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26
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. Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS One 2007;2:e1314. [PMID: 18091988 PMCID: PMC2117343 DOI: 10.1371/journal.pone.0001314] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 11/06/2007] [Indexed: 12/31/2022]  Open
27
Zhao J, Wang J, An L, Doerge RW, Chen ZJ, Grau CR, Meng J, Osborn TC. Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus. PLANTA 2007;227:13-24. [PMID: 17665211 DOI: 10.1007/s00425-007-0586-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Accepted: 07/05/2007] [Indexed: 05/16/2023]
28
van Leeuwen H, Kliebenstein DJ, West MAL, Kim K, van Poecke R, Katagiri F, Michelmore RW, Doerge RW, St Clair DA. Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid. THE PLANT CELL 2007;19:2099-110. [PMID: 17630278 PMCID: PMC1955704 DOI: 10.1105/tpc.107.050641] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
29
West MAL, Kim K, Kliebenstein DJ, van Leeuwen H, Michelmore RW, Doerge RW, St Clair DA. Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics 2007;175:1441-50. [PMID: 17179097 PMCID: PMC1840073 DOI: 10.1534/genetics.106.064972] [Citation(s) in RCA: 256] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Accepted: 12/01/2006] [Indexed: 01/09/2023]  Open
30
Jiang H, Doerge RW. A two-step multiple comparison procedure for a large number of tests and multiple treatments. Stat Appl Genet Mol Biol 2006;5:Article28. [PMID: 17402912 DOI: 10.2202/1544-6115.1223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
31
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. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 2006;27:2409-23. [PMID: 16952911 DOI: 10.1093/carcin/bgl161] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
32
Kliebenstein DJ, West MAL, van Leeuwen H, Loudet O, Doerge RW, St Clair DA. Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics 2006;7:308. [PMID: 16780591 PMCID: PMC1540440 DOI: 10.1186/1471-2105-7-308] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Accepted: 06/16/2006] [Indexed: 11/17/2022]  Open
33
West MAL, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW. High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res 2006;16:787-95. [PMID: 16702412 PMCID: PMC1473188 DOI: 10.1101/gr.5011206] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
34
Wang J, Tian L, Lee HS, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 2006;172:507-17. [PMID: 16172500 PMCID: PMC1456178 DOI: 10.1534/genetics.105.047894] [Citation(s) in RCA: 390] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 09/19/2005] [Indexed: 12/21/2022]  Open
35
Teuscher C, Doerge RW, Fillmore PD, Blankenhorn EP. eae36, a locus on mouse chromosome 4, controls susceptibility to experimental allergic encephalomyelitis in older mice and mice immunized in the winter. Genetics 2005;172:1147-53. [PMID: 16299394 PMCID: PMC1456213 DOI: 10.1534/genetics.105.049049] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
36
Kliebenstein DJ, West MAL, van Leeuwen H, Kim K, Doerge RW, Michelmore RW, St Clair DA. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics 2005;172:1179-89. [PMID: 16204207 PMCID: PMC1456216 DOI: 10.1534/genetics.105.049353] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
37
Bogdan M, Doerge RW. Biased estimators of quantitative trait locus heritability and location in interval mapping. Heredity (Edinb) 2005;95:476-84. [PMID: 16189542 DOI: 10.1038/sj.hdy.6800747] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
38
Martienssen RA, Doerge RW, Colot V. Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res 2005;13:299-308. [PMID: 15868423 DOI: 10.1007/s10577-005-1507-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
39
Munneke B, Schlauch KA, Simonsen KL, Beavis WD, Doerge RW. Adding confidence to gene expression clustering. Genetics 2005;170:2003-11. [PMID: 15944369 PMCID: PMC1449753 DOI: 10.1534/genetics.104.031500] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
40
Bradley KC, Boulware MB, Jiang H, Doerge RW, Meisel RL, Mermelstein PG. Changes in gene expression within the nucleus accumbens and striatum following sexual experience. GENES BRAIN AND BEHAVIOR 2005;4:31-44. [PMID: 15660666 DOI: 10.1111/j.1601-183x.2004.00093.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
41
Bogdan M, Ghosh JK, Doerge RW. Modifying the Schwarz Bayesian information criterion to locate multiple interacting quantitative trait loci. Genetics 2005;167:989-99. [PMID: 15238547 PMCID: PMC1470914 DOI: 10.1534/genetics.103.021683] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
42
Stevens JR, Doerge RW. Combining Affymetrix microarray results. BMC Bioinformatics 2005;6:57. [PMID: 15774008 PMCID: PMC1274254 DOI: 10.1186/1471-2105-6-57] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Accepted: 03/17/2005] [Indexed: 11/10/2022]  Open
43
Cao D, Craig BA, Doerge RW. A model selection-based interval-mapping method for autopolyploids. Genetics 2005;169:2371-82. [PMID: 15687274 PMCID: PMC1449588 DOI: 10.1534/genetics.104.035410] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
44
Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, Doerge RW, Martienssen R, Comai L. Genomic changes in synthetic Arabidopsis polyploids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005. [PMID: 15634199 DOI: 10.1111/j.1365-313x.2004.02297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
45
Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, Doerge RW, Martienssen R, Comai L. Genomic changes in synthetic Arabidopsis polyploids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005;41:221-30. [PMID: 15634199 DOI: 10.1111/j.1365-313x.2004.02297.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
46
Wang J, Lee JJ, Tian L, Lee HS, Chen M, Rao S, Wei EN, Doerge RW, Comai L, Chen ZJ. Methods for genome-wide analysis of gene expression changes in polyploids. Methods Enzymol 2005;395:570-96. [PMID: 15865985 PMCID: PMC1986650 DOI: 10.1016/s0076-6879(05)95030-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
47
Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O'Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpää MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FPM, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 2004;36:1133-7. [PMID: 15514660 DOI: 10.1038/ng1104-1133] [Citation(s) in RCA: 754] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
48
Tian L, Fong MP, Wang JJ, Wei NE, Jiang H, Doerge RW, Chen ZJ. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics 2004;169:337-45. [PMID: 15371352 PMCID: PMC1448893 DOI: 10.1534/genetics.104.033142] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
49
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. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol J Linn Soc Lond 2004;82:689-700. [PMID: 18079994 DOI: 10.1111/j.1095-8312.2004.00351.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
50
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004;430:471-6. [PMID: 15269773 DOI: 10.1038/nature02651] [Citation(s) in RCA: 822] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2004] [Accepted: 05/07/2004] [Indexed: 11/09/2022]
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