96 Shrock, E., Fujimura, E., Kula, T., Timms, R.T., Lee, I.-H., Leng, Y., Robinson, M.L., Sie, B.M., Li, M.Z., Chen, Y., et al. (2020). Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science 370, eabd4250. Xu, G.J., Kula, T., Xu, Q., Li, M.Z., Vernon, S.D., Ndung’u, T., Ruxrungtham, K., Sanchez, J., Brander, C., Chung, R.T., et al. (2015). Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. Science 348, aaa0698. Angkeow, J.W., Monaco, D.R., Chen, A., and Venkataraman, T. (2021). Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors. bioRxiv, 10.1101/2021.10.01.462481. Vogl, T., Klompus, S., Leviatan, S., Kalka, I.N., Weinberger, A., Wijmenga, C., Fu, J., Zhernakova, A., Weersma, R.K., and Segal, E. (2021). Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. Nat. Med. 27, 1442–1450. Tigchelaar, E.F., Zhernakova, A., Dekens, J.A.M., Hermes, G., Baranska, A., Mujagic, Z., Swertz, M.A., Muñoz, A.M., Deelen, P., Cénit, M.C., et al. (2015). Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. BMJ Open 5, e006772. Leviatan, S., Vogl, T., Klompus, S., et al. (2022). Food proteins elicit distinct systemic antibody responses, that associate with dietary intake in healthy individuals. Immunity 2022 (provisionally accepted). Vita, R., Overton, J.A., Greenbaum, J.A., Ponomarenko, J., Clark, J.D., Cantrell, J.R., Wheeler, D.K., Gabbard, J.L., Hix, D., Sette, A., et al. (2015). The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 43, D405-12. Scholtens, S., Smidt, N., Swertz, M.A., Bakker, S.J.L., Dotinga, A., Vonk, J.M., van Dijk, F., van Zon, S.K.R., Wijmenga, C., Wolffenbuttel, B.H.R., et al. (2015). Cohort Profile: LifeLines, a three-generation cohort study and biobank. Int. J. Epidemiol. 44, 1172–1180. Lambers, W., Arends, S., Roozendaal, C., Brouwer, E., Bootsma, H., Westra, J., and de Leeuw, K. (2021). Prevalence of systemic lupus erythematosus-related symptoms assessed by using the Connective Tissue Disease Screening Questionnaire in a large population-based cohort. Lupus Science & Medicine 8, e000555. van Zanten, A., Arends, S., Roozendaal, C., Limburg, P.C., Maas, F., Trouw, L.A., Toes, R.E.M., Huizinga, T.W.J., Bootsma, H., and Brouwer, E. (2017). Presence of anticitrullinated protein antibodies in a large populationbased cohort from the Netherlands. Ann. Rheum. Dis. 76, 1184–1190. Imhann, F., Van der Velde, K.J., Barbieri, R., Alberts, R., Voskuil, M.D., Vich Vila, A., Collij, V., Spekhorst, L.M., Van der Sloot, K.W.J., Peters, V., et al. (2019). The 1000IBD project: multiomics data of 1000 inflammatory bowel disease patients; data release 1. BMC Gastroenterol. 19, 5. Bourgonje, A.R., Andreu-Sánchez, S., Vogl, T., Hu, S., Vich Vila, A., Gacesa, R., Leviatan, S., Kurilshikov, A., Klompus, S., Kalka, I.N., et al. In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing. bioRxiv, 10.1101/2021.12.07.471581. Dixon, P. (2003). VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930. Csardi, G., Nepusz, T., and Others (2006). The igraph software package for complex network research. InterJournal, Complex Systems 1695, 1–9. Langfelder, P., and Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559. Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7, 539. Wilbur, W.J., and Lipman, D.J. (1983). Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. U. S. A. 80, 726–730. 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 Chapter 3
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