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Items: 1 to 50 of 113

1.

Systems Genetics for Evolutionary Studies.

Prins P, Smant G, Arends D, Mulligan MK, Williams RW, Jansen RC.

Methods Mol Biol. 2019;1910:635-652. doi: 10.1007/978-1-4939-9074-0_21.

PMID:
31278680
2.

FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support.

Zych K, Gort G, Maliepaard CA, Jansen RC, Voorrips RE.

BMC Bioinformatics. 2019 Mar 20;20(1):148. doi: 10.1186/s12859-019-2703-y.

3.

reGenotyper: Detecting mislabeled samples in genetic data.

Zych K, Snoek BL, Elvin M, Rodriguez M, Van der Velde KJ, Arends D, Westra HJ, Swertz MA, Poulin G, Kammenga JE, Breitling R, Jansen RC, Li Y.

PLoS One. 2017 Feb 13;12(2):e0171324. doi: 10.1371/journal.pone.0171324. eCollection 2017.

4.

Toward effective software solutions for big biology.

Prins P, de Ligt J, Tarasov A, Jansen RC, Cuppen E, Bourne PE.

Nat Biotechnol. 2015 Jul;33(7):686-7. doi: 10.1038/nbt.3240. No abstract available.

PMID:
26154002
5.

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.

van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ, Colomé-Tatché M, Johannes F.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6676-81. doi: 10.1073/pnas.1424254112. Epub 2015 May 11.

6.

Cell Specific eQTL Analysis without Sorting Cells.

Westra HJ, Arends D, Esko T, Peters MJ, Schurmann C, Schramm K, Kettunen J, Yaghootkar H, Fairfax BP, Andiappan AK, Li Y, Fu J, Karjalainen J, Platteel M, Visschedijk M, Weersma RK, Kasela S, Milani L, Tserel L, Peterson P, Reinmaa E, Hofman A, Uitterlinden AG, Rivadeneira F, Homuth G, Petersmann A, Lorbeer R, Prokisch H, Meitinger T, Herder C, Roden M, Grallert H, Ripatti S, Perola M, Wood AR, Melzer D, Ferrucci L, Singleton AB, Hernandez DG, Knight JC, Melchiotti R, Lee B, Poidinger M, Zolezzi F, Larbi A, Wang de Y, van den Berg LH, Veldink JH, Rotzschke O, Makino S, Salomaa V, Strauch K, Völker U, van Meurs JB, Metspalu A, Wijmenga C, Jansen RC, Franke L.

PLoS Genet. 2015 May 8;11(5):e1005223. doi: 10.1371/journal.pgen.1005223. eCollection 2015 May.

7.

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

Zych K, Li Y, van der Velde JK, Joosen RV, Ligterink W, Jansen RC, Arends D.

BMC Bioinformatics. 2015 Feb 19;16:51. doi: 10.1186/s12859-015-0475-6.

8.

Gene expression analysis identifies global gene dosage sensitivity in cancer.

Fehrmann RS, Karjalainen JM, Krajewska M, Westra HJ, Maloney D, Simeonov A, Pers TH, Hirschhorn JN, Jansen RC, Schultes EA, van Haagen HH, de Vries EG, te Meerman GJ, Wijmenga C, van Vugt MA, Franke L.

Nat Genet. 2015 Feb;47(2):115-25. doi: 10.1038/ng.3173. Epub 2015 Jan 12.

PMID:
25581432
9.

Worm variation made accessible: Take your shopping cart to store, link, and investigate!

Snoek LB, Joeri van der Velde K, Li Y, Jansen RC, Swertz MA, Kammenga JE.

Worm. 2014 Jan 1;3(1):e28357. doi: 10.4161/worm.28357. Epub 2014 Mar 6.

10.

Natural variation of histone modification and its impact on gene expression in the rat genome.

Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N.

Genome Res. 2014 Jun;24(6):942-53. doi: 10.1101/gr.169029.113. Epub 2014 May 2.

11.

Re: "The rise and fall of the 'minimum clinically important difference'".

Jansen RC.

Spine J. 2014 Apr;14(4):726. doi: 10.1016/j.spinee.2010.06.022. No abstract available.

PMID:
24655561
12.

Mapping the epigenetic basis of complex traits.

Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, Roudier F, Jansen RC, Colot V, Johannes F.

Science. 2014 Mar 7;343(6175):1145-8. doi: 10.1126/science.1248127. Epub 2014 Feb 6.

PMID:
24505129
13.

Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles.

Dharuri H, Henneman P, Demirkan A, van Klinken JB, Mook-Kanamori DO, Wang-Sattler R, Gieger C, Adamski J, Hettne K, Roos M, Suhre K, Van Duijn CM; EUROSPAN Consortia, van Dijk KW, 't Hoen PA.

BMC Genomics. 2013 Dec 9;14:865. doi: 10.1186/1471-2164-14-865.

14.

WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.

van der Velde KJ, de Haan M, Zych K, Arends D, Snoek LB, Kammenga JE, Jansen RC, Swertz MA, Li Y.

Nucleic Acids Res. 2014 Jan;42(Database issue):D794-801. doi: 10.1093/nar/gkt1044. Epub 2013 Nov 11.

15.

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.

16.

Pulmonary function after less invasive anterior instrumentation and fusion for idiopathic thoracic scoliosis.

Huitema GC, Jansen RC, Dompeling E, Willems P, Punt I, van Rhijn LW.

Scoliosis. 2013 Aug 21;8(1):14. doi: 10.1186/1748-7161-8-14.

17.
18.

Controlling complexity: the clinical relevance of mouse complex genetics.

Schughart K, Libert C; SYSGENET consortium, Kas MJ.

Eur J Hum Genet. 2013 Nov;21(11):1191-6. doi: 10.1038/ejhg.2013.79. Epub 2013 May 1. Review.

19.

Identifying genotype-by-environment interactions in the metabolism of germinating arabidopsis seeds using generalized genetical genomics.

Joosen RV, Arends D, Li Y, Willems LA, Keurentjes JJ, Ligterink W, Jansen RC, Hilhorst HW.

Plant Physiol. 2013 Jun;162(2):553-66. doi: 10.1104/pp.113.216176. Epub 2013 Apr 19.

20.

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

Snoek LB, Van der Velde KJ, Arends D, Li Y, Beyer A, Elvin M, Fisher J, Hajnal A, Hengartner MO, Poulin GB, Rodriguez M, Schmid T, Schrimpf S, Xue F, Jansen RC, Kammenga JE, Swertz MA.

Nucleic Acids Res. 2013 Jan;41(Database issue):D738-43. doi: 10.1093/nar/gks1124. Epub 2012 Nov 24.

21.

Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia.

Lendvai Á, Johannes F, Grimm C, Eijsink JJ, Wardenaar R, Volders HH, Klip HG, Hollema H, Jansen RC, Schuuring E, Wisman GB, van der Zee AG.

Epigenetics. 2012 Nov;7(11):1268-78. doi: 10.4161/epi.22301. Epub 2012 Sep 27.

22.

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.

Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16240-5. doi: 10.1073/pnas.1212955109. Epub 2012 Sep 17.

23.

Chronic pain, associated factors, and impact on daily life: are there differences between the sexes?

Vieira EB, Garcia JB, Silva AA, Araújo RL, Jansen RC, Bertrand AL.

Cad Saude Publica. 2012 Aug;28(8):1459-67.

24.

Prevalence, characteristics, and factors associated with chronic pain with and without neuropathic characteristics in São Luís, Brazil.

de Moraes Vieira EB, Garcia JB, da Silva AA, Mualem Araújo RL, Jansen RC.

J Pain Symptom Manage. 2012 Aug;44(2):239-51. doi: 10.1016/j.jpainsymman.2011.08.014.

PMID:
22871508
25.

Quantile-based permutation thresholds for quantitative trait loci hotspots.

Neto EC, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS.

Genetics. 2012 Aug;191(4):1355-65. doi: 10.1534/genetics.112.139451. Epub 2012 Jun 1.

26.

Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS.

Diekstra FP, Saris CG, van Rheenen W, Franke L, Jansen RC, van Es MA, van Vught PW, Blauw HM, Groen EJ, Horvath S, Estrada K, Rivadeneira F, Hofman A, Uitterlinden AG, Robberecht W, Andersen PM, Melki J, Meininger V, Hardiman O, Landers JE, Brown RH Jr, Shatunov A, Shaw CE, Leigh PN, Al-Chalabi A, Ophoff RA, van den Berg LH, Veldink JH.

PLoS One. 2012;7(4):e35333. doi: 10.1371/journal.pone.0035333. Epub 2012 Apr 11.

27.

Genetical genomics for evolutionary studies.

Prins P, Smant G, Jansen RC.

Methods Mol Biol. 2012;856:469-85. doi: 10.1007/978-1-61779-585-5_19.

PMID:
22399471
28.

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs.

Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der Velde KJ, Jansen RC, Schughart K.

Brief Bioinform. 2012 Mar;13(2):135-42. doi: 10.1093/bib/bbr026. Epub 2011 Jul 8. Review.

29.

Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.

Demirkan A, van Duijn CM, Ugocsai P, Isaacs A, Pramstaller PP, Liebisch G, Wilson JF, Johansson Å, Rudan I, Aulchenko YS, Kirichenko AV, Janssens AC, Jansen RC, Gnewuch C, Domingues FS, Pattaro C, Wild SH, Jonasson I, Polasek O, Zorkoltseva IV, Hofman A, Karssen LC, Struchalin M, Floyd J, Igl W, Biloglav Z, Broer L, Pfeufer A, Pichler I, Campbell S, Zaboli G, Kolcic I, Rivadeneira F, Huffman J, Hastie ND, Uitterlinden A, Franke L, Franklin CS, Vitart V; DIAGRAM Consortium, Nelson CP, Preuss M; CARDIoGRAM Consortium, Bis JC, O'Donnell CJ, Franceschini N; CHARGE Consortium, Witteman JC, Axenovich T, Oostra BA, Meitinger T, Hicks AA, Hayward C, Wright AF, Gyllensten U, Campbell H, Schmitz G; EUROSPAN consortium.

PLoS Genet. 2012;8(2):e1002490. doi: 10.1371/journal.pgen.1002490. Epub 2012 Feb 16.

30.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

Arends D, van der Velde KJ, Prins P, Broman KW, Möller S, Jansen RC, Swertz MA.

Bioinformatics. 2012 Apr 1;28(7):1042-4. doi: 10.1093/bioinformatics/bts049. Epub 2012 Feb 3.

31.

Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression.

Fu J, Wolfs MG, Deelen P, Westra HJ, Fehrmann RS, Te Meerman GJ, Buurman WA, Rensen SS, Groen HJ, Weersma RK, van den Berg LH, Veldink J, Ophoff RA, Snieder H, van Heel D, Jansen RC, Hofker MH, Wijmenga C, Franke L.

PLoS Genet. 2012 Jan;8(1):e1002431. doi: 10.1371/journal.pgen.1002431. Epub 2012 Jan 19.

32.

Visualizing the genetic landscape of Arabidopsis seed performance.

Joosen RV, Arends D, Willems LA, Ligterink W, Jansen RC, Hilhorst HW.

Plant Physiol. 2012 Feb;158(2):570-89. doi: 10.1104/pp.111.186676. Epub 2011 Dec 12.

33.

Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA.

Fehrmann RS, Jansen RC, Veldink JH, Westra HJ, Arends D, Bonder MJ, Fu J, Deelen P, Groen HJ, Smolonska A, Weersma RK, Hofstra RM, Buurman WA, Rensen S, Wolfs MG, Platteel M, Zhernakova A, Elbers CC, Festen EM, Trynka G, Hofker MH, Saris CG, Ophoff RA, van den Berg LH, van Heel DA, Wijmenga C, Te Meerman GJ, Franke L.

PLoS Genet. 2011 Aug;7(8):e1002197. doi: 10.1371/journal.pgen.1002197. Epub 2011 Aug 4.

34.

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects.

Westra HJ, Jansen RC, Fehrmann RS, te Meerman GJ, van Heel D, Wijmenga C, Franke L.

Bioinformatics. 2011 Aug 1;27(15):2104-11. doi: 10.1093/bioinformatics/btr323. Epub 2011 Jun 7.

PMID:
21653519
35.

Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F.

Genetics. 2011 Aug;188(4):1015-7. doi: 10.1534/genetics.111.128744. Epub 2011 May 19.

36.

RNAi-induced off-target effects in Drosophila melanogaster: frequencies and solutions.

Seinen E, Burgerhof JG, Jansen RC, Sibon OC.

Brief Funct Genomics. 2011 Jul;10(4):206-14. doi: 10.1093/bfgp/elr017. Epub 2011 May 19.

PMID:
21596801
37.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R.

Anal Chem. 2011 Apr 1;83(7):2786-93. doi: 10.1021/ac2000994. Epub 2011 Mar 14.

PMID:
21401061
38.

Big data, but are we ready?

Trelles O, Prins P, Snir M, Jansen RC.

Nat Rev Genet. 2011 Mar;12(3):224. doi: 10.1038/nrg2857-c1. Epub 2011 Feb 8. No abstract available.

PMID:
21301471
39.

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.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12. doi: 10.1186/1471-2105-11-S12-S12.

40.

Simple data-reduction method for high-resolution LC-MS data in metabolomics.

Scheltema R, Decuypere S, Dujardin J, Watson D, Jansen R, Breitling R.

Bioanalysis. 2009 Dec;1(9):1551-7. doi: 10.4155/bio.09.146.

PMID:
21083103
41.

R/qtl: high-throughput multiple QTL mapping.

Arends D, Prins P, Jansen RC, Broman KW.

Bioinformatics. 2010 Dec 1;26(23):2990-2. doi: 10.1093/bioinformatics/btq565. Epub 2010 Oct 21.

42.

RNAi experiments in D. melanogaster: solutions to the overlooked problem of off-targets shared by independent dsRNAs.

Seinen E, Burgerhof JG, Jansen RC, Sibon OC.

PLoS One. 2010 Oct 1;5(10). pii: e13119. doi: 10.1371/journal.pone.0013119.

43.

Critical reasoning on causal inference in genome-wide linkage and association studies.

Li Y, Tesson BM, Churchill GA, Jansen RC.

Trends Genet. 2010 Dec;26(12):493-8. doi: 10.1016/j.tig.2010.09.002. Epub 2010 Oct 15.

44.

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules.

Tesson BM, Breitling R, Jansen RC.

BMC Bioinformatics. 2010 Oct 6;11:497. doi: 10.1186/1471-2105-11-497.

45.

SYSGENET: a meeting report from a new European network for systems genetics.

Schughart K; SYSGENET consortium.

Mamm Genome. 2010 Aug;21(7-8):331-6. doi: 10.1007/s00335-010-9273-7. Epub 2010 Jul 11.

46.

Global genetic robustness of the alternative splicing machinery in Caenorhabditis elegans.

Li Y, Breitling R, Snoek LB, van der Velde KJ, Swertz MA, Riksen J, Jansen RC, Kammenga JE.

Genetics. 2010 Sep;186(1):405-10. doi: 10.1534/genetics.110.119677. Epub 2010 Jul 6.

47.

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor.

Alam MT, Merlo ME; STREAM Consortium, Hodgson DA, Wellington EM, Takano E, Breitling R.

BMC Genomics. 2010 Mar 26;11:202. doi: 10.1186/1471-2164-11-202.

48.

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE; Coordination of Mouse Informatics Resources (CASIMIR); Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.

Genome Biol. 2010;11(3):R27. doi: 10.1186/gb-2010-11-3-r27. Epub 2010 Mar 9.

49.

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.

Bioinformatics. 2010 Apr 15;26(8):1000-6. doi: 10.1093/bioinformatics/btq087. Epub 2010 Mar 5.

PMID:
20208068
50.

The dynamic architecture of the metabolic switch in Streptomyces coelicolor.

Nieselt K, Battke F, Herbig A, Bruheim P, Wentzel A, Jakobsen ØM, Sletta H, Alam MT, Merlo ME, Moore J, Omara WA, Morrissey ER, Juarez-Hermosillo MA, Rodríguez-García A, Nentwich M, Thomas L, Iqbal M, Legaie R, Gaze WH, Challis GL, Jansen RC, Dijkhuizen L, Rand DA, Wild DL, Bonin M, Reuther J, Wohlleben W, Smith MC, Burroughs NJ, Martín JF, Hodgson DA, Takano E, Breitling R, Ellingsen TE, Wellington EM.

BMC Genomics. 2010 Jan 6;11:10. doi: 10.1186/1471-2164-11-10.

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