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  1. 2020
  2. Hu, S., Vich Vila, A., Gacesa, R., Collij, V., Stevens, C., Fu, J. M., Wong, I., Talkowski, M. E., Rivas, M. A., Imhann, F., Bolte, L., van Dullemen, H., Dijkstra, G., Visschedijk, M. C., Festen, E. A., Xavier, R. J., Fu, J., Daly, M. J., Wijmenga, C., ... Weersma, R. K. (2020). Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut, [319706]. https://doi.org/10.1136/gutjnl-2019-319706
  3. Peters, V., Tigchelaar-Feenstra, E. F., Imhann, F., Dekens, J. A. M., Swertz, M. A., Franke, L. H., Wijmenga, C., Weersma, R. K., Alizadeh, B. Z., Dijkstra, G., & Campmans-Kuijpers, M. J. E. (2020). Habitual dietary intake of IBD patients differs from population controls: a case-control study. European journal of nutrition. https://doi.org/10.1007/s00394-020-02250-z
  4. Vich Vila, A., Collij, V., Sanna, S., Sinha, T., Imhann, F., Bourgonje, A. R., Mujagic, Z., Jonkers, D. M. A. E., Masclee, A. A. M., Fu, J., Kurilshikov, A., Wijmenga, C., Zhernakova, A., & Weersma, R. K. (2020). Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nature Communications, 11(1), [362]. https://doi.org/10.1038/s41467-019-14177-z
  5. 2019
  6. Franzosa, E. A., Sirota-Madi, A., Avila-Pacheco, J., Fornelos, N., Haiser, H. J., Reinker, S., Vatanen, T., Hall, A. B., Mallick, H., McIver, L. J., Sauk, J. S., Wilson, R. G., Stevens, B. W., Scott, J. M., Pierce, K., Deik, A. A., Bullock, K., Imhann, F., Porter, J. A., ... Xavier, R. J. (2019). Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nature Microbiology, 4(5), 898. https://doi.org/10.1038/s41564-019-0442-5
  7. Peters, V., Tigchelaar, E., Imhann, F., Dekens, J., Swertz, M., Franke, L., Wijmenga, C., Weersma, R. K., Alizadeh, B., Dijkstra, G., & Campmans-Kuijpers, M. J. (2019). Sa2029 – Habitual dietary intake of dutch IBD patients differs from population controls: A case-control study. Gastroenterology, 156(6), S477-S478. https://doi.org/10.1016/S0016-5085(19)38052-7 Abstract
  8. Klaassen, M. A. Y., Imhann, F., Collij, V., Fu, J., Wijmenga, C., Zhernakova, A., Dijkstra, G., Festen, E. A. M., Gacesa, R., Vich Vila, A., & Weersma, R. K. (2019). Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn's Disease Exacerbations. Journal of Crohn's and Colitis, 13(11), 1439-1449. https://doi.org/10.1093/ecco-jcc/jjz077
  9. Imhann, F., Van der Velde, K. J., Barbieri, R., Alberts, R., Voskuil, M. D., Vila, A. V., Collij, V., Spekhorst, L. M., Van der Sloot, K. W. J., Peters, V., Van Dullemen, H. M., Visschedijk, M. C., Festen, E. A. M., Swertz, M. A., Dijkstra, G., & Weersma, R. K. (2019). Correction to: The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. Bmc gastroenterology, 19(1), [44]. https://doi.org/10.1186/s12876-019-0938-8
  10. van der Velde, K. J., Imhann, F., Charbon, B., Pang, C., van Enckevort, D., Slofstra, M., Barbieri, R., Alberts, R., Hendriksen, D., Kelpin, F., de Haan, M., de Boer, T., Haakma, S., Stroomberg, C., Scholtens, S., van de Geijn, G-J., Festen, E. A. M., Weersma, R. K., & Swertz, M. A. (2019). MOLGENIS Research: Advanced bioinformatics data software for non-bioinformaticians. Bioinformatics (Oxford, England), 35(6), 1076-1078. https://doi.org/10.1093/bioinformatics/bty742
  11. Aschard, H., Laville, V., Tchetgen, E. T., Knights, D., Imhann, F., Seksik, P., Zaitlen, N., Silverberg, M. S., Cosnes, J., Weersma, R. K., Xavier, R., Beaugerie, L., Skurnik, D., & Sokol, H. (2019). Genetic effects on the commensal microbiota in inflammatory bowel disease patients. PLoS genetics, 15(3), [e1008018]. https://doi.org/10.1371/journal.pgen.1008018
  12. Franzosa, E. A., Sirota-Madi, A., Avila-Pacheco, J., Fornelos, N., Haiser, H. J., Reinker, S., Vatanen, T., Hall, A. B., Mallick, H., McIver, L. J., Sauk, J. S., Wilson, R. G., Stevens, B. W., Scott, J. M., Pierce, K., Deik, A. A., Bullock, K., Imhann, F., Porter, J. A., ... Xavier, R. J. (2019). Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nature Microbiology, 4(2), 293-305. https://doi.org/10.1038/s41564-018-0306-4
  13. Collij, V., Imhann, F., Vich Vila, A., Fu, J., Dijkstra, G., Festen, E. A. M., Voskuil, M. D., Daly, M. J., Xavier, R. J., Wijmenga, C., Zhernakova, A., & Weersma, R. K. (2019). SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects. PLoS ONE, 14(1), [0211328]. https://doi.org/10.1371/journal.pone.0211328
  14. Imhann, F., Van der Velde, K. J., Barbieri, R., Alberts, R., Voskuil, M. D., Vich Vila, A., Collij, V., Spekhorst, L. M., der Sloot Kwj, V., Peters, V., Van Dullemen, H. M., Visschedijk, M. C., Eam, F., Swertz, M. A., Dijkstra, G., & Weersma, R. K. (2019). The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. Bmc gastroenterology, 19(5), [5]. https://doi.org/10.1186/s12876-018-0917-5
  15. Sinha, T., Vila, A. V., Garmaeva, S., Jankipersadsing, S. A., Imhann, F., Collij, V., Bonder, M. J., Jiang, X., Gurry, T., Alm, E. J., D'Amato, M., Weersma, R. K., Scherjon, S., Wijmenga, C., Fu, J., Kurilshikov, A., & Zhernakova, A. (2019). Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut Microbes, 10(3), 358-366. https://doi.org/10.1080/19490976.2018.1528822
  16. 2018
  17. Vich Vila, A., Imhann, F., Collij, V., Jankipersadsing, S. A., Gurry, T., Mujagic, Z., Kurilshikov, A., Bonder, M. J., Jiang, X., Tigchelaar, E. F., Dekens, J., Peters, V., Voskuil, M. D., Visschedijk, M. C., van Dullemen, H. M., Keszthelyi, D., Swertz, M. A., Franke, L., Alberts, R., ... Weersma, R. K. (2018). Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Science Translational Medicine, 10(472). https://doi.org/10.1126/scitranslmed.aap8914
  18. Alberts, R., de Vries, E. M. G., Goode, E. C., Jiang, X., Sampaziotis, F., Rombouts, K., Böttcher, K., Folseraas, T., Weismüller, T. J., Mason, A. L., Wang, W., Alexander, G., Alvaro, D., Bergquist, A., Björkström, N. K., Beuers, U., Björnsson, E., Boberg, K. M., Bowlus, C. L., ... International PSC Study Group, The UK PSC Consortium (2018). Genetic association analysis identifies variants associated with disease progression in primary sclerosing cholangitis. Gut, 67(8), 1517-1524. https://doi.org/10.1136/gutjnl-2016-313598
  19. Visschedijk, M. C., Spekhorst, L. M., Cheng, S-C., van Loo, E. S., Jansen, B. H. D., Blokzijl, T., Kil, H., de Jong, D. J., Pierik, M., Maljaars, J. P. W. J., van der Woude, C. J., van Bodegraven, A. A., Oldenburg, B., Löwenberg, M., Nieuwenhuijs, V. B., Imhann, F., van Sommeren, S., Alberts, R., Xavier, R. J., ... Festen, E. A. M. (2018). Genomic and Expression Analyses Identify a Disease-Modifying Variant for Fibrostenotic Crohn's Disease. Journal of Crohn's and Colitis, 12(5), 582-588. https://doi.org/10.1093/ecco-jcc/jjy001
  20. Vich Vila, A., Imhann, F., Collij, V., Jankipersadsing, S. A., Gurry, T., Mujagic, Z., Kurilshikov, A., Bonder, M. J., Xiaofang, J., Tigchelaar, E., Dekens, J., Peters, V., Voskuil, M. D., Visschedijk, M. C., Eleonora, F. A. M., Dijkstra, G., Masclee, A. A., Hofker, M. H., Xavier, R., ... Weersma, R. K. (2018). OP014 - Analysis of 1792 gut metagenomes reveals microbial treatment targets for inflammatory bowel disease and irritable bowel syndrome. Journal of Crohn's and Colitis, 12, S10. [OP014]. https://doi.org/10.1093/ecco-jcc/jjx180.013
  21. Peters, V., Tigchelaar, E., Campmans-Kuijpers, M., Sheedfar, F., Imhann, F., Dekens, J., Wijmenga, C., Swertz, M., Franke, L., Weersma, R., Dijkstra, G., & Alizadeh, B. (2018). P831 - Habitual dietary intake of Dutch IBD patients differs from population controls: A case-control study. Journal of Crohn's and Colitis, 12, S536-S536. [P831]. https://doi.org/10.1093/ecco-jcc/jjx180.958
  22. Imhann, F., Vich Vila, A., Bonder, M. J., Fu, J., Gevers, D., Visschedijk, M. C., Spekhorst, L. M., Alberts, R., Franke, L., van Dullemen, H. M., Ter Steege, R. W. F., Huttenhower, C., Dijkstra, G., Xavier, R. J., Festen, E. A. M., Wijmenga, C., Zhernakova, A., & Weersma, R. K. (2018). Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut, 67(1), 108-119. https://doi.org/10.1136/gutjnl-2016-312135
  23. 2017
  24. Parelsnoer Institute, & Dutch Initiative on Crohn and Colitis (2017). Prevalence of- and risk factors for work disability in Dutch patients with inflammatory bowel disease. World Journal of Gastroenterology, 23(46), 8182-8192. https://doi.org/10.3748/wjg.v23.i46.8182
  25. Spekhorst, L. M., Severs, M., de Boer, N. K. H., Festen, E. A. M., Fidder, H. H., Hoentjen, F., Imhann, F., de Jong, D. J., van der Meulen-de Jong, A. E., Pierik, M. J., van der Woude, C. J., Dijkstra, G., Ponsioen, C. Y., Lowenberg, M., Oldenburg, B., Weersma, R. K., Parelsnoer Inst, & Dutch Initiative on Crohn and Colitis (2017). The Impact of Ethnicity and Country of Birth on Inflammatory Bowel Disease Phenotype: A Prospective Cohort Study. Journal of Crohn's and Colitis, 11(12), 1463-1470. https://doi.org/10.1093/ecco-jcc/jjx098
  26. Spekhorst, L. M., Imhann, F., Festen, E. A., Bodegraven, A. A. V., Boer, N. K. D., Bouma, G., Fidder, H. H., D'Haens, G., Hoentjen, F., Hommes, D. W., Jong, D. J. D., Löwenberg, M., Maljaars, P. J., Meulen-de Jong, A. E. V. D., Oldenburg, B., Pierik, M. J., Ponsioen, C. Y., Stokkers, P. C., Verspaget, H. W., ... Parelsnoer Institute (PSI) and the Dutch Initiative on Crohn and Colitis (ICC) (2017). Cohort profile: design and first results of the Dutch IBD Biobank: A prospective, nationwide biobank of patients with inflammatory bowel disease. BMJ Open, 7(11), [e016695]. https://doi.org/10.1136/bmjopen-2017-016695
  27. Spekhorst, L., Severs, M., de Boer, N. K. H., Festen, E. A. M., Fidder, H. H., Hoentjen, F., Imhann, F., de Jong, D. J., van der Meulen-de Jong, A. E., Pierik, M., van der Woude, C. J., Dijkstra, G., Ponsioen, C. Y., Lowenberg, M., Oldenburg, B., & Weersma, R. K. (2017). Ethnicity and country of birth are associated with phenotypic differences in patients with inflammatory bowel disease. Journal of Crohn's and Colitis, 11(suppl_1), S28. [DOP004 ]. https://doi.org/10.1093/ecco-jcc/jjx002.041
  28. Imhann, F., Vich Vila, A., Bonder, M. J., Lopez Manosalva, A. G., Koonen, D. P. Y., Fu, J., Wijmenga, C., Zhernakova, A., & Weersma, R. K. (2017). The influence of proton pump inhibitors and other commonly used medication on the gut microbiota. Gut Microbes, 8(4), 351-358. https://doi.org/10.1080/19490976.2017.1284732
  29. 2016
  30. Bonder, M. J., Kurilshchikov, A., Tigchelaar-Feenstra, E., Mujagic, Z., Imhann, F., Vich Vila, A., Deelen, P., Vatanen, T., Schirmer, M., Smeekens, S. P., Zhernakova, D. V., Jankipersadsing, S. A., Jaeger, M., Oosting, M., Cenit, M. C., Masclee, A. A. M., Swertz, M. A., Li, Y., Kumar, V., ... Zhernakova, A. (2016). The effect of host genetics on the gut microbiome. Nature Genetics, 48(11), 1407-1412. https://doi.org/10.1038/ng.3663
  31. Visschedijk, M. C., Alberts, R., Mucha, S., Deelen, P., de Jong, D. J., Pierik, M., Spekhorst, L. M., Imhann, F., van der Meulen-de Jong, A. E., van der Woude, C. J., van Bodegraven, A. A., Oldenburg, B., Lowenberg, M., Dijkstra, G., Ellinghaus, D., Schreiber, S., Wijmenga, C., Rivas, M. A., Franke, A., ... Dutch Initiative on Crohn and Colitis (2016). Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2. PLoS ONE, 11(8), [e0159609]. https://doi.org/10.1371/journal.pone.0159609
  32. Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., Feenstra, E. T., Jankipersadsing, S. A., Cenit, M. C., Harmsen, H. J. M., Dijkstra, G., Franke, L., Xavier, R. J., Jonkers, D., Wijmenga, C., Weersma, R. K., & Zhernakova, A. (2016). Proton pump inhibitors affect the gut microbiome. Gut, 65(5), 740-748. https://doi.org/10.1136/gutjnl-2015-310376
  33. Zhernakova, A., Kurilshchikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vich Vila, A., Falony, G., Vieira-Silva, S., Wang, J., Imhann, F., Brandsma, E., Jankipersadsing, S. A., Joossens, M., Cenit, M. C., Deelen, P., Swertz, M. A., Weersma, R. K., ... Lifelines Cohort Study (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352(6285), 565-569. https://doi.org/10.1126/science.aad3369
  34. Spekhorst, L. M., Imhann, F., Festen, E. A., van Bodegraven, A., de Boer, N., Bouma, G., Fidder, H. H., D'Haens, G. R., Hoentjen, F., Hommes, D., de Jong, D. J., Lowenberg, M., Van der Meulen, A., Oldenburg, B., Pierik, M., Ponsioen, C., Stokkers, P., Visschedijk, M. C., Van der Woude, C. J., ... Weersma, R. K. (2016). First Results and Information Model From the Parelsnoer Institute IBD Biobank: A Nationwide Standardized Inflammatory Bowel Disease Collection by All University Medical Centers in the Netherlands. Gastroenterology, 150(4), S789-S790. https://doi.org/10.1016/S0016-5085(16)32680-4
  35. Imhann, F., Vila, A. V., Bonder, M. J., Gevers, D., Fu, J., Visschedijk, M. C., Spekhorst, L. M., Franke, L., van Dullemen, H., Ter Steege, R., Huttenhower, C., Dijkstra, G., Xavier, R., Wijmenga, C., Festen, E. A., Zhernakova, A., & Weersma, R. K. (2016). Gene-Microbiome Interactions Underlying the Onset and the Clinical Phenotypes of Inflammatory Bowel Disease. Gastroenterology, 150(4), S22-S22. https://doi.org/10.1016/S0016-5085(16)30198-6
  36. Regeling, A., Imhann, F., Volders, H. H., Blokzijl, T., Bloks, V. W., Weersma, R. K., Dijkstra, G., & Faber, K. N. (2016). HSPA6 is an ulcerative colitis susceptibility factor that is induced by cigarette smoke and protects intestinal epithelial cells by stabilizing anti-apoptotic Bcl-XL. Biochimica et biophysica acta-Molecular basis of disease, 1862(4), 788-796. https://doi.org/10.1016/j.bbadis.2016.01.020
  37. Visschedijk, M. C., Spekhorst, L. M., Dijkstra, G., van Loo, E. S., de Jong, D. J., Van Der Meulen, A., Verspaget, H. W., Ponsioen, C., Nieuwenhuijs, V. B., Oldenburg, B., Pierik, M., de Boer, N., Van Der Woude, C. J., Imhann, F., Alberts, R., van Sommeren, S., Faber, K. N., Aldaz, C. M., Weersma, R. K., & Festen, E. A. (2016). Identification of a Genetic Risk Variant in the WWOX Gene Associated With Recurrent Fibrostenotic Crohn's Disease. Gastroenterology, 150(4), S570-S570. https://doi.org/10.1093/ecco-jcc/jjw019.838
  38. Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., Tigchelaar, E., Jankipersadsing, S. A., Cenit, M. C., Harmsen, H. J. M., Dijkstra, G., Franke, L., Xavier, R. J., Jonkers, D., Wijmenga, C., Weersma, R. K., & Zhernakova, A. (2016). Proton pump inhibitors affect the gut microbiome. Journal of Crohn's and Colitis, 10, S487-S487.
  39. Neelis, E. G., Roskott, A. M., Dijkstra, G., Wanten, G. J., Serlie, M. J., Tabbers, M. M., Damen, G., Olthof, E. D., Jonkers, C. F., Kloeze, J. H., Ploeg, R. J., Imhann, F., Nieuwenhuijs, V. B., & Rings, E. H. H. M. (2016). Presentation of a nationwide multicenter registry of intestinal failure and intestinal transplantation. Clinical Nutrition, 35(1), 225-229. https://doi.org/10.1016/j.clnu.2015.01.010
  40. 2015
  41. Fu, J., Bonder, M. J., Cenit, M. C., Tigchelaar-Feenstra, E., Maatman, A., Dekens, J. A. M., Brandsma, E., Marczynska, J., Imhann, F., Weersma, R. K., Franke, L., Poon, T. W., Xavier, R. J., Gevers, D., Hofker, M. H., Wijmenga, C., & Zhernakova, A. (2015). The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids. Circulation research, 117(9), 817-824. https://doi.org/10.1161/CIRCRESAHA.115.306807
  42. 2014
  43. Knights, D., Silverberg, M. S., Weersma, R. K., Gevers, D., Dijkstra, G., Huang, H., Tyler, A. D., van Sommeren, S., Imhann, F., Stempak, J. M., Huang, H., Vangay, P., Al-Ghalith, G. A., Russell, C., Sauk, J., Knight, J., Daly, M. J., Huttenhower, C., & Xavier, R. J. (2014). Complex host genetics influence the microbiome in inflammatory bowel disease. Genome medicine, 6, [107]. https://doi.org/10.1186/s13073-014-0107-1

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