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Items: 22

1.

Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.

Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J; LifeLines cohort study; BIOS consortium.

Nat Genet. 2018 Dec;50(12):1752. doi: 10.1038/s41588-018-0275-9.

PMID:
30341443
2.

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.

Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J; LifeLines cohort study; BIOS consortium.

Nat Genet. 2018 Nov;50(11):1524-1532. doi: 10.1038/s41588-018-0224-7. Epub 2018 Sep 24. Erratum in: Nat Genet. 2018 Oct 19;:.

PMID:
30250126
3.

Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.

Zhernakova DV, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Dobrynin P, Yurchenko AA, Shimansky V, Shcherbakova IV, Glotov AS, Valle DL, Tang M, Shin E, Schwarz KB, O'Brien SJ.

PLoS One. 2018 Jul 11;13(7):e0200423. doi: 10.1371/journal.pone.0200423. eCollection 2018.

4.

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Kliver S, Rayko M, Komissarov A, Bakin E, Zhernakova D, Prasad K, Rushworth C, Baskar R, Smetanin D, Schmutz J, Rokhsar DS, Mitchell-Olds T, Grossniklaus U, Brukhin V.

Genes (Basel). 2018 Mar 28;9(4). pii: E185. doi: 10.3390/genes9040185.

5.

Identified OAS3 gene variants associated with coexistence of HBsAg and anti-HBs in chronic HBV infection.

Wang S, Wang J, Fan MJ, Li TY, Pan H, Wang X, Liu HK, Lin QF, Zhang JG, Guan LP, Zhernakova DV, O'Brien SJ, Feng ZR, Chang L, Dai EH, Lu JH, Xi HL, Zeng Z, Yu YY, Wang BB.

J Viral Hepat. 2018 Aug;25(8):904-910. doi: 10.1111/jvh.12899. Epub 2018 May 29.

PMID:
29582521
6.

A SNP panel for identification of DNA and RNA specimens.

Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P; BIOS consortium, 't Hoen PAC.

BMC Genomics. 2018 Jan 25;19(1):90. doi: 10.1186/s12864-018-4482-7.

7.

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.

Nat Genet. 2017 Jan;49(1):131-138. doi: 10.1038/ng.3721. Epub 2016 Dec 5.

PMID:
27918535
8.

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.

Nat Genet. 2017 Jan;49(1):139-145. doi: 10.1038/ng.3737. Epub 2016 Dec 5.

PMID:
27918533
9.

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A; BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC; LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC.

Nat Genet. 2016 Dec;48(12):1462-1472. doi: 10.1038/ng.3698. Epub 2016 Oct 31.

10.

The effect of host genetics on the gut microbiome.

Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A.

Nat Genet. 2016 Nov;48(11):1407-1412. doi: 10.1038/ng.3663. Epub 2016 Oct 3.

PMID:
27694959
11.

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.

Genome Biol. 2016 Sep 22;17(1):191.

12.

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.

Genome Biol. 2016 Jun 27;17(1):138. doi: 10.1186/s13059-016-1000-6.

13.

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.

J Autoimmun. 2016 Apr;68:62-74. doi: 10.1016/j.jaut.2016.01.002. Epub 2016 Feb 18.

14.

Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis.

Gutierrez-Achury J, Zorro MM, Ricaño-Ponce I, Zhernakova DV; Coeliac Disease Immunochip Consortium, RACI Consortium, Diogo D, Raychaudhuri S, Franke L, Trynka G, Wijmenga C, Zhernakova A.

Hum Mol Genet. 2016 Jan 1;25(1):180-90. doi: 10.1093/hmg/ddv455. Epub 2015 Nov 5.

15.

An integrative systems genetics approach reveals potential causal genes and pathways related to obesity.

Kogelman LJ, Zhernakova DV, Westra HJ, Cirera S, Fredholm M, Franke L, Kadarmideen HN.

Genome Med. 2015 Oct 20;7:105. doi: 10.1186/s13073-015-0229-0.

16.

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels.

Deelen P, Zhernakova DV, de Haan M, van der Sijde M, Bonder MJ, Karjalainen J, van der Velde KJ, Abbott KM, Fu J, Wijmenga C, Sinke RJ, Swertz MA, Franke L.

Genome Med. 2015 Mar 27;7(1):30. doi: 10.1186/s13073-015-0152-4. eCollection 2015.

17.

Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity.

Hrdlickova B, Kumar V, Kanduri K, Zhernakova DV, Tripathi S, Karjalainen J, Lund RJ, Li Y, Ullah U, Modderman R, Abdulahad W, Lähdesmäki H, Franke L, Lahesmaa R, Wijmenga C, Withoff S.

Genome Med. 2014 Oct 28;6(10):88. doi: 10.1186/s13073-014-0088-0. eCollection 2014.

18.

Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model.

Kogelman LJ, Cirera S, Zhernakova DV, Fredholm M, Franke L, Kadarmideen HN.

BMC Med Genomics. 2014 Sep 30;7:57. doi: 10.1186/1755-8794-7-57.

19.

Systematic annotation of celiac disease loci refines pathological pathways and suggests a genetic explanation for increased interferon-gamma levels.

Kumar V, Gutierrez-Achury J, Kanduri K, Almeida R, Hrdlickova B, Zhernakova DV, Westra HJ, Karjalainen J, Ricaño-Ponce I, Li Y, Stachurska A, Tigchelaar EF, Abdulahad WH, Lähdesmäki H, Hofker MH, Zhernakova A, Franke L, Lahesmaa R, Wijmenga C, Withoff S.

Hum Mol Genet. 2015 Jan 15;24(2):397-409. doi: 10.1093/hmg/ddu453. Epub 2014 Sep 4.

PMID:
25190711
20.

Systematic identification of trans eQTLs as putative drivers of known disease associations.

Westra HJ, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, Christiansen MW, Fairfax BP, Schramm K, Powell JE, Zhernakova A, Zhernakova DV, Veldink JH, Van den Berg LH, Karjalainen J, Withoff S, Uitterlinden AG, Hofman A, Rivadeneira F, Hoen PAC', Reinmaa E, Fischer K, Nelis M, Milani L, Melzer D, Ferrucci L, Singleton AB, Hernandez DG, Nalls MA, Homuth G, Nauck M, Radke D, Völker U, Perola M, Salomaa V, Brody J, Suchy-Dicey A, Gharib SA, Enquobahrie DA, Lumley T, Montgomery GW, Makino S, Prokisch H, Herder C, Roden M, Grallert H, Meitinger T, Strauch K, Li Y, Jansen RC, Visscher PM, Knight JC, Psaty BM, Ripatti S, Teumer A, Frayling TM, Metspalu A, van Meurs JBJ, Franke L.

Nat Genet. 2013 Oct;45(10):1238-1243. doi: 10.1038/ng.2756. Epub 2013 Sep 8.

21.

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.

PLoS Genet. 2013 Jun;9(6):e1003594. doi: 10.1371/journal.pgen.1003594. Epub 2013 Jun 20. Erratum in: PLoS Genet. 2013 Sep;9(9). doi: 10.1371/annotation/296056cb-f80c-4b04-985b-180f6d3cc4ae.

22.

Human disease-associated genetic variation impacts large intergenic non-coding RNA expression.

Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Võsa U, Hofker MH, Fehrmann RS, Fu J, Withoff S, Metspalu A, Franke L, Wijmenga C.

PLoS Genet. 2013;9(1):e1003201. doi: 10.1371/journal.pgen.1003201. Epub 2013 Jan 17.

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