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The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H. Swertz MA, et al. BMC Bioinformatics. 2010 Dec 21;11 Suppl 12(Suppl 12):S12. doi: 10.1186/1471-2105-11-S12-S12. BMC Bioinformatics. 2010. PMID: 21210979 Free PMC article.
Molgenis-impute: imputation pipeline in a box.
Kanterakis A, Deelen P, van Dijk F, Byelas H, Dijkstra M, Swertz MA. Kanterakis A, et al. BMC Res Notes. 2015 Aug 19;8:359. doi: 10.1186/s13104-015-1309-3. BMC Res Notes. 2015. PMID: 26286716 Free PMC article.
Population-specific genotype imputations using minimac or IMPUTE2.
van Leeuwen EM, Kanterakis A, Deelen P, Kattenberg MV; Genome of the Netherlands Consortium, Slagboom PE, de Bakker PI, Wijmenga C, Swertz MA, Boomsma DI, van Duijn CM, Karssen LC, Hottenga JJ. van Leeuwen EM, et al. Nat Protoc. 2015 Sep;10(9):1285-96. doi: 10.1038/nprot.2015.077. Epub 2015 Jul 30. Nat Protoc. 2015. PMID: 26226460
Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'.
Deelen P, Menelaou A, van Leeuwen EM, Kanterakis A, van Dijk F, Medina-Gomez C, Francioli LC, Hottenga JJ, Karssen LC, Estrada K, Kreiner-Møller E, Rivadeneira F, van Setten J, Gutierrez-Achury J, Westra HJ, Franke L, van Enckevort D, Dijkstra M, Byelas H, van Duijn CM; Genome of Netherlands Consortium, de Bakker PI, Wijmenga C, Swertz MA. Deelen P, et al. Eur J Hum Genet. 2014 Nov;22(11):1321-6. doi: 10.1038/ejhg.2014.19. Epub 2014 Jun 4. Eur J Hum Genet. 2014. PMID: 24896149 Free PMC article.
Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant.
Almeida R, Ricaño-Ponce I, Kumar V, Deelen P, Szperl A, Trynka G, Gutierrez-Achury J, Kanterakis A, Westra HJ, Franke L, Swertz MA, Platteel M, Bilbao JR, Barisani D, Greco L, Mearin L, Wolters VM, Mulder C, Mazzilli MC, Sood A, Cukrowska B, Núñez C, Pratesi R, Withoff S, Wijmenga C. Almeida R, et al. Hum Mol Genet. 2014 May 1;23(9):2481-9. doi: 10.1093/hmg/ddt619. Epub 2013 Dec 11. Hum Mol Genet. 2014. PMID: 24334606 Free PMC article.
Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes.
Franke L, el Bannoudi H, Jansen DT, Kok K, Trynka G, Diogo D, Swertz M, Fransen K, Knevel R, Gutierrez-Achury J, Ärlestig L, Greenberg JD, Kremer J, Pappas DA, Kanterakis A, Weersma RK, van der Helm-van Mil AH, Guryev V, Rantapää-Dahlqvist S, Gregersen PK, Plenge RM, Wijmenga C, Huizinga TW, Ioan-Facsinay A, Toes RE, Zhernakova A. Franke L, et al. Eur J Hum Genet. 2016 Feb;24(2):263-70. doi: 10.1038/ejhg.2015.95. Epub 2015 May 13. Eur J Hum Genet. 2016. PMID: 25966632 Free PMC article.
Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.
van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BW, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Mateo Leach I, Beekman M, de Craen AJ, Uh HW, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rotter JI, Mychaleckyj JC, Campbell H, Duan Q, Lange LA, Wilson JF, Hayward C, Polasek O, Vitart V, Rudan I, Wright AF, Rich SS, Psaty BM, Borecki IB, Kearney PM, Stott DJ, Adrienne Cupples L; Genome of The Netherlands Consortium, Jukema JW, van der Harst P, Sijbrands EJ, Hottenga JJ, Uitterlinden AG, Swertz MA, van Ommen GJ, de Bakker PI, Eline Slagboom P, Boomsma DI, Wijmenga C, van Duijn CM. van Leeuwen EM, et al. Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065. Nat Commun. 2015. PMID: 25751400 Free PMC article.
Exome sequencing in a family segregating for celiac disease.
Szperl AM, Ricaño-Ponce I, Li JK, Deelen P, Kanterakis A, Plagnol V, van Dijk F, Westra HJ, Trynka G, Mulder CJ, Swertz M, Wijmenga C, Zheng HC. Szperl AM, et al. Clin Genet. 2011 Aug;80(2):138-47. doi: 10.1111/j.1399-0004.2011.01714.x. Epub 2011 Jun 21. Clin Genet. 2011. PMID: 21627641
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