584063-Bourgonje

98 Dominguez, C., Boelens, R., and Bonvin, A.M.J.J. (2003). HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731–1737. Adasme, M.F., Linnemann, K.L., Bolz, S.N., Kaiser, F., Salentin, S., JoachimHaupt, V., and Schroeder, M. (2021). PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA. Nucleic Acids Research 49, W530–W534. Honorato, R.V., Koukos, P.I., Jiménez-García, B., Tsaregorodtsev, A., Verlato, M., Giachetti, A., Rosato, A., and Bonvin, A.M.J.J. (2021). Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. Front Mol Biosci 8, 729513. Vangone, A., and Bonvin, A.M. (2015). Contacts-based prediction of binding affinity in proteinprotein complexes. Elife 4, e07454. Zhernakova, A., Kurilshikov, A., Bonder, M.J., Tigchelaar, E.F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A.V., Falony, G., Vieira-Silva, S., et al. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565–569. Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359. Beghini, F., McIver, L.J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A.M., et al. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife 10. Schwarzer, G., and Others (2007). meta: An R package for meta-analysis. R News 7, 40–45. Korndewal, M.J., Mollema, L., Tcherniaeva, I., van der Klis, F., Kroes, A.C.M., OudesluysMurphy, A.M., Vossen, A.C.T.M., and de Melker, H.E. (2015). Cytomegalovirus infection in the Netherlands: seroprevalence, risk factors, and implications. J. Clin. Virol. 63, 53–58. Erles, K., Sebökovà, P., and Schlehofer, J.R. (1999). Update on the prevalence of serum antibodies (IgG and IgM) to adeno-associated virus (AAV). J. Med. Virol. 59, 406–411. Hendrikx, L.H., Oztürk, K., de Rond, L.G.H., Veenhoven, R.H., Sanders, E.A.M., Berbers, G.A.M., and Buisman, A.-M. (2011). Identifying long-term memory B-cells in vaccinated children despite waning antibody levels specific for Bordetella pertussis proteins. Vaccine 29, 1431– 1437. Kontio, M., Jokinen, S., Paunio, M., Peltola, H., and Davidkin, I. (2012). Waning antibody levels and avidity: implications for MMR vaccine-induced protection. J. Infect. Dis. 206, 1542–1548. Genome of the Netherlands Consortium (2014). Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 46, 818–825. Grundbacher, F.J. (1974). Heritability estimates and genetic and environmental correlations for the human immunoglobulins G, M, and A. Am. J. Hum. Genet. 26, 1–12. Kalff, M.W., and Hijmans, W. (1969). Serum immunoglobulin levels in twins. Clin. Exp. Immunol. 5, 469– 477. Rowe, D.S., Boyle, J.A., and Buchanan, W.W. (1968). Plasma immunoglobulin concentrations in twins. Clin. Exp. Immunol. 3, 233–244. Venkataraman, T., Valencia, C., and Mangino, M. (2021). Antiviral Antibody Epitope Selection is a Heritable Trait. bioRxiv, 10.1101/2021.03.25.436790. Reynisson, B., Barra, C., Kaabinejadian, S., Hildebrand, W.H., Peters, B., and Nielsen, M. (2020b). Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data. J. Proteome Res. 19, 2304– 2315. Tian, C., Hromatka, B.S., Kiefer, A.K., Eriksson, N., Noble, S.M., Tung, J.Y., and Hinds, D.A. (2017). Genomewide association and HLA region fine-mapping studies identify susceptibility loci for multiple common infections. Nat. Commun. 8, 599. 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 Chapter 3

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