Nair V, Heredia M, Samsom J, Huehn J. Impact of gut microenvironment on epigenetic signatures of intestinal T helper cell subsets. Imm. Lett. 2022; doi:10.1016/j.imlet.2022.04.006

van Unen V., Ouboter LF., Li N., Schreurs M., Abdelaal T., Kooy-Winkelaar Y., et al. Identification of a Disease-Associated Network of Intestinal Immune Cells in Treatment-Naive Inflammatory Bowel Disease. Front Immunol 2022;13. Doi: 10.3389/fimmu.2022.893803

van Heck JIP, Gacesa R, Stienstra R, Fu J, Zhernakova A, Harmsen HJM, Weersma RK, Joosten LAB, Tack CJ. The Gut Microbiome Composition Is Altered in Long-standing Type 1 Diabetes and Associates With Glycemic Control and Disease-Related Complications. Diabetes Care. 2022 Sep 1;45(9):2084-2094. doi: 10.2337/dc21-2225. PMID: 35766965

Bourgonje AR, Hu S, Spekhorst LM, Zhernakova DV, Vich Vila A, Li Y, Voskuil MD, van Berkel LA, Bley Folly B, Charrout M, Mahfouz A, Reinders MJT, van Heck JIP, Joosten LAB, Visschedijk MC, van Dullemen HM, Faber KN, Samsom JN, Festen EAM, Dijkstra G, Weersma RK. OP39 The effect of phenotype and genotype on the plasma proteome in patients with Inflammatory Bowel Disease. J Crohns Colitis 2021; 15(Suppl 1), S036-S039.

Bourgonje AR, Hu S, Spekhorst LM, Zhernakova DV, Vich Vila A, Li Y, Voskuil MD, van Berkel LA, Bley Folly B, Charrout M, Mahfouz A, Reinders MJT, van Heck JIP, Joosten LAB, Visschedijk MC, van Dullemen HM, Faber KN, Samsom JN, Festen EAM, Dijkstra G, Weersma RK. The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease. J Crohns Colitis 2021 Sep 7.

Guo N, Unen V, Ijsselsteijn ME, Ouboter LF, van der Meulen AE, Lopes SMCS, de Miranda NFCC, Koning F, Li N. 34-Marker Panel for Imaging Mass Cytometric Analysis of Human Snap-Frozen Tissue. Front. Immunol., 16 July 2020.

Sollid LM, Koning F. Lack of relationship of AT1001 to zonulin and prehaptoglobin-2: clinical implications. Gut 2020; 0:1.

M Charrout, MJT Reinders, A Mahfouz. Untangling biological factors influencing trajectory inference from single cell data. NAR Genomics and Bioinformatics, (2,3), 2020

T Abdelaal, S Mourragui, A Mahfouz, MJT Reinders. SpaGE: Spatial Gene Enhancement using scRNA-seq. Nucleic Acids Research (48, 18), 2020

R. Gacesa, A. Kurilshikov, A. Vich Vila, T. Sinha, M.A.Y. Klaassen, L.A. Bolte, S. Andreu-Sánchez, L. Chen, V. Collij, S. Hu, J.A.M. Dekens, V.C. Lenters, J.R. Björk, J.C. Swarte, M.A. Swertz, B.H. Jansen, J. Gelderloos-Arends, Lifelines cohort study, M. Hofker, R.C.H. Vermeulen, S. Sanna, H.J.M. Harmsen, C. Wijmenga, J. Fu, A. Zhernakova, R.K. Weersma. The Dutch Microbiome Project defines factors that shape the healthy gut microbiome. Biorxiv (under review at Nature)