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Cholesterol Sulfotransferase SULT2B1b Modulates Sensitivity to Death Receptor Ligand TNFα in Castration-Resistant Prostate Cancer.

Vickman RE, Yang J, Lanman NA, Cresswell GM, Zheng F, Zhang C, Doerge RW, Crist SA, Mesecar AD, Hu CD, Ratliff TL.

Mol Cancer Res. 2019 Jun;17(6):1253-1263. doi: 10.1158/1541-7786.MCR-18-1054. Epub 2019 Mar 1.


Multiple testing with discrete data: Proportion of true null hypotheses and two adaptive FDR procedures.

Chen X, Doerge RW, Heyse JF.

Biom J. 2018 Jul;60(4):761-779. doi: 10.1002/bimj.201700157. Epub 2018 May 11.


Novel Resampling Improves Statistical Power for Multiple-Trait QTL Mapping.

Cheng R, Doerge RW, Borevitz J.

G3 (Bethesda). 2017 Mar 10;7(3):813-822. doi: 10.1534/g3.116.037531.


Environmental Regulation of Heterosis in the Allopolyploid Arabidopsis suecica.

Solhaug EM, Ihinger J, Jost M, Gamboa V, Marchant B, Bradford D, Doerge RW, Tyagi A, Replogle A, Madlung A.

Plant Physiol. 2016 Apr;170(4):2251-63. doi: 10.1104/pp.16.00052. Epub 2016 Feb 19.


Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank.

Pardo I, Lillemoe HA, Blosser RJ, Choi M, Sauder CA, Doxey DK, Mathieson T, Hancock BA, Baptiste D, Atale R, Hickenbotham M, Zhu J, Glasscock J, Storniolo AM, Zheng F, Doerge RW, Liu Y, Badve S, Radovich M, Clare SE; Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center.

Breast Cancer Res. 2014 Mar 17;16(2):R26. doi: 10.1186/bcr3627.


MAGI: Methylation analysis using genome information.

Baumann DD, Doerge RW.

Epigenetics. 2014 May;9(5):698-703. doi: 10.4161/epi.28322. Epub 2014 Mar 31.


Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics.

Lin F, Zhao M, Baumann DD, Ping J, Sun L, Liu Y, Zhang B, Tang Z, Hughes E, Doerge RW, Hughes TJ, Ma J.

BMC Genomics. 2014 Jan 10;15:18. doi: 10.1186/1471-2164-15-18.


Cytokinins secreted by Agrobacterium promote transformation by repressing a plant myb transcription factor.

Sardesai N, Lee LY, Chen H, Yi H, Olbricht GR, Stirnberg A, Jeffries J, Xiong K, Doerge RW, Gelvin SB.

Sci Signal. 2013 Nov 19;6(302):ra100. doi: 10.1126/scisignal.2004518.


Robust adjustment of sequence tag abundance.

Baumann DD, Doerge RW.

Bioinformatics. 2014 Mar 1;30(5):601-5. doi: 10.1093/bioinformatics/btt575. Epub 2013 Oct 9.


Selecting informative traits for multivariate quantitative trait locus mapping helps to gain optimal power.

Cheng R, Borevitz J, Doerge RW.

Genetics. 2013 Nov;195(3):683-91. doi: 10.1534/genetics.113.155937. Epub 2013 Aug 26.


Non-trisomic homeobox gene expression during craniofacial development in the Ts65Dn mouse model of Down syndrome.

Billingsley CN, Allen JR, Baumann DD, Deitz SL, Blazek JD, Newbauer A, Darrah A, Long BC, Young B, Clement M, Doerge RW, Roper RJ.

Am J Med Genet A. 2013 Aug;161A(8):1866-74. doi: 10.1002/ajmg.a.36006. Epub 2013 Jul 10.


The fate of duplicated genes in a polyploid plant genome.

Roulin A, Auer PL, Libault M, Schlueter J, Farmer A, May G, Stacey G, Doerge RW, Jackson SA.

Plant J. 2013 Jan;73(1):143-53. doi: 10.1111/tpj.12026. Epub 2012 Oct 22.


Differential expression--the next generation and beyond.

Auer PL, Srivastava S, Doerge RW.

Brief Funct Genomics. 2012 Jan;11(1):57-62. doi: 10.1093/bfgp/elr041. Epub 2011 Dec 30. Review.


Dynamic clustering of gene expression.

An L, Doerge RW.

ISRN Bioinform. 2012 Oct 16;2012:537217. doi: 10.5402/2012/537217. eCollection 2012.


A semi-nonparametric mixture model for selecting functionally consistent proteins.

Yu L, Doerge R.

BMC Bioinformatics. 2010 Sep 28;11:486. doi: 10.1186/1471-2105-11-486.


The nonsense-mediated decay pathway maintains synapse architecture and synaptic vesicle cycle efficacy.

Long AA, Mahapatra CT, Woodruff EA 3rd, Rohrbough J, Leung HT, Shino S, An L, Doerge RW, Metzstein MM, Pak WL, Broadie K.

J Cell Sci. 2010 Oct 1;123(Pt 19):3303-15. doi: 10.1242/jcs.069468. Epub 2010 Sep 7.


Statistical design and analysis of RNA sequencing data.

Auer PL, Doerge RW.

Genetics. 2010 Jun;185(2):405-16. doi: 10.1534/genetics.110.114983. Epub 2010 May 3.


Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling.

Pignatta D, Dilkes BP, Yoo SY, Henry IM, Madlung A, Doerge RW, Jeffrey Chen Z, Comai L.

New Phytol. 2010 Apr;186(1):194-206. doi: 10.1111/j.1469-8137.2010.03198.x.


An empirical Bayesian method for estimating biological networks from temporal microarray data.

Rau A, Jaffrézic F, Foulley JL, Doerge RW.

Stat Appl Genet Mol Biol. 2010;9:Article 9. doi: 10.2202/1544-6115.1513. Epub 2010 Jan 15.


The KM-Algorithm Identifies Regulated Genes in Time Series Expression Data.

Bremer M, Doerge RW.

Adv Bioinformatics. 2009:284251. doi: 10.1155/2009/284251. Epub 2009 Oct 7.


Gene expression analysis at the intersection of ploidy and hybridity in maize.

Riddle NC, Jiang H, An L, Doerge RW, Birchler JA.

Theor Appl Genet. 2010 Jan;120(2):341-53. doi: 10.1007/s00122-009-1113-3.


Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays.

Gaeta RT, Yoo SY, Pires JC, Doerge RW, Chen ZJ, Osborn TC.

PLoS One. 2009;4(3):e4760. doi: 10.1371/journal.pone.0004760. Epub 2009 Mar 10.


Epigenomic consequences of immortalized plant cell suspension culture.

Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA.

PLoS Biol. 2008 Dec 9;6(12):2880-95. doi: 10.1371/journal.pbio.0060302.


Moving AHEAD with an international human epigenome project.

American Association for Cancer Research Human Epigenome Task Force; European Union, Network of Excellence, Scientific Advisory Board.

Nature. 2008 Aug 7;454(7205):711-5. doi: 10.1038/454711a. No abstract available.


Meta-analysis combines affymetrix microarray results across laboratories.

Stevens JR, Doerge RW.

Comp Funct Genomics. 2005;6(3):116-22. doi: 10.1002/cfg.460.


DAG lipase activity is necessary for TRP channel regulation in Drosophila photoreceptors.

Leung HT, Tseng-Crank J, Kim E, Mahapatra C, Shino S, Zhou Y, An L, Doerge RW, Pak WL.

Neuron. 2008 Jun 26;58(6):884-96. doi: 10.1016/j.neuron.2008.05.001.


Presynaptic calcium channel localization and calcium-dependent synaptic vesicle exocytosis regulated by the Fuseless protein.

Long AA, Kim E, Leung HT, Woodruff E 3rd, An L, Doerge RW, Pak WL, Broadie K.

J Neurosci. 2008 Apr 2;28(14):3668-82. doi: 10.1523/JNEUROSCI.5553-07.2008.


Extending the modified bayesian information criterion (mBIC) to dense markers and multiple interval mapping.

Bogdan M, Frommlet F, Biecek P, Cheng R, Ghosh JK, Doerge RW.

Biometrics. 2008 Dec;64(4):1162-9. doi: 10.1111/j.1541-0420.2008.00989.x. Epub 2008 Feb 11.


Naive application of permutation testing leads to inflated type I error rates.

Churchill GA, Doerge RW.

Genetics. 2008 Jan;178(1):609-10. doi: 10.1534/genetics.107.074609.


Estimating the proportion of true null hypotheses for multiple comparisons.

Jiang H, Doerge RW.

Cancer Inform. 2008;6:25-32. Epub 2008 Feb 14.


Identification of novel high-frequency DNA methylation changes in breast cancer.

Ordway JM, Budiman MA, Korshunova Y, Maloney RK, Bedell JA, Citek RW, Bacher B, Peterson S, Rohlfing T, Hall J, Brown R, Lakey N, Doerge RW, Martienssen RA, Leon J, McPherson JD, Jeddeloh JA.

PLoS One. 2007 Dec 19;2(12):e1314.


The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects.

Jeffrey Chen Z, Wang J, Tian L, Lee HS, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B, Lippman Z, Vaughn M, Chris Pires J, Colot V, Doerge RW, Martienssen RA, Comai L, Osborn TC.

Biol J Linn Soc Lond. 2004 Aug;82(4):689-700.


Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus.

Zhao J, Wang J, An L, Doerge RW, Chen ZJ, Grau CR, Meng J, Osborn TC.

Planta. 2007 Dec;227(1):13-24. Epub 2007 Jul 31.


Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid.

van Leeuwen H, Kliebenstein DJ, West MA, Kim K, van Poecke R, Katagiri F, Michelmore RW, Doerge RW, St Clair DA.

Plant Cell. 2007 Jul;19(7):2099-110. Epub 2007 Jul 13.


Epigenetic natural variation in Arabidopsis thaliana.

Vaughn MW, Tanurdzić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW, Martienssen RA.

PLoS Biol. 2007 Jul;5(7):e174. Epub 2007 Jun 19.


A two-step multiple comparison procedure for a large number of tests and multiple treatments.

Jiang H, Doerge RW.

Stat Appl Genet Mol Biol. 2006;5:Article28. Epub 2006 Dec 18.


Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis.

West MA, Kim K, Kliebenstein DJ, van Leeuwen H, Michelmore RW, Doerge RW, St Clair DA.

Genetics. 2007 Mar;175(3):1441-50. Epub 2006 Dec 18.


Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species.

Lee HS, Wang J, Tian L, Jiang H, Black MA, Madlung A, Watson B, Lukens L, Pires JC, Wang JJ, Comai L, Osborn TC, Doerge RW, Chen ZJ.

Plant Biotechnol J. 2004 Jan;2(1):45-57.


Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets.

Ordway JM, Bedell JA, Citek RW, Nunberg A, Garrido A, Kendall R, Stevens JR, Cao D, Doerge RW, Korshunova Y, Holemon H, McPherson JD, Lakey N, Leon J, Martienssen RA, Jeddeloh JA.

Carcinogenesis. 2006 Dec;27(12):2409-23. Epub 2006 Sep 4.


Identification of QTLs controlling gene expression networks defined a priori.

Kliebenstein DJ, West MA, van Leeuwen H, Loudet O, Doerge RW, St Clair DA.

BMC Bioinformatics. 2006 Jun 16;7:308.


High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.

West MA, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW.

Genome Res. 2006 Jun;16(6):787-95. Epub 2006 May 15.


Genomic survey of gene expression diversity in Arabidopsis thaliana.

Kliebenstein DJ, West MA, van Leeuwen H, Kim K, Doerge RW, Michelmore RW, St Clair DA.

Genetics. 2006 Feb;172(2):1179-89. Epub 2005 Oct 3.


Genomewide nonadditive gene regulation in Arabidopsis allotetraploids.

Wang J, Tian L, Lee HS, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ.

Genetics. 2006 Jan;172(1):507-17. Epub 2005 Sep 19.


Adding confidence to gene expression clustering.

Munneke B, Schlauch KA, Simonsen KL, Beavis WD, Doerge RW.

Genetics. 2005 Aug;170(4):2003-11. Epub 2005 Jun 8.


Epigenomic mapping in Arabidopsis using tiling microarrays.

Martienssen RA, Doerge RW, Colot V.

Chromosome Res. 2005;13(3):299-308. Review.


Methods for genome-wide analysis of gene expression changes in polyploids.

Wang J, Lee JJ, Tian L, Lee HS, Chen M, Rao S, Wei EN, Doerge RW, Comai L, Chen ZJ.

Methods Enzymol. 2005;395:570-96.


Model selection in binary trait locus mapping.

Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte CK, Wolfinger RD, McIntyre LM.

Genetics. 2005 Jul;170(3):1281-97. Epub 2005 Apr 16.

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