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Sen P, Orešič M. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine. Metabolites. 2023 Jul 18;13(7):855. doi: 10.3390/metabo13070855. PMID: 37512562; PMCID: PMC10383060.

Salihovic S, Lamichane S, Hyötyläinen T, Orešič M. Recent advances towards mass spectrometry-based clinical lipidomics. Curr Opin Chem Biol. 2023 Oct;76:102370. doi: 10.1016/j.cbpa.2023.102370. Epub 2023 Jul 18. PMID: 37473482.

Lamichhane S, Härkönen T, Vatanen T, Hyötyläinen T, Knip M, Orešič M. Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads. Environ Int. 2023 Jun;176:107965. doi: 10.1016/j.envint.2023.107965. Epub 2023 May 11. PMID: 37210808.

Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S; Lifelines Cohort Study; Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity. 2023 Jun 13;56(6):1376-1392.e8. doi: 10.1016/j.immuni.2023.04.003. Epub 2023 May 9. PMID: 37164013.

Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity. 2023 Jun 13;56(6):1393-1409.e6. doi: 10.1016/j.immuni.2023.04.017. Epub 2023 May 9. PMID: 37164015.

Koren O, Konnikova L, Brodin P, Mysorekar IU, Collado MC. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat Rev Gastroenterol Hepatol. 2023 Dec 14. doi: 10.1038/s41575-023-00864-2. Epub ahead of print. PMID: 38097774.

Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS; Lifelines Cohort Study; Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J. Host genetic regulation of human gut microbial structural variation. Nature. 2024 Jan 3. doi: 10.1038/s41586-023-06893-w. Epub ahead of print. PMID: 38172637.

Hyötyläinen T, McGlinchey A, Salihovic S, Schubert A, Douglas A, Hay DC, O’Shaughnessy PJ, Iredale JP, Shaw S, Fowler PA, Orešič M. In utero exposures to perfluoroalkyl substances and the human fetal liver metabolome in Scotland: a cross-sectional study. Lancet Planet Health. 2024 Jan;8(1):e5-e17. doi: 10.1016/S2542-5196(23)00257-7. PMID: 38199723.

Bruzzaniti S, Piemonte E, Bruzzese D, Lepore MT, Strollo R, Izzo L, Di Candia F, Franzese A, Bifulco M, Mozzillo E, Ludvigsson J, Matarese G, Galgani M. Progression of type 1 diabetes is associated with high levels of soluble PD-1 in islet autoantibody-positive children. Diabetologia. 2024 Jan 12. doi: 10.1007/s00125-023-06075-3. Epub ahead of print. PMID: 38214712.

Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A. Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. Sci Rep. 2024 Feb 16;14(1):3911. doi: 10.1038/s41598-024-54353-w. PMID: 38366085; PMCID: PMC10873414.

Ahrens AP, Hyötyläinen T, Petrone JR, Igelström K, George CD, Garrett TJ, Orešič M, Triplett EW, Ludvigsson J. Infant microbes and metabolites point to childhood neurodevelopmental disorders. Cell. 2024 Apr 11;187(8):1853-1873.e15. doi: 10.1016/j.cell.2024.02.035. Epub 2024 Apr 3. PMID: 38574728.