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Franke, prof.dr. Lude

Lude Franke
Lude Franke

Lude Franke (1980) is adjunct-hoogleraar aan de afdeling Genetica van de Rijksuniversiteit Groningen/Universitair Medisch Centrum Groningen en hoofd Research and Education van de afdeling Genetica aan het UMCG. Als statistisch geneticus richt hij zich op het analyseren van gegevens over de genetica van complexe ziekten en auto-immuunziekten (zoals coeliakie). Dankzij een ERC Starting Grant (2014), een NWO VIDI-beurs (2014), een NWO VENI-beurs (2009) en een Horizon-beurs (2009) kan hij onderzoek uitvoeren naar moleculaire effecten van mutaties die ziektes veroorzaken.

In zijn vrije tijd is Franke grafisch ontwerper (zie het ontwerp van zijn proefschrift). Deze gelukkige combinatie van vaardigheden kan het leven van een genetisch onderzoeker behoorlijk makkelijker maken: als je je onderzoek visueel kunt uitleggen, begrijpen meer mensen wat je bedoelt. Lude Franke is een van de 'founding members' van de Young Academy Groningen. Lude Franke is in 2017 benoemd tot lid van De Jonge Akademie van de KNAW.

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Publicaties

2018

LifeLines Cohort study, Ligthart, S., Vaez, A., Võsa, U., Stathopoulou, M. G., de Vries, P. S., ... 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. DOI: 10.1016/j.ajhg.2018.09.009
LifeLines Cohort study (2018). Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nature Genetics, 50(11), 1524-+. DOI: 10.1038/s41588-018-0224-7
Bios consortium, Luijk, R., Wu, H., Ward-Caviness, C. K., Hannon, E., Carnero-Montoro, E., ... 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]. DOI: 10.1038/s41467-018-05714-3
Bios consortium, Luijk, R., Dekkers, K. F., van Iterson, M., Arindrarto, W., Claringbould, A., ... van Zwet, E. W. (2018). Genome-wide identification of directed gene networks using large-scale population genomics data. Nature Communications, 9(1), 3097. [3097]. DOI: 10.1038/s41467-018-05452-6
Bolling, M. C., Jan, S. Z., Pasmooij, A. M. G., Lemmink, H. H., Franke, L. H., Yenamandra, V. K., ... Jonkman, M. F. (2018). Generalized Ichthyotic Peeling Skin Syndrome due to FLG2 Mutations. Journal of Investigative Dermatology, 138(8), 1881-1884. DOI: 10.1016/j.jid.2018.01.038
van Setten, J., Brody, J. A., Jamshidi, Y., Swenson, B. R., Butler, A. M., Campbell, H., ... 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]. DOI: 10.1038/s41467-018-04766-9
Bakker, O. B., Aguirre-Gamboa, R., Sanna, S., Oosting, M., Smeekens, S. P., Jaeger, M., ... Li, Y. (2018). Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. Nature Immunology, 19(7), 776-786. DOI: 10.1038/s41590-018-0121-3
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. DOI: 10.1093/bib/bbw139
Pirastu, N., Joshi, P. K., de Vries, P. S., Cornelis, M. C., Keum, N., Franceschini, N., ... Wilson, J. F. (2018). Reply to 'Misestimation of heritability and prediction accuracy of male-pattern baldness'. Nature Communications, 9(1), 2538. [2538]. DOI: 10.1038/s41467-018-04808-2
Pirastu, N., Joshi, P. K., de Vries, P. S., Cornelis, M. C., McKeigue, P. M., Keum, N., ... 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. DOI: 10.1038/s41467-018-04857-7
MiBioGen Consortium Initiative (2018). Meta-analysis of human genome-microbiome association studies: The MiBioGen consortium initiative. Microbiome, 6(1), [101]. DOI: 10.1186/s40168-018-0479-3
Bolling, M., Jan, S., Pasmooij, A., Lemmink, H., Franke, L., Yenamandra, V., ... Jonkman, M. F. (2018). Generalized ichthyotic peeling skin syndrome due to FLG2 mutations. Journal of Investigative Dermatology, 138(5), S128.
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. DOI: 10.1038/s41588-018-0089-9
Amini, M., Vonk, J. M., Abbasi, A., Prins, B. P., Bruinenberg, M., Franke, L., ... 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. DOI: 10.1017/thg.2018.6
Bolling, M. C., Jan, S. Z., Pasmooij, A. M. G., Lemmink, H. H., Franke, L. H., Yenamandra, V. K., ... Jonkman, M. F. (2018). Generalized ichthyotic peeling skin syndrome due to FLG2 mutations. Journal of Investigative Dermatology. DOI: 10.1016/j.jid.2018.01.038
Barbieri, R., Venema, W. U., Vich Vila, A., Li, Y., Franke, L., van Dijk, F., ... 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.
Peters, V., Tigchelaar, E., Campmans-Kuijpers, M., Sheedfar, F., Imhann, F., Dekens, J., ... Alizadeh, B. (2018). 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].
Bios consortium (2018). A SNP panel for identification of DNA and RNA specimens. BMC Genomics, 19(90). DOI: 10.1186/s12864-018-4482-7
Imhann, F., Vich Vila, A., Bonder, M. J., Fu, J., Gevers, D., Visschedijk, M. C., ... 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. DOI: 10.1136/gutjnl-2016-312135
LifeLines Cohort study (2018). Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nature Genetics. DOI: 10.1038/s41588-018-0275-9

2017

Linner, R. K., Marioni, R. E., Rietveld, C. A., Simpkin, A. J., Davies, N. M., Watanabe, K., ... BIOS Consortium (2017). An epigenome-wide association study meta-analysis of educational attainment. Molecular Psychiatry, 22(12), 1680-1690. DOI: 10.1038/mp.2017.210
Pirastu, N., Joshi, P. K., de Vries, P. S., Cornelis, M. C., McKeigue, P. M., Keum, N., ... Wilson, J. F. (2017). GWAS for male-pattern baldness identifies 71 susceptibility loci explaining 38% of the risk. Nature Communications, 8, [1584]. DOI: 10.1038/s41467-017-01490-8
Nibbeling, E. A. R., Duarri, A., Verschuuren-Bemelmans, C. C., Fokkens, M. R., Karjalainen, J. M., Smeets, C. J. L. M., ... Verbeek, D. S. (2017). Exome sequencing and network analysis identifies shared mechanisms underlying spinocerebellar ataxia. Brain, 140(11), 2860-2878. DOI: 10.1093/brain/awx251
van Dongen, J., Suderman, M., Sugden, K., Ismail, K., Mulder, R. H., Kupper, L. K., ... BIOS Consortium (2017). Epigenome-wide association study meta-analysis of aggressive behavior. Behavior Genetics, 47(6), 662-663.
Mandaviya, P. R., Joehanes, R., Aissi, D., Kuehnel, B., Marioni, R. E., Truong, V., ... 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]. DOI: 10.1371/journal.pone.0182472
Macé, A., Tuke, M. A., Deelen, P., Kristiansson, K., Mattsson, H., Nõukas, M., ... Kutalik, Z. (2017). CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits. Nature Communications, 8(1), [744]. DOI: 10.1038/s41467-017-00556-x
Kreiner, E., Waage, J., Standl, M., Brix, S., Pers, T. H., Couto Alves, 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. DOI: 10.1016/j.jaci.2016.10.055
Matzaraki, V., Gresnigt, M. S., Jaeger, M., Ricano-Ponce, I., Johnson, M. D., Oosting, M., ... Kumar, V. (2017). An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. Plos one, 12(7), [e0180824]. DOI: 10.1371/journal.pone.0180824
Nolte, I. M., van der Most, P. J., Alizadeh, B. Z., de Bakker, P. I. W., Boezen, H. M., Bruinenberg, M., ... 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. DOI: 10.1038/ejhg.2017.50
Day, F. R., Thompson, D. J., Helgason, H., Chasman, D. I., Finucane, H., Sulem, P., ... 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. DOI: 10.1038/ng.3841
Tang, A. T., Hoi, J. P. C., Kotzin, J. J., Yang, Y., Hong, C. C., Hobson, N., ... Kahn, M. L. (2017). Endothelial TLR4 and the microbiome drive cerebral cavernous malformations. Nature, 545(7654), 305-310. DOI: 10.1038/nature22075
Wild, P. S., Felix, J. F., Schillert, A., Teumer, A., Chen, M-H., Leening, M. J. G., ... KNHI Investigators (2017). Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function. CLIN Journal, 127(5), 1798-1812. DOI: 10.1172/JCI84840
Nolte, I. M., van der Most, P. J., Alizadeh, B. Z., de Bakker, P. I., Boezen, H. M., Bruinenberg, M., ... 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. DOI: 10.1038/ejhg.2017.50
Acuna-Hidalgo, R., Deriziotis, P., Steehouwer, M., Gilissen, C., Graham, S. A., van Dam, S., ... van Bon, B. W. M. (2017). Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies. Plos Genetics, 13(3). DOI: 10.1371/journal.pgen.1006683
Kasela, S., Kisand, K., Tserel, L., Kaleviste, E., Remm, A., Fischer, K., ... Milani, L. (2017). Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4(+) versus CD8(+) T cells. Plos Genetics, 13(3). DOI: 10.1371/journal.pgen.1006643
Soderquest, K., Hertweck, A., Giambartolomei, C., Henderson, S., Mohamed, R., Goldberg, R., ... Lord, G. M. (2017). Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease. Plos Genetics, 13(2), [e1006587]. DOI: 10.1371/journal.pgen.1006587
Claringbould, A., de Klein, N., & Franke, L. (2017). The genetic architecture of molecular traits. Current Opinion in Systems Biology, 1, 25-31. DOI: 10.1016/j.coisb.2017.01.002
van der Velde, K. J., de Boer, E. N., van Diemen, C. C., Sikkema-Raddatz, B., Abbott, K. M., Knopperts, A., ... Swertz, M. A. (2017). GAVIN: Gene-Aware Variant INterpretation for medical sequencing. Genome Biology, 18(1), [6]. DOI: 10.1186/s13059-016-1141-7
Wahl, S., Drong, A. W., Lehne, B., Loh, M., Scott, W. R., Kunze, S., ... Chambers, J. C. (2017). Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature, 541(81), 81-86. DOI: 10.1038/nature20784
Bonder, M. J., Luijk, R., Pital-Zhernakova, D., Moed, M., Deelen, P., Vermaat, M., ... BIOS Consortium (2017). Disease variants alter transcription factor levels and methylation of their binding sites. Nature Genetics, 49(1), 131-138. DOI: 10.1038/ng.3721
Pital-Zhernakova, D., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., ... Franke, L. (2017). Identification of context-dependent expression quantitative trait loci in whole blood. Nature Genetics, 49(1), 139-145. DOI: 10.1038/ng.3737
Marshall, C. R., Howrigan, D. P., Merico, D., Thiruvahindrapuram, B., Wu, W., Greer, D. S., ... 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. DOI: 10.1038/ng.3725

2016

Kassam, I., Qi, T., Lloyd-Jones, L., Holloway, A., Bonder, M. J., Henders, A. K., ... McRae, A. F. (2016). Evidence for mitochondrial genetic control of autosomal gene expression. Human Molecular Genetics, 25(24), 5332-5338. DOI: 10.1093/hmg/ddw347
Amini, M., Bashirova, D., Prins, B. P., Corpeleijn, E., Bruinenberg, M., Franke, L., ... 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]. DOI: 10.1371/journal.pone.0168480
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]. DOI: 10.1371/journal.pone.0167519
Barban, N., Jansen, R., de Vlaming, R., Vaez, A., Mandemakers, J. J., Tropf, F. C., ... BIOS Consortium (2016). Genome-wide analysis identifies 12 loci influencing human reproductive behavior. Nature Genetics, 48(12), 1462-1472. DOI: 10.1038/ng.3698
Okbay, A., Baselmans, B. M. L., De Neve, J-E., Turley, P., Nivard, M. G., Fontana, M. 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. DOI: 10.1038/ng1216-1587b
Aguirre-Gamboa, R., Joosten, I., Urbano, P. C. M., van der Molen, R. G., van Rijssen, E., van Cranenbroek, B., ... 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. DOI: 10.1016/j.celrep.2016.10.053
van der Zwaag, P. A., Herkert, J. C., Sarvaas, G. J. D. M., Bartelds, B., van Diemen, C. C., de Koning, T. J., ... Kerstjens-Frederikse, W. S. (2016). Rapid Whole Genome Sequencing for Critically Ill Children With Cardiomyopathy. Circulation, 134.
Li, Y., Oosting, M., Smeekens, S. P., Jaeger, M., Aguirre-Gamboa, R., Le, K. T. T., ... Netea, M. G. (2016). A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell, 167(4), 1099-1110. DOI: 10.1016/j.cell.2016.10.017
Iotchkova, V., Huang, J., Morris, J. A., Jain, D., Barbieri, C., Walter, K., ... UK10K Consortium (2016). Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps. Nature Genetics, 48(11), 1303-1312. DOI: 10.1038/ng.3668
Bonder, M. J., Kurilshchikov, A., Tigchelaar-Feenstra, E., Mujagic, Z., Imhann, F., Vich Vila, A., ... Zhernakova, A. (2016). The effect of host genetics on the gut microbiome. Nature Genetics, 48(11), 1407-1412. DOI: 10.1038/ng.3663
Amin, N., Allebrandt, K. V., van der Spek, A., Mueller-Myhsok, B., Hek, K., Teder-Laving, M., ... van Duijn, C. M. (2016). Genetic variants in RBFOX3 are associated with sleep latency. European Journal of Human Genetics, 24(10), 1488-1495. DOI: 10.1038/ejhg.2016.31
Ehret, G. B., Ferreira, T., Chasman, D. I., Jackson, A. U., Schmidt, E. M., Johnson, T., ... 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. DOI: 10.1038/ng.3667
Li, Y., Oosting, M., Deelen, P., Ricano-Ponce, I., Smeekens, S., Jaeger, M., ... 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. DOI: 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. DOI: 10.1038/ng1016-1296c
van der Harst, P., van Setten, J., Verweij, N., Vogler, G., Franke, L., Maurano, M. T., ... de Bakker, P. I. W. (2016). 52 Genetic Loci Influencing Myocardial Mass. Journal of the American College of Cardiology, 68(13), 1435-1448. DOI: 10.1016/j.jacc.2016.07.729
Slieker, R. C., van Iterson, M., Luijk, R., Beekman, M., Zhernakova, D. V., Moed, M. H., ... BIOS Consortium (2016). Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. Genome Biology, 17, [191]. DOI: 10.1186/s13059-016-1053-6
van Rheenen, W., Shatunov, A., Dekker, A. M., McLaughlin, R. L., Diekstra, F. P., Pulit, S. L., ... 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-+. DOI: 10.1038/ng.3622
Okbay, A., Baselmans, B. M. L., De Neve, J-E., Turley, P., Nivard, M. G., Fontana, M. 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), 970-970. DOI: 10.1038/ng.3552
Netea, M. G., Joosten, L. A. B., Li, Y., Kumar, V., Oosting, M., Smeekens, S., ... Wijmenga, C. (2016). Understanding human immune function using the resources from the Human Functional Genomics Project. Nature Medicine, 22(8), 831-833. DOI: 10.1038/nm.4140
Li, Y., Oosting, M., Deelen, P., Ricano-Ponce, I., Smeekens, S., Jaeger, M., ... Netea, M. G. (2016). Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi. Nature Medicine, 22(8), 952-+. DOI: 10.1038/nm.4139
Gormley, P., Anttila, V., Winsvold, B. S., Palta, P., Esko, T., Pers, T. H., ... Int Headache Genetics Consortium (2016). Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. Nature Genetics, 48(8), 856-+. DOI: 10.1038/ng.3598
Okbay, A., Baselmans, B. M. L., Neve, J-E. D., Turley, P., Nivard, M. G., Fontana, M. 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. DOI: 10.1038/ng0816-970c
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]. DOI: 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]. DOI: 10.1158/1538-7445.AM2016-2683
Dekkers, K. F., van Iterson, M., Slieker, R. C., Moed, M. H., Bonder, M. J., van Galen, M., ... BIOS Consortium (2016). Blood lipids influence DNA methylation in circulating cells. Genome Biology, 17, [138]. DOI: 10.1186/s13059-016-1000-6
Okbay, A., Baselmans, B. M. L., De Neve, J-E., Turley, P., Nivard, M. G., Fontana, M. 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-+. DOI: 10.1038/ng.3552
Winkler, T. W., Justice, A. E., Graff, M., Barata, L., Feitosa, M. F., Chu, S., ... 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]. DOI: 10.1371/journal.pgen.1006166
Okbay, A., Beauchamp, J. P., Fontana, M. A., Lee, J. J., Pers, T. H., Rietveld, C. A., ... LifeLines Cohort Study (2016). Genome-wide association study identifies 74 loci associated with educational attainment. Nature, 533(7604), 539-+. DOI: 10.1038/nature17671
Verweij, N., Leach, I. M., Isaacs, A., Arking, D. E., Bis, J. C., Pers, T. H., ... LifeLines Cohort Study (2016). Twenty-eight genetic loci associated with ST-T-wave amplitudes of the electrocardiogram. Human Molecular Genetics, 25(10), 2093-2103. DOI: 10.1093/hmg/ddw058
Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., ... Zhernakova, A. (2016). Proton pump inhibitors affect the gut microbiome. Gut, 65(5), 740-748. DOI: 10.1136/gutjnl-2015-310376
Ellinghaus, D., Jostins, L., Spain, S. L., Cortes, A., Bethune, J., Han, B., ... 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. DOI: 10.1038/ng.3528
Zhernakova, A., Kurilshchikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., ... LifeLines Cohort Study (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352(6285), 565-569. DOI: 10.1126/science.aad3369
Ricano-Ponce, I., Zhernakova, D., Deelen, P., Luo, O., Li, X., Isaacs, A., ... 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. DOI: 10.1016/j.jaut.2016.01.002
Imhann, F., Vila, A. V., Bonder, M. J., Gevers, D., Fu, J., Visschedijk, M. C., ... Weersma, R. K. (2016). Gene-Microbiome Interactions Underlying the Onset and the Clinical Phenotypes of Inflammatory Bowel Disease. Gastroenterology, 150(4), S22-S22. DOI: 10.1016/S0016-5085(16)30198-6
Pers, T. H., Timshel, P., Ripke, S., Lent, S., Sullivan, P. F., O'Donovan, M. C., ... 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. DOI: 10.1093/hmg/ddw007
Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., ... Zhernakova, A. (2016). Proton pump inhibitors affect the gut microbiome. Journal of Crohn's and Colitis, 10, S487-S487.
Lu, Y., Day, F. R., Gustafsson, S., Buchkovich, M. L., Na, J., Bataille, V., ... Loos, R. J. F. (2016). New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk. Nature Communications, 7, [10495]. DOI: 10.1038/ncomms10495
Ibrahim-Verbaas, C. A., Bressler, J., Debette, S., Schuur, M., Smith, A. V., Bis, J. C., ... Generation Scotland (2016). GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Molecular Psychiatry, 21(2), 189-197. DOI: 10.1038/mp.2015.37
Pattaro, C., Teumer, A., Gorski, M., Chu, A. Y., Li, M., Mijatovic, V., ... ICBP Consortium (2016). Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nature Communications, 7(10023). DOI: 10.1038/ncomms10023
Felix, J. F., Bradfield, J. P., Monnereau, C., van der Valk, R. J. P., Stergiakouli, E., Chesi, 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. DOI: 10.1093/hmg/ddv472
Gutierrez-Achury, J., Zorro , M. M., Ricano-Ponce, I., Zhernakova, D. V., Diogo, D., Raychaudhuri, S., ... 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. DOI: 10.1093/hmg/ddv455
Franke, L., El Bannoudi, H., Jansen, D. T. S. L., Kok, K., Trynka, G., Diogo, D., ... 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, 263-270. DOI: 10.1038/ejhg.2015.95

2015

Day, F. R., Ruth, K. S., Thompson, D. J., Lunetta, K. L., Pervjakova, N., Chasman, D. I., ... 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. DOI: 10.1097/01.ogx.0000473766.71624.99
Kato, N., Loh, M., Takeuchi, F., Verweij, N., Wang, X., Zhang, W., ... 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-+. DOI: 10.1038/ng.3405
Day, F. R., Ruth, K. S., Thompson, D. J., Lunetta, K. L., Pervjakova, N., Chasman, D. I., ... 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. DOI: 10.1038/ng.3412
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]. DOI: 10.1186/s13073-015-0229-0
Fu, J., Bonder, M. J., Cenit, M. C., Tigchelaar-Feenstra, E., Maatman, A., Dekens, J. A. M., ... Zhernakova, A. (2015). The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids. Circulation research, 117(9), 817-824. DOI: 10.1161/CIRCRESAHA.115.306807
Peters, M. J., Joehanes, R., Pilling, L. C., Schurmann, C., Conneely, K. N., Powell, J., ... NABEC UKBEC Consortium (2015). The transcriptional landscape of age in human peripheral blood. Nature Communications, 6, [8570]. DOI: 10.1038/ncomms9570
Winkler, T. W., Justice, A. E., Graff, M., Barata, L., Feitosa, M. F., Chu, S., ... 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]. DOI: 10.1371/journal.pgen.1005378
Liu, J. Z., van Sommeren, S., Huang, H., Ng, S. C., Alberts, R., Takahashi, A., ... 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. DOI: 10.1038/ng.3359
Shah, S., Bonder, M. J., Marioni, R. E., Zhu, Z., McRae, A. F., Zhernakova, A., ... BIOS Consortium (2015). Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations. American Journal of Human Genetics, 97(1), 75-85. DOI: 10.1016/j.ajhg.2015.05.014
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. DOI: 10.1038/onc.2014.276
van Gerven, N. M. F., de Boer, Y. S., Zwiers, A., Verwer, B. J., Drenth, J. P. H., van Hoek, B., ... 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. DOI: 10.1038/gene.2014.82
Surakka, I., Horikoshi, M., Magi, R., Sarin, A-P., Mahajan, A., Lagou, V., ... ENGAGE Consortium (2015). The impact of low-frequency and rare variants on lipid levels. Nature Genetics, 47(6), 589-597. DOI: 10.1038/ng.3300
Jin, P., Andiappan, A. K., Quek, J. M., Lee, B., Au, B., Sio, Y. Y., ... 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-U151. DOI: 10.1016/j.jaci.2014.12.1870
Draisma, H. H. M., Pool, R., Kobl, M., Jansen, R., Petersen, A-K., Vaarhorst, A. A. M., ... Boomsma, D. I. (2015). Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. Nature Communications, 6, [7208]. DOI: 10.1038/ncomms8208
Chan, Y., Salem, R. M., Hsu, Y-H. H., McMahon, G., Pers, T. H., Vedantam, S., ... 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. DOI: 10.1016/j.ajhg.2015.02.018
Cornelis, M. C., Byrne, E. M., Esko, T., Nalls, M. A., Ganna, A., Paynter, N., ... UK Brain Expression Consortium (2015). Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption. Molecular Psychiatry, 20(5), 647-656. DOI: 10.1038/mp.2014.107
Westra, H-J., Arends, D., Esko, T., Peters, M. J., Schurmann, C., Schramm, K., ... Franke, L. (2015). Cell Specific eQTL Analysis without Sorting Cells. PLOS Genetics, 11(5), [1005223]. DOI: 10.1371/journal.pgen.1005223
Senapati, S., Gutierrez-Achury, J., Sood, A., Midha, V., Szperl, A., Romanos, J., ... Trynka, G. (2015). Evaluation of European coeliac disease risk variants in a north Indian population. European Journal of Human Genetics, 23(4), 530-535. DOI: 10.1038/ejhg.2014.137
Deelen, P., Zhernakova, D. V., de Haan, M., van der Sijde, M., Bonder, M. J., Karjalainen, J., ... 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]. DOI: 10.1186/s13073-015-0152-4
van der Valk, R. J. P., Kreiner-Moller, E., Kooijman, M. N., Guxens, M., Stergiakouli, E., Saaf, A., ... 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. DOI: 10.1093/hmg/ddu510
Locke, A. E., Kahali, B., Berndt, S. I., Justice, A. E., Pers, T. H., Day, F. R., ... LifeLines Cohort Study (2015). Genetic studies of body mass index yield new insights for obesity biology. Nature, 518(7538), 197-206. DOI: 10.1038/nature14177
Shungin, D., Winkler, T. W., Croteau-Chonka, D. C., Ferreira, T., Lockes, A. E., Maegi, R., ... ReproGen Consortium (2015). New genetic loci link adipose and insulin biology to body fat distribution. Nature, 518(7538), 187-96. DOI: 10.1038/nature14132
Fehrmann, R. S. N., Karjalainen, J. M., Krajewska, M., Westra, H-J., Maloney, D., Simeonov, A., ... Franke, L. (2015). Gene expression analysis identifies global gene dosage sensitivity in cancer. Nature Genetics, 47(2), 115-125. DOI: 10.1038/ng.3173
Andiappan, A. K., Narayanan, S., Myers, R. A., Lee, B., Nieuwenhuis, M. A., Nardin, A., ... Chew, F. T. (2015). Genetic variants of inducible costimulator are associated with allergic asthma susceptibility. Journal of Allergy and Clinical Immunology, 135(2), 556-+. DOI: 10.1016/j.jaci.2014.06.028
Wolfs, M. G. M., Gruben, N., Rensen, S. S., Verdam, F. J., Greve, J. W., Driessen, A., ... 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]. DOI: 10.1038/nutd.2014.43
Kumar, V., Gutierrez-Achury, J., Kanduri, K., Almeida, R., Hrdlickova, B., Zhernakova, D. V., ... 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. DOI: 10.1093/hmg/ddu453
Brandsma, C-A., van den Berge, M., Postma, D. S., Jonker, M. R., Brouwer, S., Pare, P. D., ... 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. DOI: 10.1136/thoraxjnl-2014-205091
Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H-J., Wood, A. R., Yang, J., ... Genetic Invest ANthropometric Trai (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature Communications, 6, [5890]. DOI: 10.1038/ncomms6890
Tigchelaar-Feenstra, E. F., Zhernakova, A., Dekens, J. A. M., Hermes, G., Baranska, A., Mujagic, Z., ... 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]. DOI: 10.1136/bmjopen-2014-006772

2014

Deelen, P., Bonder, M. J., van der Velde, K. J., Westra, H-J., Winder, E., Hendriksen, D., ... Swertz, M. A. (2014). Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Research Notes, 7, [901]. DOI: 10.1186/1756-0500-7-901
Pierce, B. L., Tong, L., Chen, L. S., Rahaman, R., Argos, M., Jasmine, F., ... 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]. DOI: 10.1371/journal.pgen.1004818
Wood, A. R., Esko, T., Yang, J., Vedantam, S., Pers, T. H., Gustafsson, S., ... 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. DOI: 10.1038/ng.3097
Deelen, P., Menelaou, A., van Leeuwen, E. M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., ... 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. DOI: 10.1038/ejhg.2014.19
Hrdlickova, B., Kumar, V., Kanduri, K., Zhernakova, D. V., Tripathi, S., Karjalainen, J., ... 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]. DOI: 10.1186/s13073-014-0088-0
Bonder, M. J., Kasela, S., Kals, M., Tamm, R., Lokk, K., Barragan, I., ... Milani, L. (2014). Genetic and epigenetic regulation of gene expression in fetal and adult human livers. BMC Genomics, 15(860). DOI: 10.1186/1471-2164-15-860
Perry, J. R. B., Day, F., Elks, C. E., Sulem, P., Thompson, D. J., Ferreira, T., ... Early Growth Genetics EGG Consorti (2014). Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature, 514(7520). DOI: 10.1038/nature13545
Hemani, G., Shakhbazov, K., Westra, H-J., Esko, T., Henders, A. K., McRae, A. F., ... Powell, J. E. (2014). Another explanation for apparent epistasis Reply. Nature, 514(7520), E5-E6. DOI: 10.1038/nature13692
Smolonska, J., Koppelman, G. H., Wijmenga, C., Vonk, J. M., Zanen, P., Bruinenberg, M., ... Postma, D. S. (2014). Common genes underlying asthma and COPD? Genome-wide analysis on the Dutch hypothesis. European Respiratory Journal, 44(4), 860-872. DOI: 10.1183/09031936.00001914
Benyamin, B., Esko, T., Ried, J. S., Radhakrishnan, A., Vermeulen, S. H., Traglia, M., ... InterAct Consortium (2014). Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis. Nature Communications, 5, [4926]. DOI: 10.1038/ncomms5926
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. DOI: 10.1016/j.bbadis.2014.04.024
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]. DOI: 10.1186/1755-8794-7-57
Rietveld, C. A., Esko, T., Davies, G., Pers, T. H., Turley, P., Benyamin, B., ... 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. DOI: 10.1073/pnas.1404623111
Kumar, V., Cheng, S-C., Johnson, M. D., Smeekens, S. P., Wojtowicz, A., Giamarellos-Bourboulis, E., ... Netea, M. G. (2014). Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia. Nature Communications, 5, [4675]. DOI: 10.1038/ncomms5675
Geller, F., Feenstra, B., Carstensen, L., Pers, T. H., van Rooij, I. A. L. M., Korberg, I. B., ... Melbye, M. (2014). Genome-wide association analyses identify variants in developmental genes associated with hypospadias. Nature Genetics, 46(9), 957-+. DOI: 10.1038/ng.3063
Arking, D. E., Pulit, S. L., Crotti, L., Van der Harst, P., Munroe, P. B., Koopmann, T. T., ... HRGEN Consortium (2014). Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nature Genetics, 46(8), 826-836. DOI: 10.1038/ng.3014
de Boer, Y. S., van Gerven, N. M. F., Zwiers, A., Verwer, B. J., van Hoek, B., van Erpecum, K. 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. DOI: 10.1053/j.gastro.2014.04.022
Gockel, I., Becker, J., Wouters, M. M., Niebisch, S., Gockel, H. R., Hess, T., ... Schumacher, J. (2014). Common variants in the HLA-DQ region confer susceptibility to idiopathic achalasia. Nature Genetics, 46(8), 901-904. DOI: 10.1038/ng.3029
Hoggart, C. J., Venturini, G., Mangino, M., Gomez, F., Ascari, G., Zhao, J. H., ... 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]. DOI: 10.1371/journal.pgen.1004508
Ripke, S., Neale, B. M., Corvin, A., Walters, J. T. R., Farh, K-H., Holmans, P. A., ... Wellcome Trust Case-Control Consor (2014). Biological insights from 108 schizophrenia-associated genetic loci. Nature, 511(7510), 421-427. DOI: 10.1038/nature13595
Li, H., Chan, L., Bartuzi, P., Melton, S. D., Weber, A., Ben-Shlomo, S., ... 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-U302. DOI: 10.1053/j.gastro.2014.04.007
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. DOI: 10.1097/MIB.0000000000000032
Cozen, W., Timofeeva, M. N., Li, D., Diepstra, A., Hazelett, D., Delahaye-Sourdeix, M., ... Mckay, J. D. (2014). A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. Nature Communications, 5, [3856]. DOI: 10.1038/ncomms4856
de Almeida, R., Ricaño Ponce, I., Kumar, V., Deelen, P., Szperl, A., Trynka, G., ... Wijmenga, C. (2014). Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant. Human Molecular Genetics, 23(9), 2481-2489. DOI: 10.1093/hmg/ddt619
Nibbeling, E., Verschuuren-Bemelmans, C., van de Warrenburg, B., Kremer, B., van Diemen, C., Dooijes, D., ... Verbeek, D. (2014). Identification of novel spinocerebellar ataxia disease genes using next generation sequencing approaches. Movement Disorders, 29, S58-S58.
Fransen, K., van Sommeren, S., Westra, H. J., Veenstra, M., Lamberts, L. E., Modderman, R., ... 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. DOI: 10.1097/MIB.0000000000000013
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]. DOI: 10.1371/journal.pgen.1004383
de Zeeuw, E. L., van Beijsterveldt, C. E. M., Glasner, T. J., Bartels, M., Ehli, E. A., Davies, G. E., ... 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. DOI: 10.1002/ajmg.b.32254
Hemani, G., Shakhbazov, K., Westra, H-J., Esko, T., Henders, A. K., McRae, A. F., ... Powell, J. E. (2014). Detection and replication of epistasis influencing transcription in humans. Nature, 508(7495), 249-253. DOI: 10.1038/nature13005
Scholtens, S., Postma, D. S., Moffatt, M. F., Panasevich, S., Granell, R., Henderson, A. 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. DOI: 10.1016/j.jaci.2013.08.049
Romanos, J., Rosen, A., Magadi Gopalaiah, V. K., Trynka, G., Franke, L., Szperl, A., ... PreventCD Grp (2014). Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants. Gut, 63(3), 415-422. DOI: 10.1136/gutjnl-2012-304110
Okada, Y., Wu, D., Trynka, G., Raj, T., Terao, C., Ikari, K., ... GARNET Consortium (2014). Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature, 506(7488), 376-+. DOI: 10.1038/nature12873
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]. DOI: 10.1371/journal.pone.0088216
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. DOI: 10.1021/pr400765y

2013

Verweij, N., Wieringa, W. G., Mateo Leach, I., van Veldhuisen, D. J., van Gilst, W. H., Hillege, H. 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).
Cozen, W., Li, D., Timofeeva, M., Diepstra, A., Hazelett, D., Delahaye-Sourdeix, M., ... McKay, J. D. (2013). A Meta-Analysis Of Hodgkin Lymphoma Reveals 19p13.3 (TCF3) As a Novel Susceptibility Loc. Blood, 122(21).
Westra, H-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., ... Hoen, P. A. C. . (2013). Systematic identification of trans eQTLs as putative drivers of known disease associations. Nature Genetics, 45(10), 1238-1243. DOI: 10.1038/ng.2756
Trouw, L. A., Daha, N., Kurreeman, F. A. S., Boehringer, S., Goulielmos, G. N., Westra, H. 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. DOI: 10.1111/cei.12097
Rietveld, C. A., Medland, S. E., Derringer, J., Yang, J., Esko, T., Martin, N. W., ... LifeLines Cohort Study (2013). GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science, 340(6139), 1467-1471. DOI: 10.1126/science.1235488
Zhernakova, D. V., de Klerk, E., Westra, H-J., Mastrokolias, A., Amini, S., Ariyurek, Y., ... Franke, L. (2013). DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts. PLOS Genetics, 9(6), [e1003594]. DOI: 10.1371/journal.pgen.1003594
den Hoed, M., Eijgelsheim, M., Esko, T., Brundel, B. J. J. M., Peal, D. S., Evans, D. M., ... 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. DOI: 10.1038/ng.2610
Li, G., Diogo, D., Wu, D., Spoonamore, J., Dancik, V., Franke, L., ... RACI (2013). Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway. PLOS Genetics, 9(5), [e1003487]. DOI: 10.1371/journal.pgen.1003487
Berndt, S. I., Gustafsson, S., Mägi, R., Ganna, A., Wheeler, E., Feitosa, M. F., ... 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. DOI: 10.1038/ng.2606
Cvejic, A., Haer-Wigman, L., Stephens, J. C., Kostadima, M., Smethurst, P. A., Frontini, M., ... Albers, C. A. (2013). SMIM1 underlies the Vel blood group and influences red blood cell traits. Nature Genetics, 45(5), 542-545. DOI: 10.1038/ng.2603
Gockel, I., Becker, J., Wouters, M. M., Brun, P., Vigo, A. G., Trynka, G., ... 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.
Knevel, R., Krabben, A., Wilson, A. G., Brouwer, E., Leijsma, M. K., Lindqvist, E., ... 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. DOI: 10.1002/art.37808
Kumar, V., Westra, H-J., Karjalainen, J., Zhernakova, D. V., Esko, T., Hrdlickova, B., ... Vosa, U. (2013). Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression. PLOS Genetics, 9(1), [e1003201]. DOI: 10.1371/journal.pgen.1003201
Zhernakova, D., Deelen, P., van der Sijde, M., van der Velde, J., de Haan, M., Abbott, K., ... Franke, L. (2013). Resolving Variants of Unknown Significance Through Large-Scale RNA-seq. Human heredity, 76(2), 106-107.

2012

van der Harst, P., Zhang, W., Mateo Leach, I., Rendon, A., Verweij, N., Sehmi, J., ... Chambers, J. C. (2012). Seventy-five genetic loci influencing the human red blood cell. Nature, 492(7429), 369-75. DOI: 10.1038/nature11677
Eyre, S., Bowes, J., Diogo, D., Lee, A., Barton, A., Martin, P., ... Wellcome Trust Case Control Consor (2012). High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nature Genetics, 44(12), 1336-1340. DOI: 10.1038/ng.2462
de Boer, R. A., Verweij, N., van Veldhuisen, D. J., Westra, H-J., Bakker, S. J. L., Gansevoort, R. T., ... van der Harst, P. (2012). A Genome-Wide Association Study of Circulating Galectin-3. PLoS ONE, 7(10), [e47385]. DOI: 10.1371/journal.pone.0047385
Franceschini, N., van Rooij, F. J. A., Prins, B. P., Feitosa, M. F., Karakas, M., Eckfeldt, J. H., ... 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. DOI: 10.1016/j.ajhg.2012.08.021
Diekstra, F. P., Saris, C. G. J., van Rheenen, W., Franke, L., Jansen, R. C., van Es, M. A., ... Brown Jr., R. H. (2012). Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for Sporadic ALS. PLoS ONE, 7(4), [e35333]. DOI: 10.1371/journal.pone.0035333
Demirkan, A., van Duijn, C. M., Ugocsai, P., Isaacs, A., Pramstaller, P. P., Liebisch, G., ... EUROSPAN Consortium (2012). Genome-Wide Association Study Identifies Novel Loci Associated with Circulating Phospho- and Sphingolipid Concentrations. Plos Genetics, 8(2), [e1002490]. DOI: 10.1371/journal.pgen.1002490
Fu, J., Wolfs, M. G. M., Deelen, P., Westra, H. J., Fehrmann, R. S. N., te Meerman, G., ... Franke, L. (2012). Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLOS Genetics, 8(1), [e1002431]. DOI: 10.1371/journal.pgen.1002431

2011

Johnson, T., Gaunt, T. R., Newhouse, S. J., Padmanabhan, S., Tomaszewski, M., Kumari, M., ... Global BPgen Consortium (2011). Blood Pressure Loci Identified with a Gene-Centric Array. American Journal of Human Genetics, 89(6), 688-700. DOI: 10.1016/j.ajhg.2011.10.013
Sampietro, M. L., Trompet, S., Verschuren, J. J. W., Talens, R. P., Deelen, J., Heijmans, B. T., ... 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. DOI: 10.1093/hmg/ddr389
Trynka, G., Hunt, K. A., Bockett, N. A., Romanos, J., Mistry, V., Szperl, A., ... WTCCC (2011). Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nature Genetics, 43(12), 1193-U45. DOI: 10.1038/ng.998
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. DOI: 10.1111/j.1399-0004.2011.01707.x
Fehrmann, R. S. N., Jansen, R. C., Veldink, J. H., Westra, H. J., Arends, D., Bonder, M. J., ... 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]. DOI: 10.1371/journal.pgen.1002197
Westra, H-J., Jansen, R. C., Fehrmann, R. S. N., te Meerman, G. J., van Heel, D., Wijmenga, C., ... 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. DOI: 10.1093/bioinformatics/btr323
Dolmans, G. H., Werker, P. M., Hennies, H. C., Furniss, D., Festen, E. A., Franke, L., ... BSSH-GODD Consortium, . N. V. (2011). Wnt Signaling and Dupuytren's Disease. New England Journal of Medicine, 365(4), 307-317. DOI: 10.1056/NEJMoa1101029
Janse, M., Lamberts, L. E., Franke, L., Raychaudhuri, S., Ellinghaus, E., Boberg, K. M., ... 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. DOI: 10.1002/hep.24307
Knauff, E. A. H., Blauw, H. M., Pearson, P. L., Kok, K., Wijmenga, C., Veldink, J. H., ... 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. DOI: 10.1016/j.fertnstert.2011.01.018
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. DOI: 10.1016/j.rbmo.2010.12.006
Zhernakova, A., Stahl, E. A., Trynka, G., Raychaudhuri, S., Festen, E., Franke, L., ... Plenge, R. M. (2011). Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Annals of the Rheumatic Diseases, 70, A21. DOI: 10.1136/ard.2010.148965.20
Anderson, C. A., Boucher, G., Lees, C. W., Franke, A., D'Amato, M., Taylor, K. D., ... 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. DOI: 10.1038/ng.764
Zhernakova, A., Stahl, E. A., Trynka, G., Raychaudhuri, S., Festen, E. A., Franke, L., ... 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]. DOI: 10.1371/journal.pgen.1002004
Smolonska, J., Koppelman, G. H., Wijmenga, C., Vonk, J., Zanen, P., Bruinenberg, 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.

2010

Sotoodehnia, N., Isaacs, A., de Bakker, P. I. W., Doerr, M., Newton-Cheh, C., Nolte, I. M., ... Arking, D. E. (2010). Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nature Genetics, 42(12), 1068-U62. DOI: 10.1038/ng.716
Martin, J-E., Alizadeh, B. Z., Gonzalez-Gay, M. A., Balsa, A., Pascual-Salcedo, D., Fernandez-Gutierrez, B., ... 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. DOI: 10.1002/art.27648
Fransen, K., Visschedijk, M. C., van Sommeren, S., Fu, J. Y., Franke, L., Festen, E. A. M., ... 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. DOI: 10.1093/hmg/ddq264
Wolfs, M. G. M., Bruin, E. J., Rensen, S. S., Greve, J. W., Buurman, W. A., Van Haeften, T. W., ... Hofker, M. H. (2010). Plasma glucose levels are associated with gene expression levels in subcutaneous and visceral adipose tissue of morbidly obese individuals. Diabetologia, 53.
Wolfs, M. G. M., Rensen, S. S., Dijk, E. J. B-V., Verdam, F. J., Greve, J-W., Sanjabi, B., ... 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]. DOI: 10.1186/1755-8794-3-34
Zhernakova, A., Elbers, C. C., Ferwerda, B., Romanos, J., Trynka, G., Dubois, P. 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. DOI: 10.1016/j.ajhg.2010.05.004
Knauff, E. A. H., Blauw, H. M., Kok, K., Wijmenga, C., Fauser, B. C. J. M., & Franke, L. (2010). Validation of putative CNVs on the X chromosome in POF patients. Human Reproduction, 25, I329-I329.
Buizer-Voskamp, J. E., Franke, L., Staal, W. G., van Daalen, E., Kemner, C., Ophoff, R. A., ... 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. DOI: 10.1038/ejhg.2009.206
Dubois, P. C. A., Trynka, G., Franke, L., Hunt, K. A., Romanos, J., Curtotti, A., ... van Heel, D. A. (2010). Multiple common variants for celiac disease influencing immune gene expression. Nature Genetics, 42(4), 295-U42. DOI: 10.1038/ng.543

2009

Knauff, E. A. H., Franke, L., van Es, M. A., van den Berg, L. H., van der Schouw, Y. T., Laven, J. S. E., ... 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. DOI: 10.1093/humrep/dep197
Trynka, G., Zhernakova, A., Romanos, J., Franke, L., Hunt, K. A., Turner, G., ... Wijmenga, C. (2009). Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappa B signalling. Gut, 58(8), 1078-1083. DOI: 10.1136/gut.2008.169052
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. DOI: 10.1002/gepi.20395
Knauff, E. A. H., Franke, L., Laven, J. S., Lambalk, C. B., Hoek, A., Goverde, A. J., ... Fauser, B. C. J. M. (2009). Genome-Wide Association Study in Premature Ovarian Failure Patients Reveals ADAMTS19 as a Possible Candidate Gene. Reproductive Sciences, 16(3), 282A-282A.
Zhernakova, A., Hunt, K. A., Franke, L., Trynka, G., Heap, G., Romanos, J., ... Wijmenga, C. (2009). Genome-wide association study In coeliac disease: identification of novel genetic risk loci. European journal of gastroenterology & hepatology, 21(3), A45-A45.
Buizer-Voskamp, J. E., Muntjewerff, J. W., Vorstman, J. A. S., Franke, L., Hochstenbach, P. F. R., Ophoff, R. A., & Kahn, R. S. (2009). Schizophrenia and cytogenetic aberrations: in search of susceptibility genes and pathways. European Neuropsychopharmacology, 19, S5-S6.
Heap, G. A., Trynka, G., Jansen, R. C., Bruinenberg, M., Swertz, M. A., Dinesen, L. C., ... Heel, D. A. V. (2009). Complex nature of SNP genotype effects on gene expression in primary human leucocytes. BMC Medical Genomics, 2(1), [1]. DOI: 10.1186/1755-8794-2-1
Franke, L. H., & Jansen, R. C. (2009). eQTL Analysis in Humans in Methods in Molecular Biology. In Dipetrello (Ed.), Cardiovascular Genomics
Franke, L., & Jansen, R. C. (2009). eQTL Analysis in Humans. In K. DiPetrillo (Ed.), Cardiovascular Genomics. Methods and Protocols (573 ed., pp. 311-328). (Methods in Molecular Biology; No. 573).

2008

Franke, L., de Kovel, C. G. F., Aulchenko, Y. S., Trynka, G., Zhernakova, A., Heap, G., ... Wijmenga, C. (2008). Detection, imputation and association analysis of small deletions and null-alleles on oligonucleotide arrays. Annals of Human Genetics, 72, 687-687.
Franke, L., de Kovel, C. G. E., Aulchenko, Y. S., Trynka, G., Zhernakova, A., Hunt, K. 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. DOI: 10.1016/j.ajhg.2008.05.008
van Vliet-Ostaptchouk, J. V., Onland-Moret, N. C., van Haeften, T. W., Franke, L., Elbers, C. C., Shiri-Sverdlov, R., ... 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. DOI: 10.1038/sj.ejhg.5202008
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. DOI: 10.1053/j.gastro.2008.03.068
Zhernakova, A., Festen, E. M., Franke, L., Trynka, G., van Diemen, C. C., Monsuur, A. J., ... 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. DOI: 10.1016/j.ajhg.2008.03.016
Hunt, K. A., Zhernakova, A., Turner, G., Heap, G. A. R., Franke, L., Bruinenberg, M., ... van Heel, D. A. (2008). Newly identified genetic risk variants for celiac disease related to the immune response. Nature Genetics, 40(4), 395-402. DOI: 10.1038/ng.102
Knauff, E. A. H., Wijmenga, C., van't Slot, R., Franke, L., & Fauser, B. C. J. M. (2008). Genomewide high density SNP-CGH reveals several new deletion copy number variants on the x chromosome in POF patients. Reproductive Sciences, 15(2), 229A-230A.
van Es, M. A., van Vught, P. W., Blauw, H. M., Franke, L., Saris, C. G. J., Van Den Bosch, L., ... van den Berg, L. H. (2008). Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. Nature Genetics, 40(1), 29-31. DOI: 10.1038/ng.2007.52

2007

Zhernakova, A., Alizadeh, B. Z., Bevova, M., van Leeuwen, M. A., Coenen, M. J. H., Franke, B., ... 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. DOI: 10.1086/522037
van Es, M. A., Van Vught, P. W., Blauw, H. M., Franke, L., Saris, C. G., Andersen, P. M., ... 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. DOI: 10.1016/S1474-4422(07)70222-3
van Heel, D. A., Franke, L., Hunt, K. A., Gwilliam, R., Zhernakova, A., Inouye, M., ... 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. DOI: 10.1038/ng2058
Diosdado, B., Van Bakel, H., Strengman, E., Franke, L., Van Oort, E., Mulder, C. J., ... Wapenaar, M. C. (2007). Neutrophil recruitment and barrier impairment in celiac disease: A genomic study. Clinical Gastroenterology and Hepatology, 5(5), 574-581. DOI: 10.1016/j.cgh.2006.11.014

2006

Vorstman, J. A. S., Staal, W. G., van Daalen, E., van Engeland, H., Hochstenbach, P. F. R., & Franke, L. (2006). Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism. Molecular Psychiatry, 11(1), 18-28. DOI: 10.1038/sj.mp.4001757

2005

Monsuur, A. J., de Bakker, P. I. W., Alizadeh, B. Z., Zhernakova, A., Bevova, M. R., Strengman, E., ... 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. DOI: 10.1038/ng1680

2004

Diosdado, B., Wapenaar, M. C., Franke, L., Duran, K. J., Goerres, M. J., Hadithi, M., ... Wijmenga, C. (2004). A microarray screen for novel candidate genes in coeliac disease pathogenesis. Gut, 53(7), 944-951. DOI: 10.1136/gut.2003.018374
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