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Items: 48

1.

Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System.

Wendt J, Rosenbaum H, Richmond TA, Jeddeloh JA, Burgess DL.

Methods Mol Biol. 2018;1708:383-405. doi: 10.1007/978-1-4939-7481-8_20.

PMID:
29224155
2.

Heritable L1 retrotransposition in the mouse primordial germline and early embryo.

Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH Jr, Ewing AD, Faulkner GJ.

Genome Res. 2017 Aug;27(8):1395-1405. doi: 10.1101/gr.219022.116. Epub 2017 May 8.

3.

The Arabidopsis thaliana mobilome and its impact at the species level.

Quadrana L, Bortolini Silveira A, Mayhew GF, LeBlanc C, Martienssen RA, Jeddeloh JA, Colot V.

Elife. 2016 Jun 3;5. pii: e15716. doi: 10.7554/eLife.15716.

4.

Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel.

Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS.

Plant J. 2015 Nov;84(3):587-96. doi: 10.1111/tpj.13029.

5.

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.

Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL; IWGS Consortium, Sharpe AG, Sidebottom CH, Hall N, Toomajian C, Close T, Dubcovsky J, Akhunova A, Talbert L, Bansal UK, Bariana HS, Hayden MJ, Pozniak C, Jeddeloh JA, Hall A, Akhunov E.

Genome Biol. 2015 Feb 26;16:48. doi: 10.1186/s13059-015-0606-4.

6.

Genetic perturbation of the maize methylome.

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM.

Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.

7.

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2014 Sep;79(6):993-1008. doi: 10.1111/tpj.12601. Epub 2014 Aug 11.

8.

An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse.

Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E.

Genome Biol. 2013;14(9):R96.

9.

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.

Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N.

Plant J. 2013 Nov;76(3):494-505. doi: 10.1111/tpj.12294. Epub 2013 Aug 24.

10.

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome.

Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N.

Genome Biol. 2013 Jun 12;14(6):R58. doi: 10.1186/gb-2013-14-6-r58.

11.

Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers.

Chaumeil J, Micsinai M, Ntziachristos P, Deriano L, Wang JM, Ji Y, Nora EP, Rodesch MJ, Jeddeloh JA, Aifantis I, Kluger Y, Schatz DG, Skok JA.

Cell Rep. 2013 Feb 21;3(2):359-70. doi: 10.1016/j.celrep.2013.01.024. Epub 2013 Feb 14.

12.

Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton.

Salmon A, Udall JA, Jeddeloh JA, Wendel J.

G3 (Bethesda). 2012 Aug;2(8):921-30. doi: 10.1534/g3.112.003392. Epub 2012 Aug 1.

13.

Changes in genome content generated via segregation of non-allelic homologs.

Liu S, Ying K, Yeh CT, Yang J, Swanson-Wagner R, Wu W, Richmond T, Gerhardt DJ, Lai J, Springer N, Nettleton D, Jeddeloh JA, Schnable PS.

Plant J. 2012 Nov;72(3):390-9. doi: 10.1111/j.1365-313X.2012.05087.x. Epub 2012 Aug 30.

14.

Targeted re-sequencing of the allohexaploid wheat exome.

Winfield MO, Wilkinson PA, Allen AM, Barker GL, Coghill JA, Burridge A, Hall A, Brenchley RC, D'Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ.

Plant Biotechnol J. 2012 Aug;10(6):733-42. doi: 10.1111/j.1467-7652.2012.00713.x. Epub 2012 Jun 18.

15.

Structural variants in the soybean genome localize to clusters of biotic stress-response genes.

McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM.

Plant Physiol. 2012 Aug;159(4):1295-308. doi: 10.1104/pp.112.194605. Epub 2012 Jun 13.

16.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL.

Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024.

17.

Somatic retrotransposition alters the genetic landscape of the human brain.

Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ.

Nature. 2011 Oct 30;479(7374):534-7. doi: 10.1038/nature10531.

18.

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis.

Boyle S, Rodesch MJ, Halvensleben HA, Jeddeloh JA, Bickmore WA.

Chromosome Res. 2011 Oct;19(7):901-9. doi: 10.1007/s10577-011-9245-0. Epub 2011 Oct 18.

19.

B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize.

Eichten SR, Foerster JM, de Leon N, Kai Y, Yeh CT, Liu S, Jeddeloh JA, Schnable PS, Kaeppler SM, Springer NM.

Plant Physiol. 2011 Aug;156(4):1679-90. doi: 10.1104/pp.111.174748. Epub 2011 Jun 24.

20.

Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean.

Bolon YT, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP.

Plant Physiol. 2011 May;156(1):240-53. doi: 10.1104/pp.110.170811. Epub 2011 Feb 14.

21.

The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82.

Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM.

Plant Physiol. 2011 Feb;155(2):645-55. doi: 10.1104/pp.110.166736. Epub 2010 Nov 29.

22.

Whole exome capture in solution with 3 Gbp of data.

Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, Jeddeloh JA, Muzny D, Albert TJ, Gibbs RA.

Genome Biol. 2010;11(6):R62. doi: 10.1186/gb-2010-11-6-r62. Epub 2010 Jun 17.

23.

Repeat subtraction-mediated sequence capture from a complex genome.

Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS.

Plant J. 2010 Jun 1;62(5):898-909. doi: 10.1111/j.1365-313X.2010.04196.x. Epub 2010 Mar 4.

24.

The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.

25.

Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content.

Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS.

PLoS Genet. 2009 Nov;5(11):e1000734. doi: 10.1371/journal.pgen.1000734. Epub 2009 Nov 20.

26.

A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

Parikh H, Deng Z, Yeager M, Boland J, Matthews C, Jia J, Collins I, White A, Burdett L, Hutchinson A, Qi L, Bacior JA, Lonsberry V, Rodesch MJ, Jeddeloh JA, Albert TJ, Halvensleben HA, Harkins TT, Ahn J, Berndt SI, Chatterjee N, Hoover R, Thomas G, Hunter DJ, Hayes RB, Chanock SJ, Amundadottir L.

Hum Genet. 2010 Jan;127(1):91-9. doi: 10.1007/s00439-009-0751-5. Epub 2009 Oct 13.

27.

Mutation discovery in the mouse using genetically guided array capture and resequencing.

D'Ascenzo M, Meacham C, Kitzman J, Middle C, Knight J, Winer R, Kukricar M, Richmond T, Albert TJ, Czechanski A, Donahue LR, Affourtit J, Jeddeloh JA, Reinholdt L.

Mamm Genome. 2009 Jul;20(7):424-36. doi: 10.1007/s00335-009-9200-y. Epub 2009 Jul 21.

28.

Reduced-representation methylation mapping.

Jeddeloh JA, Greally JM, Rando OJ.

Genome Biol. 2008;9(8):231. doi: 10.1186/gb-2008-9-8-231. Epub 2008 Sep 1. Review.

29.

Comprehensive high-throughput arrays for relative methylation (CHARM).

Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP.

Genome Res. 2008 May;18(5):780-90. doi: 10.1101/gr.7301508. Epub 2008 Mar 3.

30.

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.

31.

MethylScreen: DNA methylation density monitoring using quantitative PCR.

Holemon H, Korshunova Y, Ordway JM, Bedell JA, Citek RW, Lakey N, Leon J, Finney M, McPherson JD, Jeddeloh JA.

Biotechniques. 2007 Nov;43(5):683-93.

32.

Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA.

Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, Ordway JM, McCombie WR, Leon J, Jeddeloh JA, McPherson JD.

Genome Res. 2008 Jan;18(1):19-29. Epub 2007 Nov 21.

33.

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.

PMID:
16952911
34.

MethylMapper: a method for high-throughput, multilocus bisulfite sequence analysis and reporting.

Ordway JM, Bedell JA, Citek RW, Nunberg AN, Jeddeloh JA.

Biotechniques. 2005 Oct;39(4):464, 466, 468 passim. No abstract available.

35.

Sorghum genome sequencing by methylation filtration.

Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA.

PLoS Biol. 2005 Jan;3(1):e13. Epub 2005 Jan 4.

37.

Quorum sensing: a transcriptional regulatory system involved in the pathogenicity of Burkholderia mallei.

Ulrich RL, Deshazer D, Hines HB, Jeddeloh JA.

Infect Immun. 2004 Nov;72(11):6589-96.

38.

Role of quorum sensing in the pathogenicity of Burkholderia pseudomallei.

Ulrich RL, Deshazer D, Brueggemann EE, Hines HB, Oyston PC, Jeddeloh JA.

J Med Microbiol. 2004 Nov;53(Pt 11):1053-64.

PMID:
15496380
39.

Mutational analysis and biochemical characterization of the Burkholderia thailandensis DW503 quorum-sensing network.

Ulrich RL, Hines HB, Parthasarathy N, Jeddeloh JA.

J Bacteriol. 2004 Jul;186(13):4350-60.

40.

Arabidopsis MET1 cytosine methyltransferase mutants.

Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ.

Genetics. 2003 Mar;163(3):1109-22.

41.

Biodefense-driven murine model of pneumonic melioidosis.

Jeddeloh JA, Fritz DL, Waag DM, Hartings JM, Andrews GP.

Infect Immun. 2003 Jan;71(1):584-7.

42.

Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei.

Woods DE, Jeddeloh JA, Fritz DL, DeShazer D.

J Bacteriol. 2002 Jul;184(14):4003-17.

43.

Burkholderia pseudomallei kills the nematode Caenorhabditis elegans using an endotoxin-mediated paralysis.

O'Quinn AL, Wiegand EM, Jeddeloh JA.

Cell Microbiol. 2001 Jun;3(6):381-93.

PMID:
11422081
44.

Maintenance of genomic methylation requires a SWI2/SNF2-like protein.

Jeddeloh JA, Stokes TL, Richards EJ.

Nat Genet. 1999 May;22(1):94-7.

PMID:
10319870
45.

The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis.

Jeddeloh JA, Bender J, Richards EJ.

Genes Dev. 1998 Jun 1;12(11):1714-25.

46.

Developmental abnormalities and epimutations associated with DNA hypomethylation mutations.

Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ.

Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12406-11. Erratum in: Proc Natl Acad Sci U S A 2001 Jun 19;98(13):7647.

47.

mCCG methylation in angiosperms.

Jeddeloh JA, Richards EJ.

Plant J. 1996 May;9(5):579-86.

48.

Characterization of an Arabidopsis thaliana DNA hypomethylation mutant.

Kakutani T, Jeddeloh JA, Richards EJ.

Nucleic Acids Res. 1995 Jan 11;23(1):130-7.

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