinen, V., Kärkkäinen, O., Layé, S., Delzenne, N., & Hanhineva, K. (2022). Microbiota-derived metabolites as drivers of gut–brain communication. Gut microbes, 14(1), 2102878. Open-access paper.
5-Aminovaleric acid betaine in health and disease
Haikonen, R., Kärkkäinen, O., Koistinen, V. M., Hanhineva, K. (2022). Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease. Trends in Endocrinology & Metabolism, 33(7), 463-480. Open-access paper.
The impact of gut microbiota on mouse tissue metabolome
Zarei, I., Koistinen, V. M., Kokla, M., Klåvus, A., Babu, A. F., Lehtonen, M., ... & Hanhineva, K. (2022). Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition. Scientific Reports, 12(1), 15018. Open-access paper.
Effect of exercise on non-alcoholic fatty liver disease
Babu, A. F., Csader, S., Männistö, V., Tauriainen, M. M., Pentikäinen, H., Savonen, K., ... & Schwab, U. (2022). Effects of exercise on NAFLD using non-targeted metabolomics in adipose tissue, plasma, urine, and stool. Scientific reports, 12(1), 1-16. Open-access paper.
Microbiota-associated metabolites in murine tissues
Pessa-Morikawa, T., Husso, A., Kärkkäinen, O., Koistinen, V., Hanhineva, K., Iivanainen, A., & Niku, M. (2022). Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta. BMC microbiology, 22(1), 1-16. Open-access paper.
Method paper on the notame R script and our metabolomics workflow
Klåvus, A., Kokla, M., Noerman, S., Koistinen, V. M., Tuomainen, M., Zarei, I., ... & Hanhineva, K. (2020). “Notame”: Workflow for non-targeted LC–MS metabolic profiling. Metabolites, 10(4), 135. Open-access paper.
Impact of malting on the phytochemical content of whole grains highlights the value of side-streams
Koistinen, V. M., Tuomainen, M., Lehtinen, P., Peltola, P., Auriola, S., Jonsson, K., & Hanhineva, K. (2020). Side-stream products of malting: a neglected source of phytochemicals. NPJ science of food, 4(1), 1-9. Open-access paper.
Comparison of imputation methods to tackle missing values in LC-MS data
Kokla, M., Virtanen, J., Kolehmainen, M., Paananen, J., & Hanhineva, K. (2019). Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study. BMC bioinformatics, 20(1), 1-11. Open-access paper.
Older classics
Wide review on nutrimetabolomics
Ulaszewska, M. M., Weinert, C. H., Trimigno, A., Portmann, R., Andres Lacueva, C., Badertscher, R., ... Hanhineva, K., ... & Vergères, G. (2019). Nutrimetabolomics: an integrative action for metabolomic analyses in human nutritional studies. Molecular nutrition & food research, 63(1), 1800384.
Position paper on phenolic acid metabolism
Bento-Silva, A., Koistinen, V. M., Mena, P., Bronze, M. R., Hanhineva, K., Sahlstrøm, S., ... & Aura, A. M. (2020). Factors affecting intake, metabolism and health benefits of phenolic acids: do we understand individual variability?. European journal of nutrition, 59(4), 1275-1293.
Potential type 2 diabetes biomarkers
De Mello, V. D., Paananen, J., Lindström, J., Lankinen, M. A., Shi, L., Kuusisto, J., ... & Uusitupa, M. (2017). Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study. Scientific reports, 7(1), 1-12. Open-access paper.
Whole grain phytochemicals and their analysis with mass spectrometry
Koistinen, V. M., & Hanhineva, K. (2017). Mass spectrometry-based analysis of whole-grain phytochemicals. Critical reviews in food science and nutrition, 57(8), 1688-1709.
Biomarkers of foods within the Nordic diet
Hanhineva, K., Lankinen, M. A., Pedret, A., Schwab, U., Kolehmainen, M., Paananen, J., ... & Mykkänen, H. (2015). Nontargeted metabolite profiling discriminates diet-specific biomarkers for consumption of whole grains, fatty fish, and bilberries in a randomized controlled trial. The Journal of nutrition, 145(1), 7-17. Open-access paper.
Dietary polyphenols and carbohydrate metabolism
Hanhineva, K., Törrönen, R., Bondia-Pons, I., Pekkinen, J., Kolehmainen, M., Mykkänen, H., & Poutanen, K. (2010). Impact of dietary polyphenols on carbohydrate metabolism. International journal of molecular sciences, 11(4), 1365-1402. Open-access paper.