Publications

 

  1. Mannochio-Russo, H., V. Charron-Lamoureux, M. van Faassen, S. Lamichhane, W. D. Gonçalves Nunes, V. Deleray, A. V. Ayala, Y. Tanaka, A. Patan, K. Vittali, P. Rajkumar, Y. El Abiead, H. N. Zhao, P. W. P. Gomes, I. Mohanty, C. Lee, A. Sund, M. Sharma, Y. Liu, D. Pattynama, G. T. Walker, G. J. Norton, L. Khatib, M. S. Andalibi, C. X. Wang, R. J. Ellis, D. J. Moore, J. E. Iudicello, D. Franklin, Jr., S. Letendre, L. Chin, C. Walker, S. Renwick, J. Zemlin, M. J. Meehan, X. Song, D. Kasper, Z. Burcham, J. J. Kim, S. Kadakia, M. Raffatellu, L. Bode, H. Chu, K. Zengler, M. Wang, D. Siegel, R. Knight and P. C. Dorrestein “The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.” Cell. 2025 Jul 24;188(15):4154-4169.e19. doi: 10.1016/j.cell.2025.05.015. Epub 2025 Jun 10.
  2. Isokääntä, H.; Pinto da Silva, L.; Karu, N.; Kallonen, T.; Aatsinki, A. K.; Hankemeier, T.; Schimmel, L.; Diaz, E.; Hyötyläinen, T.; Dorrestein, P. C.; Knight, R.; Orešič, M.; Kaddurah-Daouk, R.; Dickens, A. M.; Lamichhane, S., Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Analytical Chemistry 2024, 96 (22), 8893-8904
  3. Zhao HN, Kvitne KE, Brungs C, Mohan S, Charron-Lamoureux V, Bittremieux W, Tang R, Schmid R, Lamichhane S, El Abiead Y, Andalibi MS, Mannochio-Russo H, Ambre M, Avalon NE, Bryant M, Caraballo-Rodríguez AM, Maya MC, Chin L, Ellis RJ, Franklin D, Girod S, Gomes PWP, Hansen L, Heaton R, Iudicello JE, Jarmusch AK, Khatib L,
    Letendre S, Magyari S, McDonald D, Mohanty I, Cumsille A, Moore DJ, Rajkumar P, Ross DH, Sapre H, Shahneh MRZ, Thomas SP, Tribelhorn C, Tubb HM, Walker C, Wang CX, Xing S, Zemlin J, Zuffa S, Wishart DS, Kaddurah-Daouk R, Wang M, Raffatellu M, Zengler K, Pluskal T, Xu L, Knight R, Tsunoda SM, Dorrestein PC. A resource to empirically establish drug exposure records directly from untargeted metabolomics data. Nature communications (Accepted, soon in press).
  4. Charron-Lamoureux, V., H. Mannochio-Russo, S. Lamichhane, S. Xing, A. Patan, P. W. Portal Gomes, P. Rajkumar, V. Deleray, A. M. Caraballo-Rodríguez, K. V. Chua, L. S. Lee, Z. Liu, J. Ching, M. Wang and P. C. Dorrestein (2025). “A guide to reverse metabolomics-a framework for big data discovery strategy.” Nature Protocol.
  5. Zhang, P., J. Liu, A. Lee, I. Tsaur, M. Ohira, V. Duong, N. Vo, K. Watari, H. Su, J. Y. Kim, L. Gu, M. Zhu, S. Shalapour, M. Hosseini, G. Bandyopadhyay, S. Zeng, C. Llorente, H. N. Zhao, S. Lamichhane, S. Mohan, P. C. Dorrestein, J. M. Olefsky, B. Schnabl, P. Soroosh and M. Karin (2024). “IL-22 resolves MASLD via enterocyte STAT3 restoration of diet-perturbed intestinal homeostasis.” Cell Metabolism 36(10): 2341-2354.e2346.
  6. Lamichhane, S., P. Sen, A. M. Dickens, M. A. Alves, T. Härkönen, J. Honkanen, T. Vatanen, R. J. Xavier, T. Hyötyläinen, M. Knip and M. Orešič (2022). “Dysregulation of secondary bile acid metabolism precedes islet autoimmunity and type 1 diabetes.” Cell Reports Medicine 3(10):
  7. Aatsinki, A.-K., S. Lamichhane, H. Isokääntä, P. Sen, M. Kråkström, M. A. Alves, A. Keskitalo, E. Munukka, H. Karlsson, L. Perasto, M. Lukkarinen, M. Oresic, H.-M. Kailanto, L. Karlsson, L. Lahti and A. M. Dickens “Dynamics of Gut Metabolome and Microbiota Maturation during Early Life.” iScience. (#Share first authors)
  8. Lamichhane, S., Kemppainen, E., Trošt, K., Siljander, H., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., & Orešič, M. (2019). Circulating metabolites in progression to islet autoimmunity and type 1 diabetes. Diabetologia, 62(12), 2287–2297.
  9. Lamichhane, S., T. Härkönen, T. Vatanen, T. Hyötyläinen, M. Knip and M. Orešič (2023). “Impact of exposure to per-and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.” Environment International 176: 107965.
  10. Lamichhane, S., Sen, P., Dickens, A. M., Kråkström, M., Ilonen, J., Lempainen, J., Hyöty, H., Lahesmaa, R., Veijola, R., Toppari, J., Hyötyläinen, T., Knip, M., & Orešič, M. (2023). Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children. Frontiers in endocrinology, 14, 1211015.
  11. Lamichhane, S., Ahonen, L., Dyrlund, T. S., Kemppainen, E., Siljander, H., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., & Oresic, M. (2018). Dynamics of Plasma Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes – Type 1 Diabetes Prediction and Prevention Study (DIPP). Scientific reports, 8(1), 10635.
  12. Lamichhane, S., Siljander, H., Duberg, D., Honkanen, J., Virtanen, S. M., Orešič, M., Knip, M., & Hyötyläinen, T. (2021). Exposure to per- and polyfluoroalkyl substances associates with an altered lipid composition of breast milk. Environment international, 157, 106855.
  13. Lamichhane, S., Sen, P., Dickens, A. M., Orešič, M., & Bertram, H. C. (2018). Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods, 149, 3–12.
  14. Lamichhane, S., Sen, P., Alves, M. A., Ribeiro, H. C., Raunioniemi, P., Hyötyläinen, T., & Orešič, M. (2021). Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. Metabolites, 11(1), 55.
  15. Lamichhane, S., Dickens, A. M., Sen, P., Laurikainen, H., Borgan, F., Suvisaari, J., Hyötyläinen, T., Howes, O., Hietala, J., & Orešič, M. (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.
  16. Lamichhane S, Siljander H, Salonen M, Ruohtula T, Virtanen SM, Ilonen J, Hyötyläinen T, Knip M, Orešič M. Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life. Frontier in Nutrition. 2022 May 24;9:859627.
  17. Lamichhane, S., Ahonen, L., Dyrlund, T. S., Dickens, A. M., Siljander, H., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., & Oresic, M. (2019). Cord-Blood Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes. Biomolecules, 9(1), 33.
  18. Lamichhane, S., Yde, C. C., Jensen, H. M., Morovic, W., Hibberd, A. A., Ouwehand, A. C., Saarinen, M. T., Forssten, S. D., Wiebe, L., Marcussen, J., Bertelsen, K., Meier, S., Young, J. F., & Bertram, H. C. (2018). Metabolic Fate of 13C-Labeled Polydextrose and Impact on the Gut Microbiome: A Triple-Phase Study in a Colon Simulator. Journal of proteome research, 17(3), 1041–1053.
  19. Lamichhane, S., Ahonen, L., Dyrlund, T. S., Siljander, H., Hyöty, H., Ilonen, J., Toppari, J., Veijola, R., Hyötyläinen, T., Knip, M., & Orešič, M. (2018). A longitudinal plasma lipidomics dataset from children who developed islet autoimmunity and type 1 diabetes. Scientific data, 5, 180250.
  20. Lamichhane, S.; Sundekilde, U. K.; Blædel, T.; Dalsgaard, T. K.; Larsen, L. H.; Dragsted, L. O.; Astrup, A.; Bertram, H. C., Optimizing sampling strategies for NMR-based metabolomics of human feces: pooled vs. unpooled analyses. Analytical Methods 2017, 9 (30), 4476-4480.
  21. Lamichhane, S.; Westerhuis, J. A.; Ouwehand, A. C.; Saarinen, M. T.; Forssten, S. D.; Jensen, H. M.; Young, J. F.; Bertram, H. C.; Yde, C. C., Gut microbial activity as influenced by fiber digestion: dynamic metabolomics in an in vitro colon simulator. Metabolomics 2016, 12 (2), 25.
  22. Lamichhane, S.; Yde, C. C.; Schmedes, M. S.; Jensen, H. M.; Meier, S.; Bertram, H. C., Strategy for nuclear-magnetic-resonance-based metabolomics of human feces. Analytical chemistry 2015, 87 (12), 5930-5937.
  23. Nguyen, A. H., H. B. Beyene, G. Mocciaro, L. Hahnefeld, S. Lamichhane, M. Fabritius, H. Avela, Y. Wang, A. M. Dickens, R. Gurke, B. Yang, W. J. Griffiths, T. Hyötyläinen, P. J. Meikle and M. Orešič (2025). “Intra- and inter-individual variation of the human lipidome.” TrAC Trends in Analytical Chemistry 191: 118368.
  24. Cruz, A. K., M. A. Alves, T. Andresson, A. L. Bayless, K. J. Bloodsworth, J. A. Bowden, K. Bullock, M. C. Burnet, F. C. Neto, A. Choy, C. B. Clish, S. P. Couvillion, R. Cumeras, L. Dailey, G. Dallmann, W. C. Davis, A. A. Deik, A. M. Dickens, D. Djukovic, P. C. Dorrestein, J. G. Eder, O. Fiehn, R. Flores, H. Gika, K. A. Hagiwara, T. H. Pham, J. J. Harynuk, J. J. Aristizabal-Henao, D. W. Hoyt, F. Jean-François, M. Kråkström, A. Kumar, J. E. Kyle, Lamichhane, Y. Li, S. L. Nam, R. Mandal, A. P. de la Mata, M. J. Meehan, T. Meikopoulos, T. O. Metz, T. Mouskeftara, N. Munoz, G. A. N. Gowda, M. Orešic, M. Panitchpakdi, S. Pierre-Hugues, D. Raftery, B. Rushing, T. Schock, H. Seifried, S. Servetas, T. Shen, S. Sumner, K. S. T. Carrillo, D. Thibaut, J. B. Trejo, L. Van Meulebroek, L. Vanhaecke, C. Virgiliou, K. C. Weldon, D. S. Wishart, L. Zhang, J. Zheng and S. Da Silva (2024). “Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors.” Metabolomics 20(6): 125.
  25. Kråkström, M., A. M. Dickens, M. A. Alves, S. D. Forssten, A. C. Ouwehand, T. Hyötyläinen, M. Orešič and S. Lamichhane (2023). “Dynamics of the Lipidome in a Colon Simulator.” Metabolites 13(3).
  26. Lamichhane, S.; Yde, C. C.; Forssten, S.; Ouwehand, A. C.; Saarinen, M.; Jensen, H. M.; Gibson, G. R.; Rastall, R.; Fava, F.; Bertram, H. C., Impact of dietary polydextrose fiber on the human gut metabolome. Journal of agricultural and food chemistry 2014, 62 (40), 9944-9951.
  27. Sen, P., Dickens, A. M., López-Bascón, M. A., Lindeman, T., Kemppainen, E., Lamichhane, S., Rönkkö, T., Ilonen, J., Toppari, J., Veijola, R., Hyöty, H., Hyötyläinen, T., Knip, M., & Orešič, M. (2020). Metabolic alterations in immune cells associate with progression to type 1 diabetes. Diabetologia, 63(5), 1017–1031.
  28. Sen, P., Lamichhane, S., Mathema, V. B., McGlinchey, A., Dickens, A. M., Khoomrung, S., & Orešič, M. (2021). Deep learning meets metabolomics: a methodological perspective. Briefings in bioinformatics, 22(2), 1531–1542.
  29. Dickens, A. M., T. P. Johnson, S. Lamichhane, A. Kumar, C. A. Pardo, E. G. Gutierrez, N. Haughey and M. C. Cervenka (2023). “Changes in lipids and inflammation in adults with super-refractory status epilepticus on a ketogenic diet.” Frontiers in Molecular Biosciences 10.
  30. McGlinchey, A., Sinioja, T., Lamichhane, S., Sen, P., Bodin, J., Siljander, H., Dickens, A. M., Geng, D., Carlsson, C., Duberg, D., Ilonen, J., Virtanen, S. M., Dirven, H., Berntsen, H. F., Zimmer, K., Nygaard, U. C., Orešič, M., Knip, M., & Hyötyläinen, T. (2020). Prenatal exposure to perfluoroalkyl substances modulates neonatal serum phospholipids, increasing risk of type 1 diabetes. Environment international, 143, 105935.
  31. Huovinen, V., Aatsinki, A. K., Kataja, E. L., Munukka, E., Keskitalo, A., Lamichhane, S., Raunioniemi, P., Bridgett, D. J., Lahti, L., O’Mahony, S. M., Dickens, A., Korja, R., Karlsson, H., Nolvi, S., & Karlsson, L. (2023). Infant gut microbiota and negative and fear reactivity. Development and psychopathology, 1–16.
  32. Dickens, A. M., Borgan, F., Laurikainen, H., Lamichhane, S., Marques, T., Rönkkö, T., Veronese, M., Lindeman, T., Hyötyläinen, T., Howes, O., Hietala, J., & Orešič, M. (2020). Links between central CB1-receptor availability and peripheral endocannabinoids in patients with first episode psychosis. NPJ schizophrenia, 6(1), 21.
  33. Mathema, V. B., P. Sen, S. Lamichhane, M. Orešič and S. Khoomrung (2023). “Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine.” Computational and Structural Biotechnology Journal.
  34. Monfort-Pires, M., S. Lamichhane, C. Alonso, B. Egelandsdal, M. Orešič, V. O. Jordahl, O. Skjølsvold, I. Pérez-Ruiz, M. E. Blanco and S. Skeie (2023). “Classification of Common Food Lipid Sources Regarding Healthiness Using Advanced Lipidomics: A Four-Arm Crossover Study.” International Journal of Molecular Sciences 24(5): 4941.
  35. Alves, M. A., Lamichhane, S., Dickens, A., McGlinchey, A., Ribeiro, H. C., Sen, P., Wei, F., Hyötyläinen, T., & Orešič, M. (2021). Systems biology approaches to study lipidomes in health and disease. Biochimica et biophysica acta. Molecular and cell biology of lipids, 1866(2), 158857.
  36. Wei, F.; Lamichhane, S.; Orešič, M.; Hyötyläinen, T., Lipidomes in health and disease: Analytical strategies and considerations. TrAC Trends in Analytical Chemistry 2019, 120, 115664.
  37. García-García, A. B., Lamichhane, S., Castejón, D., Cambero, M. I., & Bertram, H. C. (2018). 1H HR-MAS NMR-based metabolomics analysis for dry-fermented sausage characterization. Food chemistry, 240, 514–523.
  38. Haukaas, T. H.; Moestue, S. A.; Vettukattil, R.; Sitter, B.; Lamichhane, S.; Segura, R.; Giskeødegård, G. F.; Bathen, T. F., Impact of freezing delay time on tissue samples for metabolomic studies. Frontiers in oncology 2016, 6, 17.
  39. Haukaas, T. H.; Euceda, L. R.; Giskeødegård, G. F.; Lamichhane, S.; Krohn, M.; Jernström, S.; Aure, M. R.; Lingjærde, O. C.; Schlichting, E.; Garred, Ø., Metabolic clusters of breast cancer in relation to gene-and protein expression subtypes. Cancer & metabolism 2016, 4 (1), 1-14.
  40. Cao, M. D.; Lamichhane, S.; Lundgren, S.; Bofin, A.; Fjøsne, H.; Giskeødegård, G. F.; Bathen, T. F., Metabolic characterization of triple negative breast cancer. BMC cancer 2014, 14 (1), 1-12.