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Franke, Prof. Lude

Lude Franke
Lude Franke

Lude Franke is Associate Professor at the Genetics Department of the University of Groningen/University Medical Centre Groningen and Head of Research and Education in the Dept. of Genetics, UMCG. He is a statistical geneticist, working on analyzing data on the genetics of complex and autoimmune diseases (e.g. celiac disease). He has been awarded an ERC Starting grant (2014), NWO VIDI grant (2014), NWO VENI grant (2009) and a Horizon Grant (2009) to work on identifying molecular effects due to disease-causing mutations.

In his spare time he is also a graphic designer (see his PhD thesis design ). This chance combination of skills can sometimes make life as a genetics researcher a bit easier: if you can explain your research visually, more people can understand what you are doing. Lude Franke is one of the founding members of the Young Academy Groningen and has also been appointed member of De Jonge Akademie (national Young Academy).

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Publications

2020

BIOS Consortium, Ouwens, K. G., Jansen, R., Nivard, M. G., van Dongen, J., Frieser, M. J., Hottenga, J-J., Arindrarto, W., Claringbould, A., van Iterson, M., Mei, H., & Franke, L. (2020). A characterization of cis- and trans-heritability of RNA-Seq-based gene expression. European Journal of Human Genetics, 28(2), 253-263. https://doi.org/10.1038/s41431-019-0511-5
BIOS Consortium, Lu, X., Fraszczyk, E., van der Meer, T. P., van Faassen, M., Bloks, V. W., Kema, I. P., van Beek, A. P., Li, S., Franke, L., Westra, H-J., Xu, X., Huo, X., Snieder, H., Wolffenbuttel, B. H. R., & van Vliet-Ostaptchouk, J. V. (2020). An epigenome-wide association study identifies multiple DNA methylation markers of exposure to endocrine disruptors. Environment international, 144, [106016]. https://doi.org/10.1016/j.envint.2020.106016
BIOS Consortium, Aguirre-Gamboa, R., de Klein, N., di Tommaso, J., Claringbould, A., van der Wijst, M. G. P., de Vries, D., Brugge, H., Oelen, R., Vosa, U., Zorro, M. M., Chu, X., Bakker, O. B., Borek, Z., Ricano-Ponce, I., Deelen, P., Xu, C-J., Swertz, M., Jonkers, I., ... Li, Y. (2020). Deconvolution of bulk blood eQTL effects into immune cell subpopulations. Bmc Bioinformatics, 21(1), [243]. https://doi.org/10.1101/548669, https://doi.org/10.1186/s12859-020-03576-5
Folkersen, L., Gustafsson, S., Wang, Q., Hansen, D. H., Hedman, Å. K., Schork, A., Page, K., Zhernakova, D. V., Wu, Y., Peters, J., Eriksson, N., Bergen, S. E., Boutin, T. S., Bretherick, A. D., Enroth, S., Kalnapenkis, A., Gådin, J. R., Suur, B. E., Chen, Y., ... Mälarstig, A. (2020). Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals. Nature Metabolism, 2(10), 1135-1148. https://doi.org/10.1038/s42255-020-00287-2
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
Huang, Y., Ollikainen, M., Muniandy, M., Zhang, T., van Dongen, J., Hao, G., van der Most, P. J., Pan, Y., Pervjakova, N., Sun, Y. V., Hui, Q., Lahti, J., Fraszczyk, E., Lu, X., Sun, D., Richard, M. A., Willemsen, G., Heikkila, K., Mateo Leach, I., ... Wang, X. (2020). Identification, Heritability, and Relation With Gene Expression of Novel DNA Methylation Loci for Blood Pressure. Hypertension (Dallas, Tex. : 1979), 76(1), 195-205. https://doi.org/10.1161/HYPERTENSIONAHA.120.14973
de Vries, D. H., Matzaraki, V., Bakker, O. B., Brugge, H., Westra, H-J., Netea, M. G., Franke, L., Kumar, V., & van der Wijst, M. G. P. (2020). Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response. PLoS Pathogens, 16(4), [1008408]. https://doi.org/10.1371/journal.ppat.1008408
Lifelines Cohort Study, Lopera Maya, E. A., van der Graaf, A., Lanting, P., van der Geest, M., Fu, J., Swertz, M., Franke, L., Wijmenga, C., Deelen, P., Zhernakova, A., & Sanna, S. (2020). Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes. Frontiers in Genetics, 11, [613]. https://doi.org/10.3389/fgene.2020.00613
Bangma, A., Voskuil, M. D., Uniken Venema, W. T. C., Brugge, H., Hu, S., Lanting, P., Franke, L., Dijkstra, G., Festen, E. A. M., & Weersma, R. K. (2020). Predicted efficacy of a pharmacogenetic passport for inflammatory bowel disease. Alimentary Pharmacology & Therapeutics, 51(11), 1105-1115. https://doi.org/10.1111/apt.15762
Van Der Wijst, M. G. P., De Vries, D. H., Groot, H. E., Trynka, G., Hon, C. C., Bonder, M. J., Stegle, O., Nawijn, M. C., Idaghdour, Y., Van Der Harst, P., Ye, C. J., Powell, J., Theis, F. J., Mahfouz, A., Heing, M., & Franke, L. (2020). The single-cell eQTLGen consortium. eLife, 9, [52155]. https://doi.org/10.7554/eLife.52155

2019

BIOS Consortium (2019). A linear mixed-model approach to study multivariate gene-environment interactions. Nature Genetics, 51(1), 180-186. https://doi.org/10.1038/s41588-018-0271-0
BIOS Consortium (2019). Allele specific expression identifies rare variants as cause for extreme allelic imbalance. European Journal of Human Genetics, 27, 601.
Clark, D. W., Okada, Y., Moore, K. H. S., Mason, D., Pirastu, N., Gandin, I., Mattsson, H., Barnes, C. L. K., Lin, K., Zhao, J. H., Deelen, P., Rohde, R., Schurmann, C., Guo, X., Giulianini, F., Zhang, W., Medina-Gomez, C., Karlsson, R., Bao, Y., ... Wilson, J. F. (2019). Associations of autozygosity with a broad range of human phenotypes. Nature Communications, 10(1), [4957]. https://doi.org/10.1038/s41467-019-12283-6
Sanna, S., van Zuydam, N. R., Mahajan, A., Kurilshikov, A., Vich Vila, A., Võsa, U., Mujagic, Z., Masclee, A. A. M., Jonkers, D. M. A. E., Oosting, M., Joosten, L. A. B., Netea, M. G., Franke, L., Zhernakova, A., Fu, J., Wijmenga, C., & McCarthy, M. I. (2019). Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nature Genetics, 51(4), 600-605. https://doi.org/10.1038/s41588-019-0350-x
Sanna, S., van Zuydam, N. R., Mahajan, A., Kurilshikov, A., Vich Vila, A., Võsa, U., Mujagic, Z., Masclee, A. A. M., Jonkers, D. M. A. E., Oosting, M., Joosten, L. A. B., Netea, M. G., Franke, L., Zhernakova, A., Fu, J., Wijmenga, C., & McCarthy, M. I. (2019). Causal relationshipsbetween gut microbiome, short-chain fatty acids and metabolicdiseases. Nature Genetics, 51, 600-605. https://www.nature.com/articles/s41588-019-0350-x#auth-1
Zeng, B., Lloyd-Jones, L. R., Montgomery, G. W., Metspalu, A., Esko, T., Franke, L., Vosa, U., Claringbould, A., Brigham, K. L., Quyyumi, A. A., Idaghdour, Y., Yang, J., Visscher, P. M., Powell, J. E., & Gibson, G. (2019). Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation. Genetics, 212(3), 905-918. https://doi.org/10.1534/genetics.119.302091
BIOS Consortium, van Dongen, J., Zilhao, N. R., Sugden, K., Hannon, E. J., Mill, J., Caspi, A., Agnew-Blais, J., Arseneault, L., Corcoran, D. L., Moffitt, T. E., Poulton, R., Franke, B., & Boomsma, D. (2019). Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults. Biological Psychiatry, 86(8), 599-607. https://doi.org/10.1016/j.biopsych.2019.02.016
BIOS Consortium, van Rooij, J., Mandaviya, P. R., Claringbould, A., Felix, J. F., van Dongen, J., Jansen, R., Franke, L., 't Hoen, P. A. C., Heijmans, B., & van Meurs, J. B. J. (2019). Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies. Genome Biology, 20(1), [235]. https://doi.org/10.1186/s13059-019-1878-x
CommonMind Consortium, Psychiat Genomics Consortium, iPSYCH-GEMS Schizophrenia Working, Huckins, L. M., Dobbyn, A., Ruderfer, D. M., Hoffman, G., Wang, W., Pardinas, A. F., Rajagopal, V. M., Als, T. D., Nguyen, H. T., Girdhar, K., Boocock, J., Roussos, P., Fromer, M., Kramer, R., Purcell, S., Demontis, D., ... Stahl, E. A. (2019). Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. Nature Genetics, 51(4), 659-674. https://doi.org/10.1038/s41588-019-0364-4
23and Me Res Team, eQTLgen Consortium, Int Cannabis Consortium, & Soc Sci Genetic Association Con (2019). Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences. Nature Genetics, 51(2), 245-257. https://doi.org/10.1038/s41588-018-0309-3
eQTLgen Consortium, Timmers, P. R., Mounier, N., Lall, K., Fischer, K., Ning, Z., Feng, X., Bretherick, A. D., & Clark, D. W. (2019). Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances. eLife, 8, [39856]. https://doi.org/10.7554/eLife.39856
van Arensbergen, J., Pagie, L., FitzPatrick, V. D., de Haas, M., Baltissen, M. P., Comoglio, F., van der Weide, R. H., Teunissen, H., Vosa, U., Franke, L., de Wit, E., Vermeulen, M., Bussemaker, H. J., & van Steensel, B. (2019). High-throughput identification of human SNPs affecting regulatory element activity. Nature Genetics, 51(7), 1160-+. https://doi.org/10.1038/s41588-019-0455-2
Deelen, P., van Dam, S., Karjalainen, J. M., Brugge, H., Folkertsma, P., van Diemen, C. C., Kerstjens-Frederikse, W. S., Herkert, J. C., Gillett, T., Swertz, M. A., & Franke, L. (2019). Improving diagnostic yield of exome-sequencing through prioritization of genes with predicted HPO assignments. European Journal of Human Genetics, 27, 537-537.
Deelen, P., van Dam, S., Herkert, J. C., Karjalainen, J. M., Brugge, H., Abbott, K. M., van Diemen, C. C., van der Zwaag, P. A., Gerkes, E. H., Zonneveld-Huijssoon, E., Boer-Bergsma, J. J., Folkertsma, P., Gillett, T., van der Velde, K. J., Kanninga, R., van den Akker, P. C., Jan, S. Z., Hoorntje, E. T., Te Rijdt, W. P., ... Franke, L. (2019). Improving the diagnostic yield of exome-sequencing by predicting gene-phenotype associations using large-scale gene expression analysis. Nature Communications, 10(1), [2837]. https://doi.org/10.1038/s41467-019-10649-4
Chu, X., Jaeger, M., Bakker, O. B., Aguirre-Gamboa, R., Oosting, M., Smeekens, S. P., Withoff, S., Netea-Maier, R. T., Koenen, H. J. P. M., Joosten, I., Xavier, R. J., Franke, L., Joosten, L. A. B., Sanna, S., Kumar, V., Wijmenga, C., Netea, M. G., & Li, Y. (2019). Integration of similar to 10,000 metabolite features with genotype data and immune phenotypes reveals genetic determinants and common regulatory modules. European Journal of Human Genetics, 27, 787-787.
BBMRI Metabolomics Consortium (2019). Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine. Neurology, 92(16), E1899-E1911. https://doi.org/10.1212/WNL.0000000000007313
Porcu, E., Rueger, S., Lepik, K., eQTLgen Consortium, & BIOS Consortium (2019). Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits. Nature Communications, 10, [3300]. https://doi.org/10.1038/s41467-019-10936-0
Kilpelainen, T. O., Nolte, I. M., van der Most, P. J., Verweij, N., Snieder, H., van der Ende, M. Y., Oldehinkel, A. J., van der Harst, P., Van Vliet-Ostaptchouk, J. V., Lifelines Cohort Study, & Wang, Y. X. (2019). Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity. Nature Communications, 10(1), [376]. https://doi.org/10.1038/s41467-018-08008-w
Vojinovic, D., Radjabzadeh, D., Kurilshikov, A., Amin, N., Wijmenga, C., Franke, L., Ikram, M. A., Uitterlinden, A. G., Zhernakova, A., Fu, J., Kraaij, R., & van Duijn, C. M. (2019). Relationship between gut microbiota and circulating metabolites in population-based cohorts. Nature Communications, 10(1), [5813]. https://doi.org/10.1038/s41467-019-13721-1
GoNL Consortium, BIOS Consortium, Jadhav, B., Monajemi, R., Gagalova, K. K., Ho, D., Draisma, H. H. M., van de Wiel, M. A., Franke, L., Heijmans, B. T., van Meurs, J., Jansen, R., t Hoen, P. A. C., Sharp, A. J., & Kielbasa, S. M. (2019). RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting. BMC Biology, 17(1), [50]. https://doi.org/10.1186/s12915-019-0674-0
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
BIOS Consortium, & GoNL Consortium (2019). Skewed X-inactivation is common in the general female population. European Journal of Human Genetics, 27(3), 455-465. https://doi.org/10.1038/s41431-018-0291-3
BIOS Consortium, KORA Study Grp, Schlicht, K., Nyczka, P., Caliebe, A., Freitag-Wolf, S., Claringbould, A., Franke, L., Vosa, U., Kardia, S. L. R., Smith, J. A., Zhao, W., Gieger, C., Peters, A., Prokisch, H., Strauch, K., Baurecht, H., Weidinger, S., Rosenstiel, P., ... Krawczak, M. (2019). The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus. HUMAN GENETICS, 138(4), 375-388. https://doi.org/10.1007/s00439-019-01994-x

2018

BIOS Consortium (2018). A SNP panel for identification of DNA and RNA specimens. BMC Genomics, 19(90). https://doi.org/10.1186/s12864-018-4482-7
van der Wijst, M. G. P., de Vries, D. H., Brugge, H., Westra, H-J., & Franke, L. (2018). An integrative approach for building personalized gene regulatory networks for precision medicine. Genome medicine, 10, [96]. https://doi.org/10.1186/s13073-018-0608-4
BIOS Consortium, GLOBAL Meth QTL, Parmar, P., Lowry, E., Cugliari, G., Suderman, M., Wilson, R., Karhunen, V., Andrew, T., Wiklund, P., Wielscher, M., Guarrera, S., Teumer, A., Lehne, B., Milani, L., de Klein, N., Mishra, P. P., Melton, P. E., Mandaviya, P. R., ... Verweij, N. (2018). Association of maternal prenatal smoking GFI1-locus and cardiometabolic phenotypes in 18,212 adults. EBioMedicine, 38, 206-216. https://doi.org/10.1016/j.ebiom.2018.10.066
Pirastu, N., Joshi, P. K., de Vries, P. S., Cornelis, M. C., McKeigue, P. M., Keum, N., Franceschini, N., Colombo, M., Giovannucci, E. L., Spiliopoulou, A., Franke, L., North, K. E., Kraft, P., Morrison, A. C., Esko, T., & Wilson, J. F. (2018). Author Correction: GWAS for male-pattern baldness identifies 71 susceptibility loci explaining 38% of the risk. Nature Communications, 9(1), 2536. https://doi.org/10.1038/s41467-018-04857-7
Lifelines Cohort Study, Zhernakova, D. V., Le, T. H., Kurilshikov, A., Atanasovska, B., Bonder, M. J., Sanna, S., Claringbould, A., Võsa, U., Deelen, P., Franke, L., de Boer, R. A., Kuipers, F., Netea, M. G., Hofker, M. H., Wijmenga, C., Zhernakova, A., & Fu, J. (2018). Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nature Genetics, 50(12), [1752]. https://doi.org/10.1038/s41588-018-0275-9
BIOS Consortium, Luijk, R., Wu, H., Ward-Caviness, C. K., Hannon, E., Carnero-Montoro, E., Min, J. L., Mandaviya, P., Mueller-Nurasyid, M., Mei, H., van der Maarel, S. M., Relton, C., Mill, J., Waldenberger, M., Bell, J. T., Jansen, R., Zhernakova, A., Franke, L., 't Hoen, P. A. C., ... Heijmans, B. T. (2018). Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation. Nature Communications, 9(1), 3738. [3738]. https://doi.org/10.1038/s41467-018-05714-3
Amini, M., Vonk, J. M., Abbasi, A., Prins, B. P., Bruinenberg, M., Franke, L., van der Harst, P., Navis, G., Koppelman, G. H., Wolffenbuttel, B. H. R., Boezen, H. M., Snieder, H., Chasman, D. I., & Alizadeh, B. Z. (2018). Blood Eosinophil Count and Metabolic, Cardiac and Pulmonary Outcomes: A Mendelian Randomization Study. Twin research and human genetics, 21(2), 89-100. https://doi.org/10.1017/thg.2018.6
Bolling, M. C., Jan, S. Z., Pasmooij, A. M. G., Lemmink, H. H., Franke, L. H., Yenamandra, V. K., Sinke, R. J., van den Akker, P. C., & Jonkman, M. F. (2018). Generalized Ichthyotic Peeling Skin Syndrome due to FLG2 Mutations. Journal of Investigative Dermatology, 138(8), 1881-1884. https://doi.org/10.1016/j.jid.2018.01.038
Bolling, M., Jan, S., Pasmooij, A., Lemmink, H., Franke, L., Yenamandra, V., Sinke, R., van den Akker, P., & Jonkman, M. F. (2018). Generalized ichthyotic peeling skin syndrome due to FLG2 mutations. Journal of Investigative Dermatology, 138(5), S128.
Lifelines Cohort Study, Ligthart, S., Vaez, A., Võsa, U., Stathopoulou, M. G., de Vries, P. S., Prins, B. P., Van der Most, P. J., Tanaka, T., Naderi, E., Rose, L. M., Wu, Y., Karlsson, R., Barbalic, M., Lin, H., Pool, R., Zhu, G., Macé, A., Sidore, C., ... Amini, M. (2018). Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders. American Journal of Human Genetics, 103(5), 691-706. https://doi.org/10.1016/j.ajhg.2018.09.009
BIOS Consortium, Luijk, R., Dekkers, K. F., van Iterson, M., Arindrarto, W., Claringbould, A., Hop, P., Boomsma, D., van Duijn, C. M., van Greevenbroek, M. M. J., Veldink, J. H., Wijmenga, C., Franke, L., 't Hoend, P. A. C., Jansen, R., van Meurs, J., Mei, H., Slagboomi, P. E., Heijmans, B. T., & van Zwet, E. W. (2018). Genome-wide identification of directed gene networks using large-scale population genomics data. Nature Communications, 9(1), 3097. [3097]. https://doi.org/10.1038/s41467-018-05452-6
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
Lifelines Cohort Study (2018). Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nature Genetics, 50(11), 1524-+. https://doi.org/10.1038/s41588-018-0224-7
Bakker, O. B., Aguirre-Gamboa, R., Sanna, S., Oosting, M., Smeekens, S. P., Jaeger, M., Zorro, M., Vosa, U., Withoff, S., Netea-Maier, R. T., Koenen, H. J. P. M., Joosten, I., Xavier, R. J., Franke, L., Joosten, L. A. B., Kumar, V., Wijmenga, C., Netea, M. G., & Li, Y. (2018). Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. Nature Immunology, 19(7), 776-786. https://doi.org/10.1038/s41590-018-0121-3
Barbieri, R., Venema, W. U., Vich Vila, A., Li, Y., Franke, L., van Dijk, F., De Klein, N., Swertz, M., Sanna, S., Voskuil, M. D., Rivas, M., Xavier, R., Daly, M., Festen, E. A., & Weersma, R. K. (2018). Integration of whole-exome sequencing and RNA sequencing of intestinal biopsies in inflammatory bowel disease identifies inflammation-dependent effects. Journal of Crohn's and Colitis, 12, S8-S9.
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
MiBioGen Consortium Initiative (2018). Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative. Microbiome, 6(1), [101]. https://doi.org/10.1186/s40168-018-0479-3
van Setten, J., Brody, J. A., Jamshidi, Y., Swenson, B. R., Butler, A. M., Campbell, H., Del Greco, F. M., Evans, D. S., Gibson, Q., Gudbjartsson, D. F., Kerr, K. F., Krijthe, B. P., Lyytikainen, L-P., Mueller, C., Mueller-Nurasyid, M., Nolte, I. M., Padmanabhan, S., Ritchie, M. D., Robino, A., ... Snieder, H. (2018). PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity. Nature Communications, 9(1), [2904]. https://doi.org/10.1038/s41467-018-04766-9
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
Pirastu, N., Joshi, P. K., de Vries, P. S., Cornelis, M. C., Keum, N., Franceschini, N., Colombo, M., Giovannucci, E. L., Spiliopoulou, A., Franke, L., North, K. E., Kraft, P., Morrison, A. C., Esko, T., & Wilson, J. F. (2018). Reply to 'Misestimation of heritability and prediction accuracy of male-pattern baldness'. Nature Communications, 9(1), 2538. [2538]. https://doi.org/10.1038/s41467-018-04808-2
Lifelines Cohort Study, & BIOS Consortium (2018). Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs. Nature Genetics, 50(4), 493-497. https://doi.org/10.1038/s41588-018-0089-9
Scholz, R. W., Bartelsman, E. J., Diefenbach, S., Franke, L., Grunwald, A., Helbing, D., Hill, R., Hilty, L., Hojer, M., Klauser, S., Montag, C., Parycek, P., Prote, J. P., Renn, O., Reichel, A., Schuh, G., Steiner, G., & Pereira, G. V. (2018). Unintended Side Effects of the Digital Transition: European Scientists' Messages from a Proposition-Based Expert Round Table. Sustainability, 10(6), [2001]. https://doi.org/10.3390/su10062001

2017

van Dam, S., Võsa, U., van der Graaf, A., Franke, L., & de Magalhães, J. P. (2018). Gene co-expression analysis for functional classification and gene-disease predictions. Briefings in Bioinformatics, 19(4), 575-592. https://doi.org/10.1093/bib/bbw139
Linner, R. K., Marioni, R. E., Rietveld, C. A., Simpkin, A. J., Davies, N. M., Watanabe, K., Armstrong, N. J., Auro, K., Baumbach, C., Bonder, M. J., Buchwald, J., Fiorito, G., Ismail, K., Iurato, S., Joensuu, A., Karell, P., Kasela, S., Lahti, J., Mcrae, A. F., ... BIOS Consortium (2017). An epigenome-wide association study meta-analysis of educational attainment. Molecular Psychiatry, 22(12), 1680-1690. https://doi.org/10.1038/mp.2017.210
Matzaraki, V., Gresnigt, M. S., Jaeger, M., Ricano-Ponce, I., Johnson, M. D., Oosting, M., Franke, L., Withoff, S., Perfect, J. R., Joosten, L. A. B., Kullberg, B. J., van de Veerdonk, F. L., Jonkers, I., Li, Y., Wijmenga, C., Netea, M. G., & Kumar, V. (2017). An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. PLoS ONE, 12(7), [e0180824]. https://doi.org/10.1371/journal.pone.0180824
Macé, A., Tuke, M. A., Deelen, P., Kristiansson, K., Mattsson, H., Nõukas, M., Sapkota, Y., Schick, U., Porcu, E., Rüeger, S., McDaid, A. F., Porteous, D., Winkler, T. W., Salvi, E., Shrine, N., Liu, X., Ang, W. Q., Zhang, W., Feitosa, M. F., ... Kutalik, Z. (2017). CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits. Nature Communications, 8(1), [744]. https://doi.org/10.1038/s41467-017-00556-x
Marshall, C. R., Howrigan, D. P., Merico, D., Thiruvahindrapuram, B., Wu, W., Greer, D. S., Antaki, D., Shetty, A., Holmans, P. A., Pinto, D., Gujral, M., Brandler, W. M., Malhotra, D., Wang, Z., Fajarado, K. V. F., Maile, M. S., Ripke, S., Agartz, I., Albus, M., ... Psychosis Endophenotypes (2017). Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nature Genetics, 49(1), 27-35. https://doi.org/10.1038/ng.3725
Tang, A. T., Hoi, J. P. C., Kotzin, J. J., Yang, Y., Hong, C. C., Hobson, N., Girard, R., Zeineddine, H. A., Lightle, R., Moore, T., Cao, Y., Shenkar, R., Chen, M., Mericko, P., Yang, J., Li, L., Tanes, C., Kobuley, D., Vosa, U., ... Kahn, M. L. (2017). Endothelial TLR4 and the microbiome drive cerebral cavernous malformations. Nature, 545(7654), 305-310. https://doi.org/10.1038/nature22075
van Dongen, J., Suderman, M., Sugden, K., Ismail, K., Mulder, R. H., Kupper, L. K., Bustamante, M., Alemany, S., Bonder, M. J., Parmar, P., Lowry, E., Jansen, R., Baselmans, B., Nivard, M., Corcoran, D., Poulton, R., Mill, J., Hannon, E., Arseneault, L., ... BIOS Consortium (2017). Epigenome-wide association study meta-analysis of aggressive behavior. Behavior Genetics, 47(6), 662-663.
Wahl, S., Drong, A. W., Lehne, B., Loh, M., Scott, W. R., Kunze, S., Tsai, P-C., Ried, J. S., Zhang, W., Yang, Y., Tan, S., Fiorito, G., Franke, L., Guarrera, S., Kasela, S., Kriebel, J., Richmond, R. C., Adamo, M., Afzal, U., ... Chambers, J. C. (2017). Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature, 541(81), 81-86. https://doi.org/10.1038/nature20784
Nibbeling, E. A. R., Duarri, A., Verschuuren-Bemelmans, C. C., Fokkens, M. R., Karjalainen, J. M., Smeets, C. J. L. M., de Boer-Bergsma, J. J., van der Vries, G., Dooijes, D., Bampi, G. B., van Diemen, C., Brunt, E., Ippel, E., Kremer, B., Vlak, M., Adir, N., Wijmenga, C., Warrenburg, B. P. C. V. D., Franke, L., ... Verbeek, D. S. (2017). Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia. Brain, 140(11), 2860-2878. https://doi.org/10.1093/brain/awx251
van der Velde, K. J., de Boer, E. N., van Diemen, C. C., Sikkema-Raddatz, B., Abbott, K. M., Knopperts, A., Franke, L., Sijmons, R. H., de Koning, T. J., Wijmenga, C., Sinke, R. J., & Swertz, M. A. (2017). GAVIN: Gene-Aware Variant INterpretation for medical sequencing. Genome Biology, 18(1), [6]. https://doi.org/10.1186/s13059-016-1141-7
Soderquest, K., Hertweck, A., Giambartolomei, C., Henderson, S., Mohamed, R., Goldberg, R., Perucha, E., Franke, L., Herrero, J., Plagnol, V., Jenner, R. G., & Lord, G. M. (2017). Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease. PLoS genetics, 13(2), [e1006587]. https://doi.org/10.1371/journal.pgen.1006587
Mandaviya, P. R., Joehanes, R., Aissi, D., Kuehnel, B., Marioni, R. E., Truong, V., Stolk, L., Beekman, M., Bonder, M. J., Franke, L., Gieger, C., Huan, T., Ikram, M. A., Kunze, S., Liang, L., Lindemann, J., Liu, C., McRae, A. F., Mendelson, M. M., ... Charge Consortium Epigenetics Grp (2017). Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes. PLoS ONE, 12(10), [e0182472]. https://doi.org/10.1371/journal.pone.0182472
Day, F. R., Thompson, D. J., Helgason, H., Chasman, D. I., Finucane, H., Sulem, P., Ruth, K. S., Whalen, S., Sarkar, A. K., Albrecht, E., Altmaier, E., Amini, M., Barbieri, C. M., Boutin, T., Campbell, A., Demerath, E., Giri, A., He, C., Hottenga, J. J., ... PRACTICAl Consortium (2017). Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nature Genetics, 49(6), 834-841. https://doi.org/10.1038/ng.3841
Pirastu, N., Joshi, P. K., de Vries, P. S., Cornelis, M. C., McKeigue, P. M., Keum, N., Franceschini, N., Colombo, M., Giovannucci, E. L., Spiliopoulou, A., Franke, L., North, K. E., Kraft, P., Morrison, A. C., Esko, T., & Wilson, J. F. (2017). GWAS for male-pattern baldness identifies 71 susceptibility loci explaining 38% of the risk. Nature Communications, 8, [1584]. https://doi.org/10.1038/s41467-017-01490-8
Wild, P. S., Felix, J. F., Schillert, A., Teumer, A., Chen, M-H., Leening, M. J. G., Voelker, U., Grossmann, V., Brody, J. A., Irvin, M. R., Shah, S. J., Pramana, S., Lieb, W., Schmidt, R., Stanton, A. V., Malzahn, D., Smith, A. V., Sundstrom, J., Minelli, C., ... KNHI Investigators (2017). Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function. CLIN Journal, 127(5), 1798-1812. https://doi.org/10.1172/JCI84840
Nolte, I. M., van der Most, P. J., Alizadeh, B. Z., de Bakker, P. I., Boezen, H. M., Bruinenberg, M., Franke, L., van der Harst, P., Navis, G., Postma, D. S., Rots, M. G., Stolk, R. R. P., Swertz, M. A., Wolffenbuttel, B. H., Wijmenga, C., & Snieder, H. (2017). Missing heritability: Is the gap closing? An analysis of 32 complex traits in the LifeLines Cohort Study. Genetic epidemiology, 39(7), 572-573. https://doi.org/10.1038/ejhg.2017.50
Nolte, I. M., van der Most, P. J., Alizadeh, B. Z., de Bakker, P. I. W., Boezen, H. M., Bruinenberg, M., Franke, L., van der Harst, P., Navis, G., Postma, D. S., Rots, M. G., Stolk, R. P., Swertz, M. A., Wolffenbuttel, B. H. R., Wijmenga, C., & Snieder, H. (2017). Missing heritability: Is the gap closing? An analysis of 32 complex traits in the Lifelines Cohort Study. European Journal of Human Genetics, 25(7), 877-885. https://doi.org/10.1038/ejhg.2017.50
Lepamets, M., Lepik, K., Kals, M., Carmeli, C., Claringbould, A., Bochud, M., Stringhini, S., Wijmenga, C., Franke, L., Magi, R., & Kutalik, Z. (2017). New Quality Measure for CNV: A Multi-Omics Approach. Human heredity, 83(1), 16-16.
Acuna-Hidalgo, R., Deriziotis, P., Steehouwer, M., Gilissen, C., Graham, S. A., van Dam, S., Hoover-Fong, J., Telegrafi, A. B., Destree, A., Smigiel, R., Lambie, L. A., Kayserili, H., Altunoglu, U., Lapi, E., Uzielli, M. L. G., Aracena, M., Nur, B. G., Mihci, E., Moreira, L. M. A., ... van Bon, B. W. M. (2017). Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies. PLoS genetics, 13(3). https://doi.org/10.1371/journal.pgen.1006683
Kasela, S., Kisand, K., Tserel, L., Kaleviste, E., Remm, A., Fischer, K., Esko, T., Westra, H-J., Fairfax, B. P., Makino, S., Knight, J. C., Franke, L., Metspalu, A., Peterson, P., & Milani, L. (2017). Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4(+) versus CD8(+) T cells. PLoS genetics, 13(3). https://doi.org/10.1371/journal.pgen.1006643
Kreiner, E., Waage, J., Standl, M., Brix, S., Pers, T. H., Couto Alves, A., Warrington, N. M., Tiesler, C. M., Fuertes, E., Franke, L., Hirschhorn, J. N., James, A., Simpson, A., Tung, J. Y., Koppelman, G. H., Postma, D. S., Pennell, C. E., Jarvelin, M-R., Custovic, A., ... Bønnelykke, K. (2017). Shared genetic variants suggest common pathways in allergy and autoimmune diseases. Journal of Allergy and Clinical Immunology, 140(3), 771-781. https://doi.org/10.1016/j.jaci.2016.10.055
Claringbould, A., de Klein, N., & Franke, L. (2017). The genetic architecture of molecular traits. Current Opinion in Systems Biology, 1, 25-31. https://doi.org/10.1016/j.coisb.2017.01.002

2016

Bonder, M. J., Luijk, R., Pital-Zhernakova, D., Moed, M., Deelen, P., Vermaat, M., van Iterson, M., van Dijk, F., van Galen, M., Bot, J., Slieker, R. C., Jhamai, P. M., Verbiest, M., Suchiman, H. E. D., Verkerk, M., van der Breggen, R., van Rooij, J., Lakenberg, N., Arindrarto, W., ... BIOS Consortium (2017). Disease variants alter transcription factor levels and methylation of their binding sites. Nature Genetics, 49(1), 131-138. https://doi.org/10.1038/ng.3721
Pital-Zhernakova, D., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., van 't Hof, P., Mei, H., van Dijk, F., Westra, H-J., Bonder, M. J., van Rooij, J., Verkerk, M., Jhamai, P. M., Moed, M., Kielbasa, S. M., Bot, J., Nooren, I., Pool, R., ... Franke, L. (2017). Identification of context-dependent expression quantitative trait loci in whole blood. Nature Genetics, 49(1), 139-145. https://doi.org/10.1038/ng.3737
Li, Y., Oosting, M., Smeekens, S. P., Jaeger, M., Aguirre-Gamboa, R., Le, K. T. T., Deelen, P., Ricano-Ponce, I., Schoffelen, T., Jansen, A. F. M., Swertz, M. A., Withoff, S., van de Vosse, E., van Deuren, M., van de Veerdonk, F., Zhernakova, A., van der Meer, J. W. M., Xavier, R. J., Franke, L., ... Netea, M. G. (2016). A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell, 167(4), 1099-1110. https://doi.org/10.1016/j.cell.2016.10.017
Slieker, R. C., van Iterson, M., Luijk, R., Beekman, M., Zhernakova, D. V., Moed, M. H., Mei, H., van Galen, M., Deelen, P., Bonder, M. J., Zhernakova, A., Uitterlinden, A. G., Tigchelaar, E. F., Stehouwer, C. D. A., Schalkwijk, C. G., van der Kallen, C. J. H., Hofman, A., van Heemst, D., de Geus, E. J., ... BIOS Consortium (2016). Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. Genome Biology, 17, [191]. https://doi.org/10.1186/s13059-016-1053-6
Ellinghaus, D., Jostins, L., Spain, S. L., Cortes, A., Bethune, J., Han, B., Park, Y. R., Raychaudhuri, S., Pouget, J. G., Huebenthal, M., Folseraas, T., Wang, Y., Esko, T., Metspalu, A., Westra, H-J., Franke, L., Pers, T. H., Weersma, R. K., Collij, V., ... PAGE (2016). Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nature Genetics, 48(5), 510-518. https://doi.org/10.1038/ng.3528
Dekkers, K. F., van Iterson, M., Slieker, R. C., Moed, M. H., Bonder, M. J., van Galen, M., Mei, H., Zhernakova, D. V., van den Berg, L. H., Deelen, J., van Dongen, J., van Heemst, D., Hofman, A., Hottenga, J. J., van der Kallen, C. J. H., Schalkwijk, C. G., Stehouwer, C. D. A., Tigchelaar, E. F., Uitterlinden, A. G., ... BIOS Consortium (2016). Blood lipids influence DNA methylation in circulating cells. Genome Biology, 17, [138]. https://doi.org/10.1186/s13059-016-1000-6
Pers, T. H., Timshel, P., Ripke, S., Lent, S., Sullivan, P. F., O'Donovan, M. C., Franke, L., Hirschhorn, J. N., & Schizophrenia Working Grp Psychiat (2016). Comprehensive analysis of schizophrenia-associated loci highlights ion channel pathways and biologically plausible candidate causal genes. Human Molecular Genetics, 25(6), 1247-1254. https://doi.org/10.1093/hmg/ddw007
Winkler, T. W., Justice, A. E., Graff, M., Barata, L., Feitosa, M. F., Chu, S., Czajkowski, J., Esko, T., Fall, T., Kilpelainen, T. O., Lu, Y., Magi, R., Mihailov, E., Pers, T. H., Rueger, S., Teumer, A., Ehret, G. B., Ferreira, T., Heard-Costa, N. L., ... MAGIC Consortium (2016). Correction: The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study (vol 11, e1005378, 2015). PLoS genetics, 12(6), [e1006166]. https://doi.org/10.1371/journal.pgen.1006166
Okbay, A., Baselmans, B. M. L., Neve, J-E. D., Turley, P., Nivard, M. G., Fontana, M. A., Meddens, S. F. W., Linnér, R. K., Rietveld, C. A., Derringer, J., Gratten, J., Lee, J. J., Liu, J. Z., de Vlaming, R., Ahluwalia, T. S., Buchwald, J., Cavadino, A., Frazier-Wood, A. C., Furlotte, N. A., ... Lifelines Cohort Study (2016). Corrigendum: Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses. Nature Genetics, 48(8), 970. https://doi.org/10.1038/ng0816-970c
Okbay, A., Baselmans, B. M. L., De Neve, J-E., Turley, P., Nivard, M. G., Fontana, M. A., Meddens, S. F. W., Linner, R. K., Rietveld, C. A., Derringer, J., Gratten, J., Lee, J. J., Liu, J. Z., de Vlaming, R., Ahluwalia, T. S., Buchwald, J., Cavadino, A., Frazier-Wood, A. C., Furlotte, N. A., ... Lifelines Cohort Study (2016). Corrigendum: Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses. Nature Genetics, 48(12), 1591. https://doi.org/10.1038/ng1216-1587b
Okbay, A., Baselmans, B. M. L., De Neve, J-E., Turley, P., Nivard, M. G., Fontana, M. A., Meddens, S. F. W., Linner, R. K., Rietveld, C. A., Derringer, J., Gratten, J., Lee, J. J., Liu, J. Z., de Vlaming, R., Ahluwalia, T. S., Buchwald, J., Cavadino, A., Frazier-Wood, A. C., Furlotte, N. A., ... Lifelines Cohort Study (2016). Corrigendum: Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses (vol 48, pg 624, 2016). Nature Genetics, 48(8), 1587-1587. https://doi.org/10.1038/ng1216-1587b
Li, Y., Oosting, M., Deelen, P., Ricano-Ponce, I., Smeekens, S., Jaeger, M., Matzaraki, V., Swertz, M. A., Xavier, R. J., Franke, L., Wijmenga, C., Joosten, L. A. B., Kumar, V., & Netea, M. G. (2016). Corrigendum: Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi (vol 22, pg 1192, 2016). Nature Medicine, 22(10), 1192. https://doi.org/10.1038/nm1016-1192b
Int Headache Genetics Consortium (2016). Corrigendum: Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine (vol 48, pg 856, 2016). Nature Genetics, 48(10), 1296. https://doi.org/10.1038/ng1016-1296c
Aguirre-Gamboa, R., Joosten, I., Urbano, P. C. M., van der Molen, R. G., van Rijssen, E., van Cranenbroek, B., Oosting, M., Smeekens, S., Jaeger, M., Zorro, M., Withoff, S., van Herwaarden, A. E., Sweep, F. C. G. J., Netea, R. T., Swertz, M. A., Franke, L., Xavier, R. J., Joosten, L. A. B., Netea, M. G., ... Koenen, H. J. P. M. (2016). Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits. Cell reports, 17(9), 2474-2487. https://doi.org/10.1016/j.celrep.2016.10.053
Iotchkova, V., Huang, J., Morris, J. A., Jain, D., Barbieri, C., Walter, K., Min, J. L., Chen, L., Astle, W., Cocca, M., Deelen, P., Elding, H., Farmaki, A-E., Franklin, C. S., Franberg, M., Gaunt, T. R., Hofman, A., Jiang, T., Kleber, M. E., ... UK10K consortium (2016). Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps. Nature Genetics, 48(11), 1303-1312. https://doi.org/10.1038/ng.3668
Amini, M., Bashirova, D., Prins, B. P., Corpeleijn, E., Bruinenberg, M., Franke, L., van der Harst, P., Navis, G., Wolffenbuttel, B. H. R., Stolk, R. P., Wijmenga, C., Postma, D. S., Koppelman, G. H., Boezen, H. M., Vonk, J., Snieder, H., Alizadeh, B. Z., & Lifelines Cohort Study (2016). Eosinophil Count Is a Common Factor for Complex Metabolic and Pulmonary Traits and Diseases: The LifeLines Cohort Study. PLoS ONE, 11(12), [e0168480]. https://doi.org/10.1371/journal.pone.0168480
Kassam, I., Qi, T., Lloyd-Jones, L., Holloway, A., Bonder, M. J., Henders, A. K., Martin, N. G., Powell, J. E., Franke, L., Montgomery, G. W., Visscher, P. M., & McRae, A. F. (2016). Evidence for mitochondrial genetic control of autosomal gene expression. Human Molecular Genetics, 25(24), 5332-5338. https://doi.org/10.1093/hmg/ddw347
Gutierrez-Achury, J., Zorro , M. M., Ricano-Ponce, I., Zhernakova, D. V., Diogo, D., Raychaudhuri, S., Franke, L., Trynka, G., Wijmenga, C., Zhernakova, A., Coeliac Dis Immunochip Consortium, & RACI Consortium (2016). Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis. Human Molecular Genetics, 25(1), 180-190. https://doi.org/10.1093/hmg/ddv455
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
Pattaro, C., Teumer, A., Gorski, M., Chu, A. Y., Li, M., Mijatovic, V., Garnaas, M., Tin, A., Sorice, R., Li, Y., Taliun, D., Olden, M., Foster, M., Yang, Q., Chen, M-H., Pers, T. H., Johnson, A. D., Ko, Y-A., Fuchsberger, C., ... ICBP Consortium (2016). Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nature Communications, 7(10023). https://doi.org/10.1038/ncomms10023
Okbay, A., Baselmans, B. M. L., De Neve, J-E., Turley, P., Nivard, M. G., Fontana, M. A., Meddens, S. F. W., Linnér, R. K., Rietveld, C. A., Derringer, J., Gratten, J., Lee, J. J., Liu, J. Z., de Vlaming, R., Ahluwalia, T. S., Buchwald, J., Cavadino, A., Frazier-Wood, A. C., Furlotte, N. A., ... Lifelines Cohort Study (2016). Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses. Nature Genetics, 48(6), 624-636. https://doi.org/10.1038/ng.3552
Amin, N., Allebrandt, K. V., van der Spek, A., Mueller-Myhsok, B., Hek, K., Teder-Laving, M., Hayward, C., Esko, T., van Mill, J. G., Mbarek, H., Watson, N. F., Melville, S. A., Del Greco, F. M., Byrne, E. M., Oole, E., Kolcic, I., Chen, T., Evans, D. S., Coresh, J., ... van Duijn, C. M. (2016). Genetic variants in RBFOX3 are associated with sleep latency. European Journal of Human Genetics, 24(10), 1488-1495. https://doi.org/10.1038/ejhg.2016.31
Barban, N., Jansen, R., de Vlaming, R., Vaez, A., Mandemakers, J. J., Tropf, F. C., Shen, X., Wilson, J. F., Chasman, D. I., Nolte, I. M., Tragante, V., van der Laan, S. W., Perry, J. R. B., Kong, A., Ahluwalia, T. S., Albrecht, E., Yerges-Armstrong, L., Atzmon, G., Auro, K., ... BIOS Consortium (2016). Genome-wide analysis identifies 12 loci influencing human reproductive behavior. Nature Genetics, 48(12), 1462-1472. https://doi.org/10.1038/ng.3698
van Rheenen, W., Shatunov, A., Dekker, A. M., McLaughlin, R. L., Diekstra, F. P., Pulit, S. L., van der Spek, R. A. A., Vosa, U., de Jong, S., Robinson, M. R., Yang, J., Fogh, I., van Doormaal, P. T. C., Tazelaar, G. H. P., Koppers, M., Blokhuis, A. M., Sproviero, W., Jones, A. R., Kenna, K. P., ... NNIPPS Study Grp (2016). Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis. Nature Genetics, 48(9), 1043-1050. https://doi.org/10.1038/ng.3622
Felix, J. F., Bradfield, J. P., Monnereau, C., van der Valk, R. J. P., Stergiakouli, E., Chesi, A., Gaillard, R., Feenstra, B., Thiering, E., Kreiner-Moller, E., Mahajan, A., Pitkanen, N., Joro, R., Cavadino, A., Huikari, V., Franks, S., Groen-Blokhuis, M. M., Cousminer, D. L., Marsh, J. A., ... Early Growth Genetics EGG (2016). Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index. Human Molecular Genetics, 25(2), 389-403. https://doi.org/10.1093/hmg/ddv472
Okbay, A., Beauchamp, J. P., Fontana, M. A., Lee, J. J., Pers, T. H., Rietveld, C. A., Turley, P., Chen, G-B., Emilsson, V., Meddens, S. F. W., Oskarsson, S., Pickrell, J. K., Thom, K., Timshel, P., de Vlaming, R., Abdellaoui, A., Ahluwalia, T. S., Bacelis, J., Baumbach, C., ... Lifelines Cohort Study (2016). Genome-wide association study identifies 74 loci associated with educational attainment. Nature, 533(7604), 539-554. https://doi.org/10.1038/nature17671
Ibrahim-Verbaas, C. A., Bressler, J., Debette, S., Schuur, M., Smith, A. V., Bis, J. C., Davies, G., Trompet, S., Smith, J. A., Wolf, C., Chibnik, L. B., Liu, Y., Vitart, V., Kirin, M., Petrovic, K., Polasek, O., Zgaga, L., Fawns-Ritchie, C., Hoffmann, P., ... Generation Scotland (2016). GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Molecular Psychiatry, 21(2), 189-197. https://doi.org/10.1038/mp.2015.37
Li, Y., Oosting, M., Deelen, P., Ricano-Ponce, I., Smeekens, S., Jaeger, M., Matzaraki, V., Swertz, M. A., Xavier, R. J., Franke, L., Wijmenga, C., Joosten, L. A. B., Kumar, V., & Netea, M. G. (2016). Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi. Nature Medicine, 22(8), 952-962. https://doi.org/10.1038/nm.4139
Kogelman, L. J. A., Fu, J., Franke, L., Greve, J. W., Hofker, M., Rensen, S. S., & Kadarmideen, H. N. (2016). Inter-Tissue Gene Co-Expression Networks between Metabolically Healthy and Unhealthy Obese Individuals. PLoS ONE, 11(12), [e0167519]. https://doi.org/10.1371/journal.pone.0167519
Gormley, P., Anttila, V., Winsvold, B. S., Palta, P., Esko, T., Pers, T. H., Farh, K-H., Cuenca-Leon, E., Muona, M., Furlotte, N. A., Kurth, T., Ingason, A., McMahon, G., Ligthart, L., Terwindt, G. M., Kallela, M., Freilinger, T. M., Ran, C., Gordon, S. G., ... Int Headache Genetics Consortium (2016). Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. Nature Genetics, 48(8), 856-869. https://doi.org/10.1038/ng.3598
Lu, Y., Day, F. R., Gustafsson, S., Buchkovich, M. L., Na, J., Bataille, V., Cousminer, D. L., Dastani, Z., Drong, A. W., Esko, T., Evans, D. M., Falchi, M., Feitosa, M. F., Ferreira, T., Hedman, Å. K., Haring, R., Hysi, P. G., Iles, M. M., Justice, A. E., ... Loos, R. J. F. (2016). New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nature Communications, 7, [10495]. https://doi.org/10.1038/ncomms10495
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
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
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.
van der Zwaag, P. A., Herkert, J. C., Sarvaas, G. J. D. M., Bartelds, B., van Diemen, C. C., de Koning, T. J., Jongbloed, J. D., Sikkema-Raddatz, B., Franke, L., Sinke, R. J., van Langen, I. M., Wijmenga, C., & Kerstjens-Frederikse, W. S. (2016). Rapid Whole Genome Sequencing for Critically Ill Children With Cardiomyopathy. Circulation, 134.
Ricano-Ponce, I., Zhernakova, D., Deelen, P., Luo, O., Li, X., Isaacs, A., Karjalainen, J., Di Tommaso, J., Borek, Z. A., Zorro, M. M., Gutierrez-Achury, J., Uitterlinden, A. G., Hofman, A., van Meurs, J., Netea, M. G., Jonkers, I. H., Withoff, S., van Duijn, C. M., Li, Y., ... BIOS Consortium Lifelines Cohort S (2016). Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs. Journal of Autoimmunity, 68, 62-74. https://doi.org/10.1016/j.jaut.2016.01.002
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
Ehret, G. B., Ferreira, T., Chasman, D. I., Jackson, A. U., Schmidt, E. M., Johnson, T., Thorleifsson, G., Luan, J., Donnelly, L. A., Kanoni, S., Petersen, A. -K., Pihurl, V., Strawbridge, R. J., Shungin, D., Hughes, M. F., Meirelles, O., Kaakinen, M., Bouatia-Naji, N., Kristiansson, K., ... Wellcome Trust Case-Control Consor (2016). The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals. Nature Genetics, 48(10), 1171-1184. https://doi.org/10.1038/ng.3667
Ben-David, U., Ha, G., Khadka, P., Jin, X., Wong, B., Franke, L., & Golub, T. R. (2016). The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis. Nature Communications, 7, [12160]. https://doi.org/10.1038/ncomms12160
Ben-David, U., Ha, G., Khadka, P., Jin, X., Franke, L., & Golub, T. R. (2016). The landscape of chromosomal aberrations in mouse models of breast cancer reveals driver-specific routes to tumor development. Cancer Research, 76, [2683]. https://doi.org/10.1158/1538-7445.AM2016-2683
Verweij, N., Leach, I. M., Isaacs, A., Arking, D. E., Bis, J. C., Pers, T. H., Van den Berg, M. E., Lyytikainen, L-P., Barnett, P., Wang, X., Soliman, E. Z., Van Duijn, C. M., Kahonen, M., Van Veldhuisen, D. J., Kors, J. A., Raitakari, O. T., Silva, C. T., Lehtimaki, T., Hillege, H. L., ... Lifelines Cohort Study (2016). Twenty-eight genetic loci associated with ST-T-wave amplitudes of the electrocardiogram. Human Molecular Genetics, 25(10), 2093-2103. https://doi.org/10.1093/hmg/ddw058
Netea, M. G., Joosten, L. A. B., Li, Y., Kumar, V., Oosting, M., Smeekens, S., Jaeger, M., ter Horst, R., Schirmer, M., Vlamakis, H., Notebaart, R., Pavelka, N., Aguirre-Gamboa, R. R., Swertz, M. A., Tunjungputri, R. N., van de Heijden, W., Franzosa, E. A., Ng, A., Graham, D., ... Wijmenga, C. (2016). Understanding human immune function using the resources from the Human Functional Genomics Project. Nature Medicine, 22(8), 831-833. https://doi.org/10.1038/nm.4140
van der Harst, P., van Setten, J., Verweij, N., Vogler, G., Franke, L., Maurano, M. T., Wang, X., Leach, I. M., Eijgelsheim, M., Sotoodehnia, N., Hayward, C., Sorice, R., Meirelles, O., Lyytikainen, L-P., Polasek, O., Tanaka, T., Arking, D. E., Ulivi, S., Trompet, S., ... de Bakker, P. I. W. (2016). 52 Genetic Loci Influencing Myocardial Mass. Journal of the American College of Cardiology, 68(13), 1435-1448. https://doi.org/10.1016/j.jacc.2016.07.729

2015

Franke, L., El Bannoudi, H., Jansen, D. T. S. L., Kok, K., Trynka, G., Diogo, D., Swertz, M., Fransen, K., Knevel, R., Gutierrez-Achury, J., Ärlestig, L., Greenberg, J. D., Kremer, J., Pappas, D. A., Kanterakis, A., Weersma, R. K., van der Helm-van Mil, A. H. M., Guryev, V., Rantapää-Dahlqvist, S., ... Zhernakova, A. (2016). Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes. European Journal of Human Genetics, 24(2), 263-270. https://doi.org/10.1038/ejhg.2015.95
Jin, P., Andiappan, A. K., Quek, J. M., Lee, B., Au, B., Sio, Y. Y., Irwanto, A., Schurmann, C., Grabe, H. J., Suri, B. K., Matta, S. A., Westra, H-J., Franke, L., Esko, T., Sun, L., Zhang, X., Liu, H., Zhang, F., Larbi, A., ... Wang, D. Y. (2015). A functional brain-derived neurotrophic factor (BDNF) gene variant increases the risk of moderate-to-severe allergic rhinitis. Journal of Allergy and Clinical Immunology, 135(6), 1486-1493.e8. https://doi.org/10.1016/j.jaci.2014.12.1870
Brandsma, C-A., van den Berge, M., Postma, D. S., Jonker, M. R., Brouwer, S., Pare, P. D., Sin, D. D., Bosse, Y., Laviolette, M., Karjalainen, J., Fehrmann, R. S. N., Nickle, D. C., Hao, K., Spanjer, A. I. R., Timens, W., & Franke, L. (2015). A large lung gene expression study identifying fibulin-5 as a novel player in tissue repair in COPD. Thorax, 70(1), 21-32. https://doi.org/10.1136/thoraxjnl-2014-205091
van der Valk, R. J. P., Kreiner-Moller, E., Kooijman, M. N., Guxens, M., Stergiakouli, E., Saaf, A., Bradfield, J. P., Geller, F., Hayes, M. G., Cousminer, D. L., Koerner, A., Thiering, E., Curtin, J. A., Myhre, R., Huikari, V., Joro, R., Kerkhof, M., Warrington, N. M., Pitkanen, N., ... Early Growth Genetics EGG (2015). A novel common variant in DCST2 is associated with length in early life and height in adulthood. Human Molecular Genetics, 24(4), 1155-1168. https://doi.org/10.1093/hmg/ddu510
Kogelman, L. J. A., Zhernakova, D. V., Westra, H-J., Cirera, S., Fredholm, M., Franke, L., & Kadarmideen, H. N. (2015). An integrative systems genetics approach reveals potential causal genes and pathways related to obesity. Genome medicine, 7, [105]. https://doi.org/10.1186/s13073-015-0229-0
Liu, J. Z., van Sommeren, S., Huang, H., Ng, S. C., Alberts, R., Takahashi, A., Ripke, S., Lee, J. C., Jostins, L., Shah, T., Abedian, S., Cheon, J. H., Cho, J., Daryani, N. E., Franke, L., Fuyuno, Y., Hart, A., Juyal, R. C., Juyal, G., ... Int IBD Genetics Consortium (2015). Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nature Genetics, 47(9), 979-986. https://doi.org/10.1038/ng.3359
Krajewska, M., Fehrmann, R. S. N., Schoonen, P. M., Labib, S., de Vries, E. G. E., Franke, L., & van Vugt, M. A. T. M. (2015). ATR inhibition preferentially targets homologous recombination-deficient tumor cells. ONCOGENE, 34(26), 3474-3481. https://doi.org/10.1038/onc.2014.276
Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H-J., Wood, A. R., Yang, J., Lui, J. C., Vedantam, S., Gustafsson, S., Esko, T., Frayling, T., Speliotes, E. K., Boehnke, M., Raychaudhuri, S., Fehrmann, R. S. N., Hirschhorn, J. N., Franke, L., & Genetic Invest ANthropometric Trai (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature Communications, 6, [5890]. https://doi.org/10.1038/ncomms6890
Deelen, P., Zhernakova, D. V., de Haan, M., van der Sijde, M., Bonder, M. J., Karjalainen, J., van der Velde, K. J., Abbott, K. M., Fu, J., Wijmenga, C., Sinke, R. J., Swertz, M. A., & Franke, L. (2015). Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels. Genome medicine, 7(1), [30]. https://doi.org/10.1186/s13073-015-0152-4
Westra, H-J., Arends, D., Esko, T., Peters, M. J., Schurmann, C., Schramm, K., Kettunen, J., Yaghootkar, H., Fairfax, B. P., Andiappan, A. K., Li, Y., Fu, J., Karjalainen, J., Platteel, M., Visschedijk, M., Weersma, R. K., Kasela, S., Milani, L., Tserel, L., ... Franke, L. (2015). Cell Specific eQTL Analysis without Sorting Cells. PLoS genetics, 11(5), [1005223]. https://doi.org/10.1371/journal.pgen.1005223
Tigchelaar-Feenstra, E. F., Zhernakova, A., Dekens, J. A. M., Hermes, G., Baranska, A., Mujagic, Z., Swertz, M. A., Muñoz Contreras, A., Deelen, P., Cenit, M. C., Franke, L., Scholtens, S., Stolk, R. P., Wijmenga, C., & Feskens, E. J. M. (2015). Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: Study design and baseline characteristics. BMJ Open, 5(8), [e006772]. https://doi.org/10.1136/bmjopen-2014-006772
Wolfs, M. G. M., Gruben, N., Rensen, S. S., Verdam, F. J., Greve, J. W., Driessen, A., Wijmenga, C., Buurman, W. A., Franke, L., Scheja, L., Koonen, D. P. Y., Shiri-Sverdlov, R., van Haeften, T. W., Hofker, M. H., & Fu, J. (2015). Determining the association between adipokine expression in multiple tissues and phenotypic features of non-alcoholic fatty liver disease in obesity. Nutrition & Diabetes, 5, [146]. https://doi.org/10.1038/nutd.2014.43
Senapati, S., Gutierrez-Achury, J., Sood, A., Midha, V., Szperl, A., Romanos, J., Zhernakova, A., Franke, L., Alonso, S., Thelma, B. K., Wijmenga, C., & Trynka, G. (2015). Evaluation of European coeliac disease risk variants in a north Indian population. European Journal of Human Genetics, 23(4), 530-535. https://doi.org/10.1038/ejhg.2014.137
Fehrmann, R. S. N., Karjalainen, J. M., Krajewska, M., Westra, H-J., Maloney, D., Simeonov, A., Pers, T. H., Hirschhorn, J. N., Jansen, R. C., Schultes, E. A., van Haagenl, H. H. H. B. M., de Vries, E. G. E., te Meerman, G., Wijmenga, C., van Vugt, M. A. T. M., & Franke, L. (2015). Gene expression analysis identifies global gene dosage sensitivity in cancer. Nature Genetics, 47(2), 115-125. https://doi.org/10.1038/ng.3173
Locke, A. E., Kahali, B., Berndt, S. I., Justice, A. E., Pers, T. H., Day, F. R., Powell, C., Vedantam, S., Buchkovich, M. L., Yang, J., Croteau-Chonka, D. C., Esko, T., Fall, T., Ferreira, T., Gustafsson, S., Kutalik, Z., Luan, J., Mägi, R., Randall, J. C., ... Lifelines Cohort Study (2015). Genetic studies of body mass index yield new insights for obesity biology. Nature, 518(7538), 197-206. https://doi.org/10.1038/nature14177
Andiappan, A. K., Narayanan, S., Myers, R. A., Lee, B., Nieuwenhuis, M. A., Nardin, A., Park, C-S., Shin, H. D., Kim, J-H., Westra, H-J., Franke, L., Esko, T., Metspalu, A., Teo, Y-Y., Saw, S. M., Khor, C. C., Liu, J., Koppelman, G. H., Postma, D. S., ... Chew, F. T. (2015). Genetic variants of inducible costimulator are associated with allergic asthma susceptibility. Journal of Allergy and Clinical Immunology, 135(2), 556-+. https://doi.org/10.1016/j.jaci.2014.06.028
Chan, Y., Salem, R. M., Hsu, Y-H. H., McMahon, G., Pers, T. H., Vedantam, S., Esko, T., Guo, M. H., Lim, E. T., Franke, L., Smith, G. D., Strachan, D. P., Hirschhorn, J. N., & GIANT Consortium (2015). Genome-wide Analysis of Body Proportion Classifies Height-Associated Variants by Mechanism of Action and Implicates Genes Important for Skeletal Development. American Journal of Human Genetics, 96(5), 695-708. https://doi.org/10.1016/j.ajhg.2015.02.018
Draisma, H. H. M., Pool, R., Kobl, M., Jansen, R., Petersen, A-K., Vaarhorst, A. A. M., Yet, I., Haller, T., Demirkan, A., Esko, T., Zhu, G., Boehringer, S., Beekman, M., van Klinken, J. B., Roemisch-Margl, W., Prehn, C., Adamski, J., de Craen, A. J. M., van Leeuwen, E. M., ... Boomsma, D. I. (2015). Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. Nature Communications, 6, [7208]. https://doi.org/10.1038/ncomms8208
Cornelis, M. C., Byrne, E. M., Esko, T., Nalls, M. A., Ganna, A., Paynter, N., Monda, K. L., Amin, N., Fischer, K., Renstrom, F., Ngwa, J. S., Huikari, V., Cavadino, A., Nolte, I. M., Teumer, A., Yu, K., Marques-Vidal, P., Rawal, R., Manichaikul, A., ... UK Brain Expression Consortium (2015). Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption. Molecular Psychiatry, 20(5), 647-656. https://doi.org/10.1038/mp.2014.107
van Gerven, N. M. F., de Boer, Y. S., Zwiers, A., Verwer, B. J., Drenth, J. P. H., van Hoek, B., van Erpecum, K. J., Beuers, U., van Buuren, H. R., den Ouden, J. W., Verdonk, R. C., Koek, G. H., Brouwer, J. T., Guichelaar, M. J., Vrolijk, J. M., Coenraad, M. J., Kraal, G., Mulder, C. J. J., van Nieuwkerk, C. M. J., ... Dutch Autoimmune Hepatitis Study G (2015). HLA-DRB1*03: 01 and HLA-DRB1*04:01 modify the presentation and outcome in autoimmune hepatitis type-1. GENES AND IMMUNITY, 16(4), 247-252. https://doi.org/10.1038/gene.2014.82
Shah, S., Bonder, M. J., Marioni, R. E., Zhu, Z., McRae, A. F., Zhernakova, A., Harris, S. E., Liewald, D., Henders, A. K., Mendelson, M. M., Liu, C., Joehanes, R., Liang, L., Levy, D., Martin, N. G., Starr, J. M., Wijmenga, C., Wray, N. R., Yang, J., ... BIOS Consortium (2015). Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations. American Journal of Human Genetics, 97(1), 75-85. https://doi.org/10.1016/j.ajhg.2015.05.014
Day, F. R., Ruth, K. S., Thompson, D. J., Lunetta, K. L., Pervjakova, N., Chasman, D. I., Stolk, L., Finucane, H. K., Sulem, P., Bulik-Sullivan, B., Esko, T., Johnson, A. D., Elks, C. E., Franceschini, N., He, C., Altmaier, E., Brody, J. A., Franke, L. L., Huffman, J. E., ... Lifelines Cohort Study (2015). Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. Nature Genetics, 47(11), 1294-303. https://doi.org/10.1038/ng.3412
Day, F. R., Ruth, K. S., Thompson, D. J., Lunetta, K. L., Pervjakova, N., Chasman, D. I., Stolk, L., Finucane, H. K., Sulem, P., Bulik-Sullivan, B., Esko, T., Johnson, A. D., Elks, C. E., Franceschini, N., He, C., Altmaier, E., Brody, J. A., Franke, L. L., Huffman, J. E., ... Lifelines Cohort Study (2015). Large-Scale Genomic Analyses Link Reproductive Aging to Hypothalamic Signaling, Breast Cancer Susceptibility, and BRCA1-Mediated DNA Repair EDITORIAL COMMENT. Obstetrical & Gynecological Survey, 70(12), 758-762. https://doi.org/10.1097/01.ogx.0000473766.71624.99
Shungin, D., Winkler, T. W., Croteau-Chonka, D. C., Ferreira, T., Lockes, A. E., Maegi, R., Strawbridge, R. J., Pers, T. H., Fischer, K., Justice, A. E., Workalemahu, T., Wu, J. M. W., Buchkovich, M. L., Heard-Costa, N. L., Roman, T. S., Drong, A. W., Song, C., Gustafsson, S., Day, F. R., ... ReproGen Consortium (2015). New genetic loci link adipose and insulin biology to body fat distribution. Nature, 518(7538), 187-196. https://doi.org/10.1038/nature14132
Kumar, V., Gutierrez-Achury, J., Kanduri, K., Almeida, R., Hrdlickova, B., Zhernakova, D. V., Westra, H-J., Karjalainen, J., Ricano-Ponce, I., Li, Y., Stachurska, A., Tigchelaar, E. F., Abdulahad, W. H., Lahdesmaki, H., Hofker, M. H., Zhernakova, A., Franke, L., Lahesmaa, R., Wijmenga, C., & Withoff, S. (2015). Systematic annotation of celiac disease loci refines pathological pathways and suggests a genetic explanation for increased interferon-gamma levels. Human Molecular Genetics, 24(2), 397-409. https://doi.org/10.1093/hmg/ddu453
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
Surakka, I., Horikoshi, M., Magi, R., Sarin, A-P., Mahajan, A., Lagou, V., Marullo, L., Ferreira, T., Miraglio, B., Timonen, S., Kettunen, J., Pirinen, M., Karjalainen, J., Thorleifsson, G., Hagg, S., Hottenga, J-J., Isaacs, A., Ladenvall, C., Beekman, M., ... ENGAGE Consortium (2015). The impact of low-frequency and rare variants on lipid levels. Nature Genetics, 47(6), 589-597. https://doi.org/10.1038/ng.3300
Winkler, T. W., Justice, A. E., Graff, M., Barata, L., Feitosa, M. F., Chu, S., Czajkowski, J., Esko, T., Fall, T., Kilpelainen, T. O., Lu, Y., Magi, R., Mihailov, E., Pers, T. H., Rueeger, S., Teumer, A., Ehret, G. B., Ferreira, T., Heard-Costa, N. L., ... MAGIC Consortium (2015). The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. PLoS genetics, 11(10), [e1005378]. https://doi.org/10.1371/journal.pgen.1005378
Peters, M. J., Joehanes, R., Pilling, L. C., Schurmann, C., Conneely, K. N., Powell, J., Reinmaa, E., Sutphin, G. L., Zhernakova, A., Schramm, K., Wilson, Y. A., Kobes, S., Tukiainen, T., Ramos, Y. F., Goering, H. H. H., Fornage, M., Liu, Y., Gharib, S. A., Stranger, B. E., ... NABEC UKBEC Consortium (2015). The transcriptional landscape of age in human peripheral blood. Nature Communications, 6, [8570]. https://doi.org/10.1038/ncomms9570
Kato, N., Loh, M., Takeuchi, F., Verweij, N., Wang, X., Zhang, W., Kelly, T. N., Saleheen, D., Lehne, B., Leach, I. M., Drong, A. W., Abbott, J., Wahl, S., Tan, S-T., Scott, W. R., Campanella, G., Chadeau-Hyam, M., Afzal, U., Ahluwalia, T. S., ... InterAct Consortium (2015). Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nature Genetics, 47(11), 1282-1293.e2. https://doi.org/10.1038/ng.3405

2014

Cozen, W., Timofeeva, M. N., Li, D., Diepstra, A., Hazelett, D., Delahaye-Sourdeix, M., Edlund, C. K., Franke, L., Rostgaard, K., Van Den Berg, D. J., Cortessis, V. K., Smedby, K. E., Glaser, S. L., Westra, H. -J., Robison, L. L., Mack, T. M., Ghesquieres, H., Hwang, A. E., Nieters, A., ... Mckay, J. D. (2014). A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. Nature Communications, 5, [3856]. https://doi.org/10.1038/ncomms4856
Hemani, G., Shakhbazov, K., Westra, H-J., Esko, T., Henders, A. K., McRae, A. F., Yang, J., Gibson, G., Martin, N. G., Metspalu, A., Franke, L., Montgomery, G. W., Visscher, P. M., & Powell, J. E. (2014). Another explanation for apparent epistasis Reply. Nature, 514(7520), E5-E6. https://doi.org/10.1038/nature13692
Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014). Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics. PLoS genetics, 10(5), [e1004383]. https://doi.org/10.1371/journal.pgen.1004383
Ripke, S., Neale, B. M., Corvin, A., Walters, J. T. R., Farh, K-H., Holmans, P. A., Lee, P., Bulik-Sullivan, B., Collier, D. A., Huang, H., Pers, T. H., Agartz, I., Agerbo, E., Albus, M., Alexander, M., Amin, F., Bacanu, S. A., Begemann, M., Belliveau, R. A., ... Wellcome Trust Case-Control Consor (2014). Biological insights from 108 schizophrenia-associated genetic loci. Nature, 511(7510), 421-427. https://doi.org/10.1038/nature13595
Geremek, M., Zietkiewicz, E., Bruinenberg, M., Franke, L., Pogorzelski, A., Wijmenga, C., & Witt, M. (2014). Ciliary Genes Are Down-Regulated in Bronchial Tissue of Primary Ciliary Dyskinesia Patients. PLoS ONE, 9(2), [e88216]. https://doi.org/10.1371/journal.pone.0088216
Smolonska, J., Koppelman, G. H., Wijmenga, C., Vonk, J. M., Zanen, P., Bruinenberg, M., Curjuric, I., Imboden, M., Thun, G-A., Franke, L., Probst-Hensch, N. M., Nuernberg, P., Riemersma, R. A., van Schayck, C. P., Loth, D. W., Brusselle, G. G., Stricker, B. H., Hofman, A., Uitterlinden, A. G., ... Postma, D. S. (2014). Common genes underlying asthma and COPD? Genome-wide analysis on the Dutch hypothesis. European Respiratory Journal, 44(4), 860-872. https://doi.org/10.1183/09031936.00001914
Rietveld, C. A., Esko, T., Davies, G., Pers, T. H., Turley, P., Benyamin, B., Chabris, C. F., Emilsson, V., Johnson, A. D., Lee, J. J., de Leeuw, C., Marioni, R. E., Medland, S. E., Miller, M. B., Rostapshova, O., van der Lee, S. J., Vinkhuyzen, A. A. E., Amin, N., Conley, D., ... Koellinger, P. D. (2014). Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. Proceedings of the National Academy of Sciences of the United States of America, 111(38), 13790-13794. https://doi.org/10.1073/pnas.1404623111
Gockel, I., Becker, J., Wouters, M. M., Niebisch, S., Gockel, H. R., Hess, T., Ramonet, D., Zimmermann, J., Vigo, A. G., Trynka, G., de Leon, A. R., de la Serna, J. P., Urcelay, E., Magadi Gopalaiah, V. K., Franke, L., Westra, H-J., Drescher, D., Kneist, W., Marquardt, J. U., ... Schumacher, J. (2014). Common variants in the HLA-DQ region confer susceptibility to idiopathic achalasia. Nature Genetics, 46(8), 901-904. https://doi.org/10.1038/ng.3029
Li, H., Chan, L., Bartuzi, P., Melton, S. D., Weber, A., Ben-Shlomo, S., Varol, C., Raetz, M., Mao, X., Starokadomskyy, P., van Sommeren, S., Mokadem, M., Schneider, H., Weisberg, R., Westra, H-J., Esko, T., Metspalu, A., Magadi Gopalaiah, V. K., Faubion, W. A., ... Burstein, E. (2014). Copper Metabolism Domain-Containing 1 Represses Genes That Promote Inflammation and Protects Mice From Colitis and Colitis-Associated Cancer. Gastroenterology, 147(1), 184-195.e3. https://doi.org/10.1053/j.gastro.2014.04.007
Fransen, K., van Sommeren, S., Westra, H. J., Veenstra, M., Lamberts, L. E., Modderman, R., Dijkstra, G., Fu, J., Wijmenga, C., Franke, L., Weersma, R. K., & van Diemen, C. C. (2014). Correlation of Genetic Risk and Messenger RNA Expression in a Th17/IL23 Pathway Analysis in Inflammatory Bowel Disease. Inflammatory Bowel Diseases, 20(5), 777-782. https://doi.org/10.1097/MIB.0000000000000013
Wood, A. R., Esko, T., Yang, J., Vedantam, S., Pers, T. H., Gustafsson, S., Chun, A. Y., Estrada, K., Luan, J., Kutalik, Z., Amin, N., Buchkovich, M. L., Croteau-Chonka, D. C., Day, F. R., Duan, Y., Fall, T., Fehrmann, R., Ferreira, T., Jackson, A. U., ... Lifelines Cohort Study (2014). Defining the role of common variation in the genomic and biological architecture of adult human height. Nature Genetics, 46(11), 1173-1186. https://doi.org/10.1038/ng.3097
Hemani, G., Shakhbazov, K., Westra, H-J., Esko, T., Henders, A. K., McRae, A. F., Yang, J., Gibson, G., Martin, N. G., Metspalu, A., Franke, L., Montgomery, G. W., Visscher, P. M., & Powell, J. E. (2014). Detection and replication of epistasis influencing transcription in humans. Nature, 508(7495), 249-253. https://doi.org/10.1038/nature13005
Hrdlickova, B., Kumar, V., Kanduri, K., Zhernakova, D. V., Tripathi, S., Karjalainen, J., Lund, R. J., Li, Y., Ullah, U., Modderman, R., Abdulahad, W., Lahdesmaki, H., Franke, L., Lahesmaa, R., Wijmenga, C., & Withoff, S. (2014). Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. Genome medicine, 6(10), [88]. https://doi.org/10.1186/s13073-014-0088-0
van Sommeren, S., Janse, M., Karjalainen, J., Fehrmann, R., Franke, L., Fu, J., & Weersma, R. K. (2014). Extraintestinal Manifestations and Complications in Inflammatory Bowel Disease: From Shared Genetics to Shared Biological Pathways. Inflammatory Bowel Diseases, 20(6), 987-994. https://doi.org/10.1097/MIB.0000000000000032
de Almeida, R., Ricaño Ponce, I., Kumar, V., Deelen, P., Szperl, A., Trynka, G., Gutierrez-Achury, J., Kanterakis, A., Westra, H. J., Franke, L., Swertz, M. A., Platteel, M., Ramon Bilbao, J., Barisani, D., Greco, L., Mearin, L., Wolters, V. M., Mulder, C., Mazzilli, M. C., ... Wijmenga, C. (2014). Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant. Human Molecular Genetics, 23(9), 2481-2489. https://doi.org/10.1093/hmg/ddt619
Westra, H-J., & Franke, L. (2014). From genome to function by studying eQTLs. Biochimica et biophysica acta-Molecular basis of disease, 1842(10), 1896-1902. https://doi.org/10.1016/j.bbadis.2014.04.024
Bonder, M. J., Kasela, S., Kals, M., Tamm, R., Lokk, K., Barragan, I., Buurman, W. A., Deelen, P., Greve, J-W., Ivanov, M., Rensen, S. S., van Vliet-Ostaptchouk, J. V., Wolfs, M. G., Fu, J., Hofker, M. H., Wijmenga, C., Zhernakova, A., Ingelman-Sundberg, M., Franke, L., & Milani, L. (2014). Genetic and epigenetic regulation of gene expression in fetal and adult human livers. BMC Genomics, 15(860). https://doi.org/10.1186/1471-2164-15-860
Arking, D. E., Pulit, S. L., Crotti, L., Van der Harst, P., Munroe, P. B., Koopmann, T. T., Sotoodehnia, N., Rossin, E. J., Morley, M., Wang, X., Johnson, A. D., Lundby, A., Gudbjartsson, D. F., Noseworthy, P. A., Eijgelsheim, M., Bradford, Y., Tarasov, K. V., Dorr, M., Miiller-Nurasyid, M., ... HRGEN Consortium (2014). Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nature Genetics, 46(8), 826-836. https://doi.org/10.1038/ng.3014
Okada, Y., Wu, D., Trynka, G., Raj, T., Terao, C., Ikari, K., Kochi, Y., Ohmura, K., Suzuki, A., Yoshida, S., Graham, R. R., Manoharan, A., Ortmann, W., Bhangale, T., Denny, J. C., Carroll, R. J., Eyler, A. E., Greenberg, J. D., Kremer, J. M., ... GARNET Consortium (2014). Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature, 506(7488), 376-381.e15. https://doi.org/10.1038/nature12873
Geller, F., Feenstra, B., Carstensen, L., Pers, T. H., van Rooij, I. A. L. M., Korberg, I. B., Choudhry, S., Karjalainen, J. M., Schnack, T. H., Hollegaard, M. V., Feitz, W. F. J., Roeleveld, N., Hougaard, D. M., Hirschhorn, J. N., Franke, L., Baskin, L. S., Nordenskjold, A., van der Zanden, L. F. M., & Melbye, M. (2014). Genome-wide association analyses identify variants in developmental genes associated with hypospadias. Nature Genetics, 46(9), 957-963.e3. https://doi.org/10.1038/ng.3063
de Boer, Y. S., van Gerven, N. M. F., Zwiers, A., Verwer, B. J., van Hoek, B., van Erpecum, K. J., Beuers, U., van Buuren, H. R., Drenth, J. P. H., den Ouden, J. W., Verdonk, R. C., Koek, G. H., Brouwer, J. T., Guichelaar, M. M. J., Vrolijk, J. M., Kraal, G., Mulder, C. J. J., van Nieuwkerk, C. M. J., Fischer, J., ... Dutch Autoimmune Hepatitis Study Group (2014). Genome-wide association study identifies variants associated with autoimmune hepatitis type 1. Gastroenterology, 147(2), 443-452.e5. https://doi.org/10.1053/j.gastro.2014.04.022
Deelen, P., Bonder, M. J., van der Velde, K. J., Westra, H-J., Winder, E., Hendriksen, D., Franke, L., & Swertz, M. A. (2014). Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Research Notes, 7, [901]. https://doi.org/10.1186/1756-0500-7-901
Kogelman, L. J. A., Cirera, S., Zhernakova, D. V., Fredholm, M., Franke, L., & Kadarmideen, H. N. (2014). Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. BMC Medical Genomics, 7, [57]. https://doi.org/10.1186/1755-8794-7-57
Nibbeling, E., Verschuuren-Bemelmans, C., van de Warrenburg, B., Kremer, B., van Diemen, C., Dooijes, D., Dijkstra, M., Franke, L., Swertz, M., Sinke, R., & Verbeek, D. (2014). Identification of novel spinocerebellar ataxia disease genes using next generation sequencing approaches. Movement Disorders, 29, S58-S58.
Kumar, V., Cheng, S-C., Johnson, M. D., Smeekens, S. P., Wojtowicz, A., Giamarellos-Bourboulis, E., Karjalainen, J., Franke, L., Withoff, S., Plantinga, T. S., de Veerdonk, F. L. V., van der Meer, J. W. M., Joosten, L. A. B., Sokol, H., Bauer, H., Herrmann, B. G., Bochud, P-Y., Marchetti, O., Perfect, J. R., ... Netea, M. G. (2014). Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia. Nature Communications, 5, [4675]. https://doi.org/10.1038/ncomms5675
Deelen, P., Menelaou, A., van Leeuwen, E. M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., Francioli, L. C., Hottenga, J. J., Karssen, L. C., Estrada, K., Kreiner-Moller, E., Rivadeneira, F., van Setten, J., Gutierrez-Achury, J., Westra, H-J., Franke, L., van Enckevort, D., Dijkstra, M., Byelas, H., ... Genome Netherlands Consortium (2014). Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'. European Journal of Human Genetics, 22(11), 1321-1326. https://doi.org/10.1038/ejhg.2014.19
Romanos, J., Rosen, A., Magadi Gopalaiah, V. K., Trynka, G., Franke, L., Szperl, A., Gutierrez Achury, J., van Diemen, C. C., Kanninga, R., Jankipersadsing, S. A., Steck, A., Eisenbarth, G., van Heel, D. A., Cukrowska, B., Bruno, V., Mazzilli, M. C., Nunez, C., Ramon Bilbao, J., Mearin, M. L., ... PreventCD Grp (2014). Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants. Gut, 63(3), 415-422. https://doi.org/10.1136/gutjnl-2012-304110
Pierce, B. L., Tong, L., Chen, L. S., Rahaman, R., Argos, M., Jasmine, F., Roy, S., Paul-Brutus, R., Westra, H-J., Franke, L., Esko, T., Zaman, R., Islam, T., Rahman, M., Baron, J. A., Kibriya, M. G., & Ahsan, H. (2014). Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians. PLoS genetics, 10(12), [e1004818]. https://doi.org/10.1371/journal.pgen.1004818
Hoggart, C. J., Venturini, G., Mangino, M., Gomez, F., Ascari, G., Zhao, J. H., Teumer, A., Winkler, T. W., Tsernikova, N., Luan, J., Mihailov, E., Ehret, G. B., Zhang, W., Lamparter, D., Esko, T., Mace, A., Rueeger, S., Bochud, P-Y., Barcella, M., ... GIANT Consortium (2014). Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index. PLoS genetics, 10(7), [1004508]. https://doi.org/10.1371/journal.pgen.1004508
Scholtens, S., Postma, D. S., Moffatt, M. F., Panasevich, S., Granell, R., Henderson, A. J., Melen, E., Nyberg, F., Pershagen, G., Jarvis, D., Ramasamy, A., Wjst, M., Svanes, C., Bouzigon, E., Demenais, F., Kauffmann, F., Siroux, V., von Mutius, E., Ege, M. J., ... GABRIELA Study Grp (2014). Novel childhood asthma genes interact with in utero and early-life tobacco smoke exposure. Journal of Allergy and Clinical Immunology, 133(3), 885-888. https://doi.org/10.1016/j.jaci.2013.08.049
Benyamin, B., Esko, T., Ried, J. S., Radhakrishnan, A., Vermeulen, S. H., Traglia, M., Goegele, M., Anderson, D., Broer, L., Podmore, C., Luan, J., Kutalik, Z., Sanna, S., van der Meer, P., Tanaka, T., Wang, F., Westra, H-J., Franke, L., Mihailov, E., ... InterAct Consortium (2014). Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis. Nature Communications, 5, [4926]. https://doi.org/10.1038/ncomms5926
Perry, J. R. B., Day, F., Elks, C. E., Sulem, P., Thompson, D. J., Ferreira, T., He, C., Chasman, D. I., Esko, T., Thorleifsson, G., Albrecht, E., Ang, W. Q., Corre, T., Cousminer, D. L., Feenstra, B., Franceschini, N., Ganna, A., Johnson, A. D., Kjellqvist, S., ... Early Growth Genetics EGG Consorti (2014). Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature, 514(7520), 92–97. https://doi.org/10.1038/nature13545
de Zeeuw, E. L., van Beijsterveldt, C. E. M., Glasner, T. J., Bartels, M., Ehli, E. A., Davies, G. E., Hudziak, J. J., Rietveld, C. A., Groen-Blokhuis, M. M., Hottenga, J. J., de Geus, E. J. C., Boomsma, D. I., & Social Science Genetic Assotiation Consortium (2014). Polygenic scores associated with educational attainment in adults predict educational achievement and ADHD symptoms in children. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 165(6), 510-520. https://doi.org/10.1002/ajmg.b.32254

2013

Horvatovich, P., Franke, L., & Bischoff, R. (2014). Proteomic studies related to genetic determinants of variability in protein concentrations. Journal of Proteome Research, 13(1), 5-14. https://doi.org/10.1021/pr400765y
Knevel, R., Krabben, A., Wilson, A. G., Brouwer, E., Leijsma, M. K., Lindqvist, E., de Rooy, D. P. C., Daha, N. A., van der Linden, M. P. M., Tsonaka, S., Zhernakova, A., Westra, H. -J., Franke, L., Houwing-Duistermaat, J. J., Toes, R. E. M., Huizinga, T. W. J., Saxne, T., & van der Helm-van Mil, A. H. M. (2013). A genetic variant in granzyme B is associated with progression of joint destruction in rheumatoid arthritis. ARTHRITIS AND RHEUMATISM, 65(3), 582-589. https://doi.org/10.1002/art.37808
Cozen, W., Li, D., Timofeeva, M., Diepstra, A., Hazelett, D., Delahaye-Sourdeix, M., Edlund, C. K., Rostgaard, K., Van Den Berg, D. J., Franke, L., Smedby, K. E., Glaser, S. L., Westra, H-J., Robison, L. L., Mack, T. M., Ghesquieres, H., Hwang, A. E., Nieters, A., de Sanjose, S., ... McKay, J. D. (2013). A Meta-Analysis Of Hodgkin Lymphoma Reveals 19p13.3 (TCF3) As a Novel Susceptibility Loc. Blood, 122(21).
Gockel, I., Becker, J., Wouters, M. M., Brun, P., Vigo, A. G., Trynka, G., Kumar, V., Franke, L., Westra, H. J., Wijmenga, C., Zaninotto, G., Drescher, D. G., Niebisch, S., Tack, J. F., Mueller, M., Eckardt, A. J., Gockel, H. R., Schulz, H. G., de Bakker, P. I., ... Schumacher, J. (2013). An Insertion of Eight Amino Acids in HLA-DQA1 and Three Amino Acid Substitutions in HLA-DQA1 and HLA-DQB1 Confer Risk to Idiopathic Achalasia. Gastroenterology, 144(5), S142-S142.
Zhernakova, D. V., de Klerk, E., Westra, H-J., Mastrokolias, A., Amini, S., Ariyurek, Y., Jansen, R., Penninx, B. W., Hottenga, J. J., Willemsen, G., de Geus, E. J., Boomsma, D. I., Veldink, J. H., van den Berg, L. H., Wijmenga, C., den Dunnen, J. T., van Ommen, G-J. B., 't Hoen, P. A. C., & Franke, L. (2013). DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts. PLoS genetics, 9(6), [e1003594]. https://doi.org/10.1371/journal.pgen.1003594
Trouw, L. A., Daha, N., Kurreeman, F. A. S., Boehringer, S., Goulielmos, G. N., Westra, H. J., Zhernakova, A., Franke, L., Stahl, E. A., Levarht, E. W. N., Stoeken-Rijsbergen, G., Verduijn, W., Roos, A., Li, Y., Houwing-Duistermaat, J. J., Huizinga, T. W. J., & Toes, R. E. M. (2013). Genetic variants in the region of the C1q genes are associated with rheumatoid arthritis. Clinical and Experimental Immunology, 173(1), 76-83. https://doi.org/10.1111/cei.12097
Berndt, S. I., Gustafsson, S., Mägi, R., Ganna, A., Wheeler, E., Feitosa, M. F., Justice, A. E., Monda, K. L., Croteau-Chonka, D. C., Day, F. R., Esko, T., Fall, T., Ferreira, T., Gentilini, D., Jackson, A. U., Luan, J., Randall, J. C., Vedantam, S., Willer, C. J., ... Ingelsson, E. (2013). Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics, 45(5), 501-512. https://doi.org/10.1038/ng.2606
Verweij, N., Wieringa, W. G., Mateo Leach, I., van Veldhuisen, D. J., van Gilst, W. H., Hillege, H. L., Fehrmann, R. S., de Bakker, P. I., de Boer, R. A., Franke, L., & van der Harst, P. (2013). GWA Meta-Analysis on ST-T Wave Changes Identifies 12 Novel Loci for Human Cardiac Repolarization. Circulation, 128(22).
Rietveld, C. A., Medland, S. E., Derringer, J., Yang, J., Esko, T., Martin, N. W., Westra, H-J., Shakhbazov, K., Abdellaoui, A., Agrawal, A., Albrecht, E., Alizadeh, B. Z., Amin, N., Barnard, J., Baumeister, S. E., Benke, K. S., Bielak, L. F., Boatman, J. A., Boyle, P. A., ... Lifelines Cohort Study (2013). GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science, 340(6139), 1467-1471. https://doi.org/10.1126/science.1235488
Kumar, V., Westra, H-J., Karjalainen, J., Zhernakova, D. V., Esko, T., Hrdlickova, B., Almeida, R., Zhernakova, A., Reinmaa, E., Hofker, M. H., Fehrmann, R. S. N., Fu, J., Withoff, S., Metspalu, A., Franke, L., Wijmenga, C., & Vosa, U. (2013). Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression. PLoS genetics, 9(1), [e1003201]. https://doi.org/10.1371/journal.pgen.1003201
Li, G., Diogo, D., Wu, D., Spoonamore, J., Dancik, V., Franke, L., Kurreeman, F., Rossin, E. J., Duclos, G., Hartland, C., Zhou, X., Li, K., Liu, J., De Jager, P. L., Siminovitch, K. A., Zhernakova, A., Raychaudhuri, S., Bowes, J., Eyre, S., ... RACI (2013). Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway. PLoS genetics, 9(5), [e1003487]. https://doi.org/10.1371/journal.pgen.1003487
den Hoed, M., Eijgelsheim, M., Esko, T., Brundel, B. J. J. M., Peal, D. S., Evans, D. M., Nolte, I. M., Segre, A. V., Holm, H., Handsaker, R. E., Westra, H-J., Johnson, T., Isaacs, A., Yang, J., Lundby, A., Zhao, J. H., Kim, Y. J., Go, M. J., Almgren, P., ... CHARGE-AF Consortium (2013). Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nature Genetics, 45(6), 621-31. https://doi.org/10.1038/ng.2610
Zhernakova, D., Deelen, P., van der Sijde, M., van der Velde, J., de Haan, M., Abbott, K., Wijmenga, C., Sinke, R., Swertz, M., Fu, J., & Franke, L. (2013). Resolving Variants of Unknown Significance Through Large-Scale RNA-seq. Human heredity, 76(2), 106-107.
Cvejic, A., Haer-Wigman, L., Stephens, J. C., Kostadima, M., Smethurst, P. A., Frontini, M., van den Akker, E., Bertone, P., Bielczyk-Maczynska, E., Farrow, S., Fehrmann, R. S. N., Gray, A., de Haas, M., Haver, V. G., Jordan, G., Karjalainen, J., Kerstens, H. H. D., Kiddle, G., Lloyd-Jones, H., ... Albers, C. A. (2013). SMIM1 underlies the Vel blood group and influences red blood cell traits. Nature Genetics, 45(5), 542-545. https://doi.org/10.1038/ng.2603
Westra, H-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., Christiansen, M. W., Fairfax, B. P., Schramm, K., Powell, J. E., Zhernakova, A., Zhernakova, D. V., Veldink, J. H., Van den Berg, L. H., Karjalainen, J., Withoff, S., Uitterlinden, A. G., Hofman, A., Rivadeneira, F., ... Hoen, P. A. C. . (2013). Systematic identification of trans eQTLs as putative drivers of known disease associations. Nature Genetics, 45(10), 1238-1243. https://doi.org/10.1038/ng.2756

2012

de Boer, R. A., Verweij, N., van Veldhuisen, D. J., Westra, H-J., Bakker, S. J. L., Gansevoort, R. T., Kobold, A. C. M., van Gilst, W. H., Franke, L., Mateo Leach, I., & van der Harst, P. (2012). A Genome-Wide Association Study of Circulating Galectin-3. PLoS ONE, 7(10), [e47385]. https://doi.org/10.1371/journal.pone.0047385
Franceschini, N., van Rooij, F. J. A., Prins, B. P., Feitosa, M. F., Karakas, M., Eckfeldt, J. H., Folsom, A. R., Kopp, J., Vaez, A., Andrews, J. S., Baumert, J., Boraska, V., Broer, L., Hayward, C., Ngwa, J. S., Okada, Y., Polasek, O., Westra, H-J., Wang, Y. A., ... Lifelines Cohort Study (2012). Discovery and Fine Mapping of Serum Protein Loci through Transethnic Meta-analysis. American Journal of Human Genetics, 91(4), 744-753. https://doi.org/10.1016/j.ajhg.2012.08.021
Demirkan, A., van Duijn, C. M., Ugocsai, P., Isaacs, A., Pramstaller, P. P., Liebisch, G., Wilson, J. F., Johansson, A., Rudan, I., Aulchenko, Y. S., Kirichenko, A. V., Janssens, A. C. J. W., Jansen, R. C., Gnewuch, C., Domingues, F. S., Pattaro, C., Wild, S. H., Jonasson, I., Polasek, O., ... EUROSPAN Consortium (2012). Genome-Wide Association Study Identifies Novel Loci Associated with Circulating Phospho- and Sphingolipid Concentrations. PLoS genetics, 8(2), [e1002490]. https://doi.org/10.1371/journal.pgen.1002490
Eyre, S., Bowes, J., Diogo, D., Lee, A., Barton, A., Martin, P., Zhernakova, A., Stahl, E., Viatte, S., McAllister, K., Amos, C. I., Padyukov, L., Toes, R. E. M., Huizinga, T. W. J., Wijmenga, C., Trynka, G., Franke, L., Westra, H-J., Alfredsson, L., ... Wellcome Trust Case-Control Consor (2012). High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nature Genetics, 44(12), 1336-1340. https://doi.org/10.1038/ng.2462
Diekstra, F. P., Saris, C. G. J., van Rheenen, W., Franke, L., Jansen, R. C., van Es, M. A., van Vught, P. W. J., Blauw, H. M., Groen, E. J. N., Horvath, S., Estrada, K., Rivadeneira, F., Hofman, A., Uitterlinden, A. G., Robberecht, W., Andersen, P. M., Melki, J., Meininger, V., Hardiman, O., ... Brown Jr., R. H. (2012). Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for Sporadic ALS. PLoS ONE, 7(4), [e35333]. https://doi.org/10.1371/journal.pone.0035333
van der Harst, P., Zhang, W., Mateo Leach, I., Rendon, A., Verweij, N., Sehmi, J., Paul, D. S., Elling, U., Allayee, H., Li, X., Radhakrishnan, A., Tan, S-T., Voss, K., Weichenberger, C. X., Albers, C. A., Al-Hussani, A., Asselbergs, F. W., Ciullo, M., Danjou, F., ... Chambers, J. C. (2012). Seventy-five genetic loci influencing the human red blood cell. Nature, 492(7429), 369-75. https://doi.org/10.1038/nature11677
Fu, J., Wolfs, M. G. M., Deelen, P., Westra, H. J., Fehrmann, R. S. N., te Meerman, G., Buurman, W. A., Rensen, S. S. M., Groen, H., Weersma, R. K., van den Berg, L. H., Veldink, J., Ophoff, R. A., Snieder, H., van Heel, D., Jansen, R. C., Hofker, M. H., Wijmenga, C., & Franke, L. (2012). Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS genetics, 8(1), [e1002431]. https://doi.org/10.1371/journal.pgen.1002431

2011

Sampietro, M. L., Trompet, S., Verschuren, J. J. W., Talens, R. P., Deelen, J., Heijmans, B. T., de Winter, R. J., Tio, R. A., Doevendans, P. A. F. M., Ganesh, S. K., Nabel, E. G., Westra, H-J., Franke, L., van den Akker, E. B., Westendorp, R. G. J., Zwinderman, A. H., Kastrati, A., Koch, W., Slagboom, P. E., ... Jukema, J. W. (2011). A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutaneous coronary intervention. Human Molecular Genetics, 20(23), 4748-4757. https://doi.org/10.1093/hmg/ddr389
Johnson, T., Gaunt, T. R., Newhouse, S. J., Padmanabhan, S., Tomaszewski, M., Kumari, M., Morris, R. W., Tzoulaki, I., O'Brien, E. T., Poulter, N. R., Sever, P., Shields, D. C., Thom, S., Wannamethee, S. G., Whincup, P. H., Brown, M. J., Connell, J. M., Dobson, R. J., Howard, P. J., ... Global BPGen Consortium (2011). Blood Pressure Loci Identified with a Gene-Centric Array. American Journal of Human Genetics, 89(6), 688-700. https://doi.org/10.1016/j.ajhg.2011.10.013
Hrdlickova, B., Westra, H-J., Franke, L., & Wijmenga, C. (2011). Celiac disease: moving from genetic associations to causal variants. Clinical Genetics, 80(3), 203-213. https://doi.org/10.1111/j.1399-0004.2011.01707.x
Knauff, E. A. H., Blauw, H. M., Pearson, P. L., Kok, K., Wijmenga, C., Veldink, J. H., van den Berg, L. H., Bouchard, P., Fauser, B. C. J. M., Franke, L., & Dutch Primary Ovarian Insufficienc (2011). Copy number variants on the X chromosome in women with primary ovarian insufficiency. Fertility and sterility, 95(5), 1584-1588. https://doi.org/10.1016/j.fertnstert.2011.01.018
Trynka, G., Hunt, K. A., Bockett, N. A., Romanos, J., Mistry, V., Szperl, A., Bakker, S. F., Bardella, M. T., Bhaw-Rosun, L., Castillejo, G., de la Concha, E. G., de Almeida, R. C., Dias, K-R. M., van Diemen, C. C., Dubois, P. C. A., Duerr, R. H., Edkins, S., Franke, L., Fransen, K., ... WTCCC (2011). Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nature Genetics, 43(12), 1193-U45. https://doi.org/10.1038/ng.998
van Disseldorp, J., Franke, L., Eijkemans, R., Broekmans, F., Macklon, N., Wijmenga, C., & Fauser, B. (2011). Genome-wide analysis shows no genomic predictors of ovarian response to stimulation by exogenous FSH for IVF. Reproductive Biomedicine Online, 22(4), 382-388. https://doi.org/10.1016/j.rbmo.2010.12.006
Smolonska, J., Koppelman, G. H., Wijmenga, C., Vonk, J., Zanen, P., Bruinenberg, M., Franke, L., Groen, H. M., Boezen, H. M., & Postma, D. S. (2011). Identification Of Novel Genes That Contribute To Both Asthma And COPD, With Replication In A Large Population-Based Cohort. American Journal of Respiratory and Critical Care Medicine, 183.
Anderson, C. A., Boucher, G., Lees, C. W., Franke, A., D'Amato, M., Taylor, K. D., Lee, J. C., Goyette, P., Imielinski, M., Latiano, A., Lagace, C., Scott, R., Amininejad, L., Bumpstead, S., Baidoo, L., Baldassano, R. N., Barclay, M., Bayless, T. M., Brand, S., ... Rioux, J. D. (2011). Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nature Genetics, 43(3), 246-U94. https://doi.org/10.1038/ng.764
Zhernakova, A., Stahl, E. A., Trynka, G., Raychaudhuri, S., Festen, E. A., Franke, L., Westra, H-J., Fehrmann, R. S. N., Kurreeman, F. A. S., Thomson, B., Gupta, N., Romanos, J., McManus, R., Ryan, A. W., Turner, G., Brouwer, E., Posthumus, M. D., Remmers, E. F., Tucci, F., ... Plenge, R. M. (2011). Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci. PLoS genetics, 7(2), [1002004]. https://doi.org/10.1371/journal.pgen.1002004
Westra, H-J., Jansen, R. C., Fehrmann, R. S. N., te Meerman, G. J., van Heel, D., Wijmenga, C., Franke, L., & te Meerman, G. (2011). MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Bioinformatics, 27(15), 2104-2111. https://doi.org/10.1093/bioinformatics/btr323
Janse, M., Lamberts, L. E., Franke, L., Raychaudhuri, S., Ellinghaus, E., Boberg, K. M., Melum, E., Folseraas, T., Schrumpf, E., Bergquist, A., Bjornsson, E., Fu, J., Westra, H. J., Groen, H. J. M., Fehrmann, R. S. N., Smolonska, J., van den Berg, L. H., Ophoff, R. A., Porte, R. J., ... Weersma, R. K. (2011). Three Ulcerative Colitis Susceptibility Loci Are Associated with Primary Sclerosing Cholangitis and Indicate a Role for IL2, REL, and CARD9. Hepatology, 53(6), 1977-1985. https://doi.org/10.1002/hep.24307
Fehrmann, R. S. N., Jansen, R. C., Veldink, J. H., Westra, H. J., Arends, D., Bonder, M. J., Fu, J., Deelen, P., Groen, H., Smolonska, J., Weersma, R. K., Hofstra, R. M. W., Buurman, W. A., Rensen, S., Wolfs, M. G. M., Platteel, M., Zhernakova, A., Elbers, C. C., Festen, E. A., ... Franke, L. (2011). Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS genetics, 7(8), [1002197]. https://doi.org/10.1371/journal.pgen.1002197
Dolmans, G. H., Werker, P. M., Hennies, H. C., Furniss, D., Festen, E. A., Franke, L., Becker, K., van der Vlies, P., Wolffenbuttel, B. H., Tinschert, S., Toliat, M. R., Nothnagel, M., Franke, A., Klopp, N., Wichmann, H-E., Nuernberg, P., Giele, H., Ophoff, R. A., Wijmenga, C., ... BSSH-GODD Consortium, N. V. (2011). Wnt Signaling and Dupuytren's Disease. New England Journal of Medicine, 365(4), 307-317. https://doi.org/10.1056/NEJMoa1101029

2010

Fransen, K., Visschedijk, M. C., van Sommeren, S., Fu, J. Y., Franke, L., Festen, E. A. M., Stokkers, P. C. F., van Bodegraven, A. A., Crusius, J. B. A., Hommes, D. W., Zanen, P., de Jong, D. J., Wijmenga, C., van Diemen, C. C., & Weersma, R. K. (2010). Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Human Molecular Genetics, 19(17), 3482-3488. https://doi.org/10.1093/hmg/ddq264
Wolfs, M. G. M., Rensen, S. S., Dijk, E. J. B-V., Verdam, F. J., Greve, J-W., Sanjabi, B., Bruinenberg, M., Wijmenga, C., van Haeften, T. W., Buurman, W. A., Franke, L., & Hofker, M. H. (2010). Co-expressed immune and metabolic genes in visceral and subcutaneous adipose tissue from severely obese individuals are associated with plasma HDL and glucose levels: a microarray study. BMC Medical Genomics, 3, [34]. https://doi.org/10.1186/1755-8794-3-34
Sotoodehnia, N., Isaacs, A., de Bakker, P. I. W., Doerr, M., Newton-Cheh, C., Nolte, I. M., van der Harst, P., Mueller, M., Eijgelsheim, M., Alonso, A., Hicks, A. A., Padmanabhan, S., Hayward, C., Smith, A. V., Polasek, O., Giovannone, S., Fu, J., Magnani, J. W., Marciante, K. D., ... Arking, D. E. (2010). Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nature Genetics, 42(12), 1068-U62. https://doi.org/10.1038/ng.716
Zhernakova, A., Elbers, C. C., Ferwerda, B., Romanos, J., Trynka, G., Dubois, P. C., de Kovel, C. G. F., Franke, L., Oosting, M., Barisani, D., Bardella, M. T., Joosten, L. A. B., Saavalainen, P., van Heel, D. A., Catassi, C., Netea, M. G., Wijmenga, C., & Finnish Celiac Dis Study Grp (2010). Evolutionary and Functional Analysis of Celiac Risk Loci Reveals SH2B3 as a Protective Factor against Bacterial Infection. American Journal of Human Genetics, 86(6), 970-977. https://doi.org/10.1016/j.ajhg.2010.05.004
Martin, J-E., Alizadeh, B. Z., Gonzalez-Gay, M. A., Balsa, A., Pascual-Salcedo, D., Fernandez-Gutierrez, B., Raya, E., Franke, L., van't Slot, R., Coenen, M. J. H., van Riel, P., Radstake, T. R. D. J., Koeleman, B. P. C., & Martin, J. (2010). Identification of the Oxidative Stress-Related Gene MSRA as a Rheumatoid Arthritis Susceptibility Locus by Genome-Wide Pathway Analysis. ARTHRITIS AND RHEUMATISM, 62(11), 3183-3190. https://doi.org/10.1002/art.27648
Dubois, P. C. A., Trynka, G., Franke, L., Hunt, K. A., Romanos, J., Curtotti, A., Zhernakova, A., Heap, G. A. R., Adany, R., Aromaa, A., Bardella, M. T., van den Berg, L. H., Bockett, N. A., de la Concha, E. G., Dema, B., Fehrmann, R. S. N., Fernandez-Arquero, M., Fiatal, S., Grandone, E., ... van Heel, D. A. (2010). Multiple common variants for celiac disease influencing immune gene expression. Nature Genetics, 42(4), 295-U42. https://doi.org/10.1038/ng.543
Buizer-Voskamp, J. E., Franke, L., Staal, W. G., van Daalen, E., Kemner, C., Ophoff, R. A., Vorstman, J. A. S., van Engeland, H., & Wijmenga, C. (2010). Systematic genotype-phenotype analysis of autism susceptibility loci implicates additional symptoms to co-occur with autism. European Journal of Human Genetics, 18(5), 588-595. https://doi.org/10.1038/ejhg.2009.206

2009

Trynka, G., Zhernakova, A., Romanos, J., Franke, L., Hunt, K. A., Turner, G., Bruinenberg, M., Heap, G. A., Platteel, M., Ryan, A. W., de Kovel, C., Holmes, G. K. T., Howdle, P. D., Walters, J. R. F., Sanders, D. S., Mulder, C. J. J., Mearin, M. L., Verbeek, W. H. M., Trimble, V., ... Wijmenga, C. (2009). Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappa B signalling. Gut, 58(8), 1078-1083. https://doi.org/10.1136/gut.2008.169052
Heap, G. A., Trynka, G., Jansen, R. C., Bruinenberg, M., Swertz, M. A., Dinesen, L. C., Hunt, K. A., Wijmenga, C., vanHeel, D. A., Franke, L., & Heel, D. A. V. (2009). Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Medical Genomics, 2(1), [1]. https://doi.org/10.1186/1755-8794-2-1
Franke, L., & Jansen, R. C. (2009). eQTL Analysis in Humans. In K. DiPetrillo (Ed.), Cardiovascular Genomics: Methods and Protocols (Vol. 573, pp. 311-328). (Methods in Molecular Biology; No. 573). Springer. https://doi.org/10.1007/978-1-60761-247-6_17
Franke, L. H., & Jansen, R. C. (2009). eQTL Analysis in Humans in Methods in Molecular Biology. In Dipetrello (Ed.), Cardiovascular Genomics
Knauff, E. A. H., Franke, L., van Es, M. A., van den Berg, L. H., van der Schouw, Y. T., Laven, J. S. E., Lambalk, C. B., Hoek, A., Goverde, A. J., Christin-Maitre, S., Hsueh, A. J., Wijmenga, C., Fauser, B. C. J. M., & Dutch POF Consortium (2009). Genome-wide association study in premature ovarian failure patients suggests ADAMTS19 as a possible candidate gene. Human Reproduction, 24(9), 2372-2378. https://doi.org/10.1093/humrep/dep197
Elbers, C. C., van Eijk, K. R., Franke, L., Mulder, F., van der Schouw, Y. T., Wijmenga, C., & Onland-Moret, N. C. (2009). Using Genome-Wide Pathway Analysis to Unravel the Etiology of Complex Diseases. Genetic epidemiology, 33(5), 419-431. https://doi.org/10.1002/gepi.20395

2008

Franke, L., de Kovel, C. G. E., Aulchenko, Y. S., Trynka, G., Zhernakova, A., Hunt, K. A., Blauw, H. M., van den Berg, L. H., Ophoff, R., Deloukas, P., van Heel, D. A., & Wijmenga, C. (2008). Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. American Journal of Human Genetics, 82(6), 1316-1333. https://doi.org/10.1016/j.ajhg.2008.05.008
Zhernakova, A., Festen, E. M., Franke, L., Trynka, G., van Diemen, C. C., Monsuur, A. J., Bevova, M., Nijmeijer, R. M., van 't Slot, R., Heijmans, R., Boezen, H., van Heel, D. A., van Bodegraven, A. A., Stokkers, P. C. F., Wijmenga, C., Crusius, J. B. A., & Weersma, R. K. (2008). Genetic analysis of innate immunity in Crohn's disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP. American Journal of Human Genetics, 82(5), 1202-1210. https://doi.org/10.1016/j.ajhg.2008.03.016
van Es, M. A., van Vught, P. W., Blauw, H. M., Franke, L., Saris, C. G. J., Van Den Bosch, L., de Jong, S. W., de Jong, V., Baas, F., van't Slot, R., Lemmens, R., Schelhaas, H. J., Birve, A., Sleegers, K., Van Broeckhoven, C., Schymick, J. C., Traynor, B. J., Wokke, J. H. J., Wijmenga, C., ... van den Berg, L. H. (2008). Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. Nature Genetics, 40(1), 29-31. https://doi.org/10.1038/ng.2007.52
van Vliet-Ostaptchouk, J. V., Onland-Moret, N. C., van Haeften, T. W., Franke, L., Elbers, C. C., Shiri-Sverdlov, R., van der Schouw, Y. T., Hofker, M. H., & Wijmenga, C. (2008). HHEX gene polymorphisms are associated with type 2 diabetes in the Dutch Breda cohort. European Journal of Human Genetics, 16(5), 652-656. https://doi.org/10.1038/sj.ejhg.5202008
Hunt, K. A., Zhernakova, A., Turner, G., Heap, G. A. R., Franke, L., Bruinenberg, M., Romanos, J., Dinesen, L. C., Ryan, A. W., Panesar, D., Gwilliam, R., Takeuchi, F., McLaren, W. M., Holmes, G. K. T., Howdle, P. D., Walters, J. R. F., Sanders, D. S., Playford, R. J., Trynka, G., ... van Heel, D. A. (2008). Newly identified genetic risk variants for celiac disease related to the immune response. Nature Genetics, 40(4), 395-402. https://doi.org/10.1038/ng.102
Hunt, K. A., Franke, L., Deloukas, P., Wjmenga, C., & van Heel, D. A. (2008). No evidence in a large UK collection for celiac disease risk variants reported by a Spanish study. Gastroenterology, 134(5), 1629-1630. https://doi.org/10.1053/j.gastro.2008.03.068

2007

van Heel, D. A., Franke, L., Hunt, K. A., Gwilliam, R., Zhernakova, A., Inouye, M., Wapenaar, M. C., Barnardo, M. C. N. M., Bethel, G., Holmes, G. K. T., Feighery, C., Jewell, D., Kelleher, D., Kumar, P., Travis, S., Walters, J. R. F., Sanders, D. S., Howdle, P., Swift, J., ... Wijmenga, C. (2007). A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nature Genetics, 39(7), 827-829. https://doi.org/10.1038/ng2058
van Es, M. A., Van Vught, P. W., Blauw, H. M., Franke, L., Saris, C. G., Andersen, P. M., Van Den Bosch, L., de Jong, S. W., van 't Slot, R., Birve, A., Lemmens, R., de Jong, V., Baas, F., Schelhaas, H. J., Sleegers, K., Van Broeckhoven, C., Wokke, J. H. J., Wijmenga, C., Robberecht, W., ... van den Berg, L. H. (2007). ITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome-wide association study. Lancet Neurology, 6(10), 869-877. https://doi.org/10.1016/S1474-4422(07)70222-3
Diosdado, B., Van Bakel, H., Strengman, E., Franke, L., Van Oort, E., Mulder, C. J., Wijmenga, C., & Wapenaar, M. C. (2007). Neutrophil recruitment and barrier impairment in celiac disease: A genomic study. Clinical Gastroenterology and Hepatology, 5(5), 574-581. https://doi.org/10.1016/j.cgh.2006.11.014
Zhernakova, A., Alizadeh, B. Z., Bevova, M., van Leeuwen, M. A., Coenen, M. J. H., Franke, B., Franke, L., Posthumus, M. D., van Heel, D. A., van der Steege, G., Radstake, T. R. D. J., Barrera, P., Roep, B. O., Koeleman, B. P. C., & Wijmenga, C. (2007). Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases. American Journal of Human Genetics, 81(6), 1284-1288. https://doi.org/10.1086/522037

2006

Vorstman, JAS., Staal, WG., van Daalen, E., van Engeland, H., Hochstenbach, PFR., & Franke, L. (2006). Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism. Molecular Psychiatry, 11(1), 18-28. https://doi.org/10.1038/sj.mp.4001757

2005

Monsuur, AJ., de Bakker, PIW., Alizadeh, BZ., Zhernakova, A., Bevova, MR., Strengman, E., Franke, L., van't Slot, R., van Belzen, MJ., Lavrijsen, ICM., Diosdado, B., Daly, MJ., Mulder, C. J. J., Mearin, ML., Meijer, J. W. R., Meijer, G. A., van Oort, E., Wapenaar, MC., Koeleman, BPC., & Wijmenga, C. (2005). Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect. Nature Genetics, 37(12), 1341-1344. https://doi.org/10.1038/ng1680

2004

Diosdado, B., Wapenaar, MC., Franke, L., Duran, KJ., Goerres, MJ., Hadithi, M., Crusius, JBA., Meijer, JWR., Duggan, DJ., Mulder, CJJ., Holstege, FCP., & Wijmenga, C. (2004). A microarray screen for novel candidate genes in coeliac disease pathogenesis. Gut, 53(7), 944-951. https://doi.org/10.1136/gut.2003.018374
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