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polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.

Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C.

Bioinformatics. 2019 Feb 1;35(3):540. doi: 10.1093/bioinformatics/bty1002. No abstract available.


Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose.

Bourke PM, Gitonga VW, Voorrips RE, Visser RGF, Krens FA, Maliepaard C.

Theor Appl Genet. 2018 Oct;131(10):2055-2069. doi: 10.1007/s00122-018-3132-4. Epub 2018 Jun 30.


A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.

Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F.

Nat Plants. 2018 Jul;4(7):473-484. doi: 10.1038/s41477-018-0166-1. Epub 2018 Jun 11.


TriPoly: haplotype estimation for polyploids using sequencing data of related individuals.

Motazedi E, de Ridder D, Finkers R, Baldwin S, Thomson S, Monaghan K, Maliepaard C.

Bioinformatics. 2018 Nov 15;34(22):3864-3872. doi: 10.1093/bioinformatics/bty442.


polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.

Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C.

Bioinformatics. 2018 Oct 15;34(20):3496-3502. doi: 10.1093/bioinformatics/bty371.


Tools for Genetic Studies in Experimental Populations of Polyploids.

Bourke PM, Voorrips RE, Visser RGF, Maliepaard C.

Front Plant Sci. 2018 Apr 18;9:513. doi: 10.3389/fpls.2018.00513. eCollection 2018. Review.


Genetical genomics of quality related traits in potato tubers using proteomics.

Acharjee A, Chibon PY, Kloosterman B, America T, Renaut J, Maliepaard C, Visser RGF.

BMC Plant Biol. 2018 Jan 23;18(1):20. doi: 10.1186/s12870-018-1229-1.


An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis.

van Geest G, Bourke PM, Voorrips RE, Marasek-Ciolakowska A, Liao Y, Post A, van Meeteren U, Visser RGF, Maliepaard C, Arens P.

Theor Appl Genet. 2017 Dec;130(12):2527-2541. doi: 10.1007/s00122-017-2974-5. Epub 2017 Aug 29.


Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels.

van der Weijde T, Kamei CLA, Severing EI, Torres AF, Gomez LD, Dolstra O, Maliepaard CA, McQueen-Mason SJ, Visser RGF, Trindade LM.

BMC Genomics. 2017 May 25;18(1):406. doi: 10.1186/s12864-017-3802-7.


Partial preferential chromosome pairing is genotype dependent in tetraploid rose.

Bourke PM, Arens P, Voorrips RE, Esselink GD, Koning-Boucoiran CF, Van't Westende WP, Santos Leonardo T, Wissink P, Zheng C, van Geest G, Visser RG, Krens FA, Smulders MJ, Maliepaard C.

Plant J. 2017 Apr;90(2):330-343. doi: 10.1111/tpj.13496. Epub 2017 Mar 20. Erratum in: Plant J. 2019 Feb;97(3):616.


Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study.

Motazedi E, Finkers R, Maliepaard C, de Ridder D.

Brief Bioinform. 2018 May 1;19(3):387-403. doi: 10.1093/bib/bbw126.


High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array.

Vukosavljev M, Arens P, Voorrips RE, van 't Westende WP, Esselink GD, Bourke PM, Cox P, van de Weg WE, Visser RG, Maliepaard C, Smulders MJ.

Hortic Res. 2016 Oct 26;3:16052. eCollection 2016.


Inheritance and QTL analysis of the determinants of flower color in tetraploid cut roses.

Gitonga VW, Stolker R, Koning-Boucoiran CF, Aelaei M, Visser RG, Maliepaard C, Krens FA.

Mol Breed. 2016;36(10):143. Epub 2016 Oct 7.


Integrating haplotype-specific linkage maps in tetraploid species using SNP markers.

Bourke PM, Voorrips RE, Kranenburg T, Jansen J, Visser RG, Maliepaard C.

Theor Appl Genet. 2016 Nov;129(11):2211-2226. Epub 2016 Aug 25.


Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms).

Gao W, Baars JJP, Maliepaard C, Visser RGF, Zhang J, Sonnenberg ASM.

AMB Express. 2016 Dec;6(1):67. doi: 10.1186/s13568-016-0239-3. Epub 2016 Sep 8.


Systems genetics reveals key genetic elements of drought induced gene regulation in diploid potato.

van Muijen D, Anithakumari AM, Maliepaard C, Visser RG, van der Linden CG.

Plant Cell Environ. 2016 Sep;39(9):1895-908. doi: 10.1111/pce.12744. Epub 2016 Jun 29.


Integration of multi-omics data for prediction of phenotypic traits using random forest.

Acharjee A, Kloosterman B, Visser RG, Maliepaard C.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:180. doi: 10.1186/s12859-016-1043-4.


Genetic Control of Water and Nitrate Capture and Their Use Efficiency in Lettuce (Lactuca sativa L.).

Kerbiriou PJ, Maliepaard CA, Stomph TJ, Koper M, Froissart D, Roobeek I, Lammerts Van Bueren ET, Struik PC.

Front Plant Sci. 2016 Mar 30;7:343. doi: 10.3389/fpls.2016.00343. eCollection 2016.


Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions.

Basnet RK, Duwal A, Tiwari DN, Xiao D, Monakhos S, Bucher J, Visser RG, Groot SP, Bonnema G, Maliepaard C.

Front Plant Sci. 2015 Dec 1;6:1032. doi: 10.3389/fpls.2015.01032. eCollection 2015.


A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed.

Basnet RK, Del Carpio DP, Xiao D, Bucher J, Jin M, Boyle K, Fobert P, Visser RG, Maliepaard C, Bonnema G.

Plant Physiol. 2016 Jan;170(1):568-85. doi: 10.1104/pp.15.00853. Epub 2015 Oct 30.


The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map.

Bourke PM, Voorrips RE, Visser RG, Maliepaard C.

Genetics. 2015 Nov;201(3):853-63. doi: 10.1534/genetics.115.181008. Epub 2015 Sep 15. Erratum in: Genetics. 2016 May;203(1):611.


Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).

Koning-Boucoiran CF, Esselink GD, Vukosavljev M, van 't Westende WP, Gitonga VW, Krens FA, Voorrips RE, van de Weg WE, Schulz D, Debener T, Maliepaard C, Arens P, Smulders MJ.

Front Plant Sci. 2015 Apr 21;6:249. doi: 10.3389/fpls.2015.00249. eCollection 2015.


Genetic variation, heritability and genotype by environment interaction of morphological traits in a tetraploid rose population.

Gitonga VW, Koning-Boucoiran CF, Verlinden K, Dolstra O, Visser RG, Maliepaard C, Krens FA.

BMC Genet. 2014 Dec 20;15:146. doi: 10.1186/s12863-014-0146-z.


A metabolomics approach to identify factors influencing glucosinolate thermal degradation rates in Brassica vegetables.

Hennig K, de Vos RC, Maliepaard C, Dekker M, Verkerk R, Bonnema G.

Food Chem. 2014 Jul 15;155:287-97. doi: 10.1016/j.foodchem.2014.01.062. Epub 2014 Jan 31.


Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.

Basnet RK, Moreno-Pachon N, Lin K, Bucher J, Visser RG, Maliepaard C, Bonnema G.

BMC Genomics. 2013 Dec 1;14:840. doi: 10.1186/1471-2164-14-840.


Capturing flavors from Capsicum baccatum by introgression in sweet pepper.

Eggink PM, Tikunov Y, Maliepaard C, Haanstra JP, de Rooij H, Vogelaar A, Gutteling EW, Freymark G, Bovy AG, Visser RG.

Theor Appl Genet. 2014 Feb;127(2):373-90. doi: 10.1007/s00122-013-2225-3. Epub 2013 Nov 2.


Relation between HLA genes, human skin volatiles and attractiveness of humans to malaria mosquitoes.

Verhulst NO, Beijleveld H, Qiu YT, Maliepaard C, Verduyn W, Haasnoot GW, Claas FH, Mumm R, Bouwmeester HJ, Takken W, van Loon JJ, Smallegange RC.

Infect Genet Evol. 2013 Aug;18:87-93. doi: 10.1016/j.meegid.2013.05.009. Epub 2013 May 18.


Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis.

Karlova R, van Haarst JC, Maliepaard C, van de Geest H, Bovy AG, Lammers M, Angenent GC, de Maagd RA.

J Exp Bot. 2013 Apr;64(7):1863-78. doi: 10.1093/jxb/ert049. Epub 2013 Mar 13.


The simulation of meiosis in diploid and tetraploid organisms using various genetic models.

Voorrips RE, Maliepaard CA.

BMC Bioinformatics. 2012 Sep 26;13:248. doi: 10.1186/1471-2105-13-248.


A taste of sweet pepper: Volatile and non-volatile chemical composition of fresh sweet pepper (Capsicum annuum) in relation to sensory evaluation of taste.

Eggink PM, Maliepaard C, Tikunov Y, Haanstra JP, Bovy AG, Visser RG.

Food Chem. 2012 May 1;132(1):301-10. doi: 10.1016/j.foodchem.2011.10.081. Epub 2011 Oct 31.


The mode of inheritance in tetraploid cut roses.

Koning-Boucoiran CF, Gitonga VW, Yan Z, Dolstra O, van der Linden CG, van der Schoot J, Uenk GE, Verlinden K, Smulders MJ, Krens FA, Maliepaard C.

Theor Appl Genet. 2012 Aug;125(3):591-607. doi: 10.1007/s00122-012-1855-1. Epub 2012 Apr 12.


Untargeted metabolic quantitative trait loci analyses reveal a relationship between primary metabolism and potato tuber quality.

Carreno-Quintero N, Acharjee A, Maliepaard C, Bachem CW, Mumm R, Bouwmeester H, Visser RG, Keurentjes JJ.

Plant Physiol. 2012 Mar;158(3):1306-18. doi: 10.1104/pp.111.188441. Epub 2012 Jan 5.


Composition of human skin microbiota affects attractiveness to malaria mosquitoes.

Verhulst NO, Qiu YT, Beijleveld H, Maliepaard C, Knights D, Schulz S, Berg-Lyons D, Lauber CL, Verduijn W, Haasnoot GW, Mumm R, Bouwmeester HJ, Claas FH, Dicke M, van Loon JJ, Takken W, Knight R, Smallegange RC.

PLoS One. 2011;6(12):e28991. doi: 10.1371/journal.pone.0028991. Epub 2011 Dec 28.


Data integration and network reconstruction with ~omics data using Random Forest regression in potato.

Acharjee A, Kloosterman B, de Vos RC, Werij JS, Bachem CW, Visser RG, Maliepaard C.

Anal Chim Acta. 2011 Oct 31;705(1-2):56-63. doi: 10.1016/j.aca.2011.03.050. Epub 2011 Apr 13.


Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Goodwin SB, M'barek SB, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canché B, Churchill AC, Conde-Ferràez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH.

PLoS Genet. 2011 Jun;7(6):e1002070. doi: 10.1371/journal.pgen.1002070. Epub 2011 Jun 9.


Comparative methods for association studies: a case study on metabolite variation in a Brassica rapa core collection.

Pino Del Carpio D, Basnet RK, De Vos RC, Maliepaard C, Paulo MJ, Bonnema G.

PLoS One. 2011;6(5):e19624. doi: 10.1371/journal.pone.0019624. Epub 2011 May 13.


The patterns of population differentiation in a Brassica rapa core collection.

Pino Del Carpio D, Basnet RK, De Vos RC, Maliepaard C, Visser R, Bonnema G.

Theor Appl Genet. 2011 Apr;122(6):1105-18. doi: 10.1007/s00122-010-1516-1. Epub 2010 Dec 31.


QTLMAS 2009: simulated dataset.

Coster A, Bastiaansen JW, Calus MP, Maliepaard C, Bink MC.

BMC Proc. 2010 Mar 31;4 Suppl 1:S3. doi: 10.1186/1753-6561-4-S1-S3.


Comparison of analyses of the QTLMAS XIII common dataset. II: QTL analysis.

Maliepaard C, Bastiaansen JW, Calus MP, Coster A, Bink MC.

BMC Proc. 2010 Mar 31;4 Suppl 1:S2.


Comparison of analyses of the QTLMAS XIII common dataset. I: genomic selection.

Bastiaansen JW, Bink MC, Coster A, Maliepaard C, Calus MP.

BMC Proc. 2010 Mar 31;4 Suppl 1:S1.


Phytophthora infestans isolates lacking class I ipiO variants are virulent on Rpi-blb1 potato.

Champouret N, Bouwmeester K, Rietman H, van der Lee T, Maliepaard C, Heupink A, van de Vondervoort PJ, Jacobsen E, Visser RG, van der Vossen EA, Govers F, Vleeshouwers VG.

Mol Plant Microbe Interact. 2009 Dec;22(12):1535-45. doi: 10.1094/MPMI-22-12-1535.


BABY BOOM target genes provide diverse entry points into cell proliferation and cell growth pathways.

Passarinho P, Ketelaar T, Xing M, van Arkel J, Maliepaard C, Hendriks MW, Joosen R, Lammers M, Herdies L, den Boer B, van der Geest L, Boutilier K.

Plant Mol Biol. 2008 Oct;68(3):225-37. doi: 10.1007/s11103-008-9364-y. Epub 2008 Jul 29.


Buthionine sulfoximine (BSO)-mediated improvement in cultured embryo quality in vitro entails changes in ascorbate metabolism, meristem development and embryo maturation.

Stasolla C, Belmonte MF, Tahir M, Elhiti M, Khamiss K, Joosen R, Maliepaard C, Sharpe A, Gjetvaj B, Boutilier K.

Planta. 2008 Jul;228(2):255-72. doi: 10.1007/s00425-008-0735-z. Epub 2008 May 6.


Estrogenic effects in the immature rat uterus after dietary exposure to ethinylestradiol and zearalenone using a systems biology approach.

Heneweer M, Houtman R, Poortman J, Groot M, Maliepaard C, Peijnenburg A.

Toxicol Sci. 2007 Sep;99(1):303-14. Epub 2007 Jun 8.


Combined transcriptome and proteome analysis identifies pathways and markers associated with the establishment of rapeseed microspore-derived embryo development.

Joosen R, Cordewener J, Supena ED, Vorst O, Lammers M, Maliepaard C, Zeilmaker T, Miki B, America T, Custers J, Boutilier K.

Plant Physiol. 2007 May;144(1):155-72. Epub 2007 Mar 23.


Integrated statistical analysis of cDNA microarray and NIR spectroscopic data applied to a hemp dataset.

Reijmers TH, Maliepaard C, van den Broeck HC, Kessler RW, Toonen MA, van der Voet H.

J Bioinform Comput Biol. 2005 Aug;3(4):891-913.


Gene expression programs during Brassica oleracea seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level.

Soeda Y, Konings MC, Vorst O, van Houwelingen AM, Stoopen GM, Maliepaard CA, Kodde J, Bino RJ, Groot SP, van der Geest AH.

Plant Physiol. 2005 Jan;137(1):354-68. Epub 2004 Dec 23.


Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry.

Aharoni A, Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R, Goodenowe DB.

OMICS. 2002;6(3):217-34.


Quantitative assessment of the presence of a single leg separation in Björk-Shiley convexoconcave prosthetic heart valves.

Vrooman HA, Maliepaard C, van der Linden LP, Jessurun ER, Ludwig JW, Plokker HW, Schalij MJ, Weeda HW, Laufer JL, Huysmans HA, Reiber JH.

Invest Radiol. 1997 Sep;32(9):540-9.


On-line automated border detection for echocardiographic quantification of right ventricular size and function in children.

Helbing WA, Bosch HG, Maliepaard C, Zwinderman KH, Rebergen SA, Ottenkamp J, de Roos A, Reiber JH.

Pediatr Cardiol. 1997 Jul-Aug;18(4):261-9.


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