29.
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1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
1001 Genomes Consortium
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28.
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Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping
Rowan B. A., Patel V., Weigel D. and Schneeberger K.
G3 (Bethesda)
(2015),
5(3) 385-398.

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27.
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Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage
Hagmann J., Becker C., Muller J., Stegle O., Meyer R. C., Wang G., Schneeberger K., Fitz J., Altmann T., Bergelson J., Borgwardt K. and Weigel D.
PLoS Genet
(2015),
11(1) e1004920.

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26.
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Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization
Seymour D. K., Koenig D., Hagmann J., Becker C. and Weigel D.
PLoS Genet
(2014),
10(11) e1004785.

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25.
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Trowel: a fast and accurate error correction module for Illumina sequencing reads
Lim E. C., Muller J., Hagmann J., Henz S. R., Kim S. T. and Weigel D.
Bioinformatics
(2014),
30(22) 3264-5.

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24.
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Accurate indel prediction using paired-end short reads
Grimm D., Hagmann J., Koenig D., Weigel D. and Borgwardt K.
BMC Genomics
(2013),
14 132.

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23.
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The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Slotte T., Hazzouri K. M., Agren J. A., Koenig D., Maumus F., Guo Y. L., Steige K., Platts A. E., Escobar J. S., Newman L. K., Wang W., Mandáková T., Vello E., Smith L. M., Henz S. R., Steffen J., Takuno S., Brandvain Y., Coop G., Andolfatto P., Hu T. T., Blanchette M., Clark R. M., Quesneville H., Nordborg M., Gaut B. S., Lysak M. A., Jenkins J., Grimwood J., Chapman J., Prochnik S., Shu S., Rokhsar D., Schmutz J., Weigel D. and Wright S. I.
Nat Genet
(2013),
45(7) 831-5.

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22.
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User guide for mapping-by-sequencing in Arabidopsis
James G. V., Patel V., Nordstrom K. J., Klasen J. R., Salome P. A., Weigel D. and Schneeberger K.
Genome Biol
(2013),
14(6) R61.

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21.
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Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1
Manavella P. A., Hagmann J., Ott F., Laubinger S., Franz M., Macek B. and Weigel D.
Cell
(2012),
151(4) 859-70.

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20.
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Synteny-based mapping-by-sequencing enabled by targeted enrichment
Galvao V. C., Nordstrom K. J., Lanz C., Sulz P., Mathieu J., Pose D., Schmid M., Weigel D. and Schneeberger K.
Plant J
(2012),
71(3) 517-26.

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19.
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Fast-forward genetics enabled by new sequencing technologies
Schneeberger K. and Weigel D.
Trends Plant Sci
(2011),
16(5) 282-8.

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18.
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Paired-end RAD-seq for de novo assembly and marker design without available reference
Willing E. M., Hoffmann M., Klein J. D., Weigel D. and Dreyer C.
Bioinformatics
(2011),
27(16) 2187-93.

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17.
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Reference-guided assembly of four diverse Arabidopsis thaliana genomes
Schneeberger K., Ossowski S., Ott F., Klein J. D., Wang X., Lanz C., Smith L. M., Cao J., Fitz J., Warthmann N., Henz S. R., Huson D. H. and Weigel D.
Proc Natl Acad Sci U S A
(2011),
108(25) 10249-54.

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16.
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Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K. and Weigel D.
Nature
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15.
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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
Hu T. T., Pattyn P., Bakker E. G., Cao J., Cheng J. F., Clark R. M., Fahlgren N., Fawcett J. A., Grimwood J., Gundlach H., Haberer G., Hollister J. D., Ossowski S., Ottilar R. P., Salamov A. A., Schneeberger K., Spannagl M., Wang X., Yang L., Nasrallah M. E., Bergelson J., Carrington J. C., Gaut B. S., Schmutz J., Mayer K. F., Van de Peer Y., Grigoriev I. V., Nordborg M., Weigel D. and Guo Y. L.
Nat Genet
(2011),
43(5) 476-81.

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14.
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Whole-genome sequencing of multiple Arabidopsis thaliana populations
Cao J., Schneeberger K., Ossowski S., Gunther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., Wang X., Ott F., Muller J., Alonso-Blanco C., Borgwardt K., Schmid K. J. and Weigel D.
Nat Genet
(2011),
43(10) 956-63.

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13.
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Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing
Laitinen R. A., Schneeberger K., Jelly N. S., Ossowski S. and Weigel D.
Plant Physiol
(2010),
153(2) 652-4.

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12.
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The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
Ossowski S., Schneeberger K., Lucas-Lledo J. I., Warthmann N., Clark R. M., Shaw R. G., Weigel D. and Lynch M.
Science
(2010),
327(5961) 92-4.

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11.
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SHOREmap: simultaneous mapping and mutation identification by deep sequencing
Schneeberger K., Ossowski S., Lanz C., Juul T., Petersen A. H., Nielsen K. L., Jorgensen J. E., Weigel D. and Andersen S. U.
Nat Methods
(2009),
6(8) 550-1.

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10.
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Simultaneous alignment of short reads against multiple genomes
Schneeberger K., Hagmann J., Ossowski S., Warthmann N., Gesing S., Kohlbacher O. and Weigel D.
Genome Biol
(2009),
10(9) R98.

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9.
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Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays
Zeller G., Henz S. R., Widmer C. K., Sachsenberg T., Ratsch G., Weigel D. and Laubinger S.
Plant J
(2009),
58(6) 1068-82.

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8.
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The 1001 genomes project for Arabidopsis thaliana
Weigel D. and Mott R.
Genome Biol
(2009),
10(5) 107.

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7.
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At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana
Laubinger S., Zeller G., Henz S. R., Sachsenberg T., Widmer C. K., Naouar N., Vuylsteke M., Scholkopf B., Ratsch G. and Weigel D.
Genome Biol
(2008),
9(7) R112.

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6.
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Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
Zeller G., Clark R. M., Schneeberger K., Bohlen A., Weigel D. and Ratsch G.
Genome Res
(2008),
18(6) 918-29.

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5.
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Sequencing of natural strains of Arabidopsis thaliana with short reads
Ossowski S., Schneeberger K., Clark R. M., Lanz C., Warthmann N. and Weigel D.
Genome Res
(2008),
18(12) 2024-33.

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4.
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Transcript normalization and segmentation of tiling array data
Zeller G., Henz S. R., Laubinger S., Weigel D. and Ratsch G.
Pac Symp Biocomput
(2008),
527-38.
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3.
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Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
Clark R. M., Schweikert G., Toomajian C., Ossowski S., Zeller G., Shinn P., Warthmann N., Hu T. T., Fu G., Hinds D. A., Chen H., Frazer K. A., Huson D. H., Scholkopf B., Nordborg M., Ratsch G., Ecker J. R. and Weigel D.
Science
(2007),
317(5836) 338-42.

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2.
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MSQT for choosing SNP assays from multiple DNA alignments
Warthmann N., Fitz J. and Weigel D.
Bioinformatics
(2007),
23(20) 2784-7.

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1.
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A gene expression map of Arabidopsis thaliana development
Schmid M., Davison T. S., Henz S. R., Pape U. J., Demar M., Vingron M., Scholkopf B., Weigel D. and Lohmann J. U.
Nat Genet
(2005),
37(5) 501-6.

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