PUB - Publikationen an der Universität Bielefeld

Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.
Ben-David S, Yaakov B, Kashkush K., Plant J. 76(2), 2013
PMID: 23855320

The contributions of transposable elements to the structure, function, and evolution of plant genomes
Bennetzen, Annu. Rev. Plant Biol. 65(), 2014

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE., Nature 452(7184), 2008
PMID: 18278030

Target DNA chromatinization modulates nicking by L1 endonuclease.
Cost GJ, Golding A, Schlissel MS, Boeke JD., Nucleic Acids Res. 29(2), 2001
PMID: 11139628

Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers.
Deragon JM, Zhang X., Syst. Biol. 55(6), 2006
PMID: 17345676

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H., Nature 505(7484), 2013
PMID: 24352233

MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res. 32(5), 2004
PMID: 15034147

A SINE family widely distributed in the plant kingdom and its evolutionary history.
Fawcett JA, Kawahara T, Watanabe H, Yasui Y., Plant Mol. Biol. 61(3), 2006
PMID: 16830182

Eukaryotic transposable elements and genome evolution.
Finnegan DJ., Trends Genet. 5(4), 1989
PMID: 2543105

Novel SINEs families in Medicago truncatula and Lotus japonicus: bioinformatic analysis.
Gadzalski M, Sakowicz T., Gene 480(1-2), 2011
PMID: 21352903

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.
Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, Dawe RK., Genome Res. 23(4), 2012
PMID: 23269663

Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons.
Gentles AJ, Kohany O, Jurka J., Mol. Biol. Evol. 22(10), 2005
PMID: 15944437

Activation of plant retrotransposons under stress conditions
Grandbastien, Trends Plant Sci. 3(), 1998

Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades.
Heitkam T, Holtgrawe D, Dohm JC, Minoche AE, Himmelbauer H, Weisshaar B, Schmidt T., Plant J. 79(3), 2014
PMID: 24862340

Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading.
Henderson IR, Jacobsen SE., Genes Dev. 22(12), 2008
PMID: 18559476

Understanding Mediterranean-Californian disjunctions: molecular evidence from Chenopodiaceae-Betoideae
Hohmann, Taxon 55(), 2006

Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression.
Hollister JD, Gaut BS., Genome Res. 19(8), 2009
PMID: 19478138

Active transposition in genomes.
Huang CR, Burns KH, Boeke JD., Annu. Rev. Genet. 46(), 2012
PMID: 23145912

Matplotlib: a 2D graphics environment
Hunter, Comput. Sci. Eng. 9(), 2007

The SRA methyl-cytosine-binding domain links DNA and histone methylation.
Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE., Curr. Biol. 17(4), 2007
PMID: 17239600

tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18957446

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A., Bioinformatics 28(12), 2012
PMID: 22543367

Mapping and analysis of the LINE and SINE type of repetitive elements in rice.
Khan MF, Yadav BS, Ahmad K, Jaitly AK., Bioinformation 7(6), 2011
PMID: 22355220

Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae).
Kolano B, Bednara E, Weiss-Schneeweiss H., Plant Cell Rep. 32(10), 2013
PMID: 23754338

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
Krueger F, Andrews SR., Bioinformatics 27(11), 2011
PMID: 21493656

Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium., Nature 409(6822), 2001
PMID: 11237011

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law JA, Jacobsen SE., Nat. Rev. Genet. 11(3), 2010
PMID: 20142834

The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana.
Lenoir A, Lavie L, Prieto JL, Goubely C, Cote JC, Pelissier T, Deragon JM., Mol. Biol. Evol. 18(12), 2001
PMID: 11719581

Epigenetic regulation of transposable elements in plants.
Lisch D., Annu Rev Plant Biol 60(), 2009
PMID: 19007329

How important are transposons for plant evolution?
Lisch D., Nat. Rev. Genet. 14(1), 2013
PMID: 23247435

Retrotransposon activation followed by rapid repression in introgressed rice plants.
Liu B, Wendel JF., Genome 43(5), 2000
PMID: 11081978

Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome.
Myouga F, Tsuchimoto S, Noma K, Ohtsubo H, Ohtsubo E., Genes Genet. Syst. 76(3), 2001
PMID: 11569500

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail.
Ohshima K, Okada N., Cytogenet. Genome Res. 110(1-4), 2005
PMID: 16093701

Transposable elements: powerful contributors to angiosperm evolution and diversity.
Oliver KR, McComb JA, Greene WK., Genome Biol Evol 5(10), 2013
PMID: 24065734

Jumping genes and epigenetics: Towards new species.
Rebollo R, Horard B, Hubert B, Vieira C., Gene 454(1-2), 2010
PMID: 20102733

Active Alu element "A-tails": size does matter.
Roy-Engel AM, Salem AH, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, Batzer MA, Deininger PL., Genome Res. 12(9), 2002
PMID: 12213770

Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics.
Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW., Proc. Natl. Acad. Sci. U.S.A. 81(24), 1984
PMID: 6096873

Sambrook, 1989

Physical mapping of rRNA genes by fluorescent in-situ hybridzation and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgaris).
Schmidt T, Schwarzacher T, Heslop-Harrison JS., Theor. Appl. Genet. 88(6/7), 1994
PMID: IND20435298

Transposable elements and the epigenetic regulation of the genome.
Slotkin RK, Martienssen R., Nat. Rev. Genet. 8(4), 2007
PMID: 17363976

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S., Mol. Biol. Evol. 24(8), 2007
PMID: 17488738

Repeat elements and the Arabidopsis DNA methylation landscape.
Teixeira FK, Colot V., Heredity (Edinb) 105(1), 2010
PMID: 20461104

MapChart: software for the graphical presentation of linkage maps and QTLs.
Voorrips RE., J. Hered. 93(1), 2002
PMID: 12011185

An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris.
Wenke T, Holtgrawe D, Horn AV, Weisshaar B, Schmidt T., Plant Mol. Biol. 71(6), 2009
PMID: 19697140

Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes.
Wenke T, Dobel T, Sorensen TR, Junghans H, Weisshaar B, Schmidt T., Plant Cell 23(9), 2011
PMID: 21908723

A unified classification system for eukaryotic transposable elements.
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH., Nat. Rev. Genet. 8(12), 2007
PMID: 17984973

The CHH motif in sugar beet satellite DNA: a modulator for cytosine methylation.
Zakrzewski F, Schubert V, Viehoever P, Minoche AE, Dohm JC, Himmelbauer H, Weisshaar B, Schmidt T., Plant J. 78(6), 2014
PMID: 24661787

BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.
Zhang X, Wessler SR., J. Mol. Evol. 60(5), 2005
PMID: 15983875

Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining.
Zingler N, Willhoeft U, Brose HP, Schoder V, Jahns T, Hanschmann KM, Morrish TA, Lower J, Schumann GG., Genome Res. 15(6), 2005
PMID: 15930490