Publications by the GCC
(1) Recent articles (2) Other papers of interest (3) Papers on tools. For all papers see PubMed, with M.A. Swertz as a co-author.
(1) Recent articles
Whole-exome sequencing is a powerful approach for establishing the etiological diagnosis in patients with intellectual disability and microcephaly Rump P, Jazayeri O, van Dijk-Bos KK, Johansson LF, van Essen AJ, Verheij JB, Veenstra-Knol HE, Redeker EJ, Mannens MM, Swertz MA, Alizadeh BZ, van Ravenswaaij-Arts CM, Sinke RJ, Sikkema-Raddatz B. BMC Med Genomics. 2016 Feb 4;9:7.
Understanding human immune function using the resources from the Human Functional Genomics Project Netea MG, Joosten LA, Li Y, Kumar V, et al. Nat Med. 2016 Aug 4;22(8):831-3.
Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG. Nat Med. 2016 Aug;22(8):952-60.
A novel biomarker panel for irritable bowel syndrome and the application in the general population Mujagic Z, Tigchelaar EF, Zhernakova A, Ludwig T, Ramiro-Garcia J, Baranska A, Swertz MA, Masclee AA, Wijmenga C, van Schooten FJ, Smolinska A, Jonkers DM. Sci Rep. 2016 Jun 6;6:26420.
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, ... Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, ...Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Science. 2016 Apr 29;352(6285):565-9.
PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols. Kanterakis A, Kuiper J, Potamias G, Swertz MA. Source Code Biol Med. 2015 Nov 19;10:14. eCollection 2015.
The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. Winkler TW, et al. PLoS Genet. 2015 Oct 1;11(10):e1005378. eCollection 2015 Oct.
Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations. Shah S, et al. Am J Hum Genet. 2015 Jul 2;97(1):75-85.
Estimation of Genetic Relationships Between Individuals Across Cohorts and Platforms: Application to Childhood Height. Fedko IO, Hottenga JJ, Medina-Gomez C, Pappa I, van Beijsterveldt CE, Ehli EA, Davies GE, Rivadeneira F, Tiemeier H, Swertz MA, Middeldorp CM, Bartels M, Boomsma DI. Behav Genet. 2015 Sep;45(5):514-28.
The hybrid synthetic microdata platform: a method for statistical disclosure control. Kuiper J, van den Heuvel ER, Swertz MA. Biopreserv Biobank. 2015 Jun;13(3):178-82.
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. eCollection 2015.
Characteristics of de novo structural changes in the human genome. Kloosterman WP, et al. Genome Res. 2015 Jun;25(6):792-801. doi: 10.1101/gr.185041.114.
Evaluation of CADD Scores in Curated Mismatch Repair Gene Variants Yields a Model for Clinical Validation and Prioritization. van der Velde KJ, et al. Hum Mutat. 2015 Jul;36(7):712-9.
Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm. Farlow JL, et al. PLoS One. 2015 Mar 24;10(3):e0121104. doi: 10.1371/journal.pone.0121104. eCollection 2015.
Genetic studies of body mass index yield new insights for obesity biology. Locke AE, et al. Nature. 2015 Feb 12;518(7538):197-206.
New genetic loci link adipose and insulin biology to body fat distribution. Shungin D, et al. Nature. 2015 Feb 12;518(7538):187-96.
Biological interpretation of genome-wide association studies using predicted gene functions. Pers TH, et al. Nat Commun. 2015 Jan 19;6:5890.
(2) Other papers of interest
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson MD, et al. Sci Data. 2016 Mar 15;3:160018.
Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. Tigchelaar EF, Zhernakova A, Dekens JA, Hermes G, Baranska A, Mujagic Z,Swertz MA, Muñoz AM, Deelen P, Cénit MC, Franke L, Scholtens S, Stolk RP, Wijmenga C, Feskens EJ. BMJ Open. 2015 Aug 28;5(8):e006772. Free PMC Article
Cohort Profile: LifeLines, a three-generation cohort study and biobank. Scholtens S, Smidt N, Swertz MA, Bakker SJ, Dotinga A, Vonk JM, van Dijk F, van Zon SK, Wijmenga C, Wolffenbuttel BH, Stolk RP. Int J Epidemiol. 2015 Aug;44(4):1172-80.
Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Van Leeuwen EM, et al. Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065.
Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. Van Leeuwen EM, et al. Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065.
The Genome of the Netherlands: design, and project goals. Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA et al. (2013). Eur J Hum Gen. doi: 10.1038/ejhg.2013.118 Position paper
Workshop on laboratory protocol standards for the Molecular Methods Database. Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, et al. N Biotechnol. 2013;30(2):109-13. Abstract
How to kickstart a national biobanking infrastructure – experiences and prospects of BBMRI-NL. Brandsma et al. Norsk Epidemiolog 2012;21(2):143-148.
Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs. Durrant C, et al. Brief Bioinform. 2012;13(2):135-42. Full text
(3) Papers on tools
CoNVaDING: Single Exon Variation Detection in Targeted NGS Data Johansson LF, van Dijk F, de Boer EN, van Dijk-Bos KK, Jongbloed JD, van der Hout AH, Westers H, Sinke RJ, Swertz MA, Sijmons RH, Sikkema-Raddatz B. Hum Mutat. 2016 May;37(5):457-64
MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks Pang C, van Enckevort D, de Haan M, Kelpin F, Jetten J, Hendriksen D, de Boer T, Charbon B, Winder E, van der Velde KJ, Doiron D, Fortier I, Hillege H, Swertz MA. Bioinformatics. 2016 Jul 15;32(14):2176-83.
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data. Pang C, Sollie A, Sijtsma A, Hendriksen D, Charbon B, de Haan M, de Boer T, Kelpin F, Jetten J, van der Velde JK, Smidt N, Sijmons R, Hillege H, Swertz MA. Database (Oxford). 2015 Sep 18;2015. 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. Nat Protoc. 2015 Sep;10(9):1285-96.
Molgenis-impute: imputation pipeline in a box. Kanterakis A, Deelen P, van Dijk F, Byelas H, Dijkstra M, Swertz MA. BMC Res Notes. 2015 Aug 19;8:359. Free PMC Article
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. Pang C, Hendriksen D, Dijkstra M, van der Velde KJ, Kuiper J, Hillege HL,Swertz MA. J Am Med Inform Assoc. 2015 Jan;22(1):65-75. Free PMC Article
Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. Deelen P, Bonder MJ, van der Velde KJ, Westra HJ, Winder E, Hendriksen D, Franke L, Swertz MA. BMC Res Notes. 2014 Dec 11;7:901. Free PMC Article
WormQTLHD --a web database for linking human disease to natural variation data in C. elegans. Van der Velde KJ, et al. Nucleic Acids Res. 2013 Nov 11. Full text
WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp. Snoek et al (2013) Nucleic Acids Research, 41, D738–D743, doi:10.1093/nar/gks1124, Full article
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. Adamusiak T et al. BMC Bioinformatics 2011;12:218 Free PMC article
O ntoCAT: an R package for ontology traversal and search. Kurbatova N, et al. Bioinformatics 2011;1;27(17):2468-70. Full text
Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information. Adamusiak et al (2012) Human Mutation 33(5):867-73, Abstract
xQTL workbench: a scalable web environment for multi-level QTL analysis. Arends, van der Velde, et al (2012) Bioinformatics , http://www.xqtl.org, Free PMC article
XGAP ‘xQTL’ data model XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Swertz et al (2010) Genome Biology 11(3):R27. doi: 10.1186/gb-2010-11-3-r27, http://www.xgap.org, Full article
MOLGENIS toolbox The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. Swertz et al (2010) BMC Bioinf. 11(Suppl 12):S12, http://www.molgenis.org, Full article
designGG: an R-package and web tool for the optimal design of genetical genomics experiments. Li Y, et al. BMC Bioinformatics. 2009;10:188. Full text
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