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DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts.
Zhernakova DV, de Klerk E, Westra HJ, Mastrokolias A, Amini S, Ariyurek Y, Jansen R, Penninx BW, Hottenga JJ, Willemsen G, de Geus EJ, Boomsma DI, Veldink JH, van den Berg LH, Wijmenga C, den Dunnen JT, van Ommen GJ, 't Hoen PA, Franke L. Zhernakova DV, et al. PLoS Genet. 2013 Jun;9(6):e1003594. doi: 10.1371/journal.pgen.1003594. Epub 2013 Jun 20. PLoS Genet. 2013. PMID: 23818875 Free PMC article.
Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels.
Draisma HHM, Pool R, Kobl M, Jansen R, Petersen AK, Vaarhorst AAM, Yet I, Haller T, Demirkan A, Esko T, Zhu G, Böhringer S, Beekman M, van Klinken JB, Römisch-Margl W, Prehn C, Adamski J, de Craen AJM, van Leeuwen EM, Amin N, Dharuri H, Westra HJ, Franke L, de Geus EJC, Hottenga JJ, Willemsen G, Henders AK, Montgomery GW, Nyholt DR, Whitfield JB, Penninx BW, Spector TD, Metspalu A, Slagboom PE, van Dijk KW, 't Hoen PAC, Strauch K, Martin NG, van Ommen GB, Illig T, Bell JT, Mangino M, Suhre K, McCarthy MI, Gieger C, Isaacs A, van Duijn CM, Boomsma DI. Draisma HHM, et al. Nat Commun. 2015 Jun 12;6:7208. doi: 10.1038/ncomms8208. Nat Commun. 2015. PMID: 26068415 Free PMC article.
Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations.
Shah S, Bonder MJ, Marioni RE, Zhu Z, McRae AF, Zhernakova A, Harris SE, Liewald D, Henders AK, Mendelson MM, Liu C, Joehanes R, Liang L; BIOS Consortium; Levy D, Martin NG, Starr JM, Wijmenga C, Wray NR, Yang J, Montgomery GW, Franke L, Deary IJ, Visscher PM. Shah S, et al. Am J Hum Genet. 2015 Jul 2;97(1):75-85. doi: 10.1016/j.ajhg.2015.05.014. Epub 2015 Jun 25. Am J Hum Genet. 2015. PMID: 26119815 Free PMC article.
Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
Ricaño-Ponce I, Zhernakova DV, Deelen P, Luo O, Li X, Isaacs A, Karjalainen J, Di Tommaso J, Borek ZA, Zorro MM, Gutierrez-Achury J, Uitterlinden AG, Hofman A, van Meurs J; BIOS Consortium; Lifelines Cohort Study; Netea MG, Jonkers IH, Withoff S, van Duijn CM, Li Y, Ruan Y, Franke L, Wijmenga C, Kumar V. Ricaño-Ponce I, et al. J Autoimmun. 2016 Apr;68:62-74. doi: 10.1016/j.jaut.2016.01.002. Epub 2016 Feb 18. J Autoimmun. 2016. PMID: 26898941 Free PMC article.
Blood lipids influence DNA methylation in circulating cells.
Dekkers KF, van Iterson M, Slieker RC, Moed MH, Bonder MJ, van Galen M, Mei H, Zhernakova DV, van den Berg LH, Deelen J, van Dongen J, van Heemst D, Hofman A, Hottenga JJ, van der Kallen CJ, Schalkwijk CG, Stehouwer CD, Tigchelaar EF, Uitterlinden AG, Willemsen G, Zhernakova A, Franke L, 't Hoen PA, Jansen R, van Meurs J, Boomsma DI, van Duijn CM, van Greevenbroek MM, Veldink JH, Wijmenga C; BIOS Consortium; van Zwet EW, Slagboom PE, Jukema JW, Heijmans BT. Dekkers KF, et al. Genome Biol. 2016 Jun 27;17(1):138. doi: 10.1186/s13059-016-1000-6. Genome Biol. 2016. PMID: 27350042 Free PMC article.
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
Slieker RC, van Iterson M, Luijk R, Beekman M, Zhernakova DV, Moed MH, Mei H, van Galen M, Deelen P, Bonder MJ, Zhernakova A, Uitterlinden AG, Tigchelaar EF, Stehouwer CD, Schalkwijk CG, van der Kallen CJ, Hofman A, van Heemst D, de Geus EJ, van Dongen J, Deelen J, van den Berg LH, van Meurs J, Jansen R, 't Hoen PA, Franke L, Wijmenga C, Veldink JH, Swertz MA, van Greevenbroek MM, van Duijn CM, Boomsma DI; BIOS consortium; Slagboom PE, Heijmans BT. Slieker RC, et al. Genome Biol. 2016 Sep 22;17(1):191. doi: 10.1186/s13059-016-1053-6. Genome Biol. 2016. PMID: 27654999 Free PMC article.
Identification of context-dependent expression quantitative trait loci in whole blood.
Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MM, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JB, Jansen R, Heijmans BT, 't Hoen PA, Franke L. Zhernakova DV, et al. Nat Genet. 2017 Jan;49(1):139-145. doi: 10.1038/ng.3737. Epub 2016 Dec 5. Nat Genet. 2017. PMID: 27918533
Disease variants alter transcription factor levels and methylation of their binding sites.
Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HE, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ; BIOS Consortium; Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MM, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JB, 't Hoen PA, Franke L, Heijmans BT. Bonder MJ, et al. Nat Genet. 2017 Jan;49(1):131-138. doi: 10.1038/ng.3721. Epub 2016 Dec 5. Nat Genet. 2017. PMID: 27918535
229 results