Genome Informatics


Group Interests

We use both phenotype-first and genotype-first approaches to understand how plants adapt to their environment. The most extensively investigated species remains Arabidopsis thaliana. To enable the rapid discovery of functionally relevant variation, we have spearheaded for almost a decade now, extensive genome sequencing using Illumina technology. The resulting 1001 Genomes Project for A. thaliana has been setting the stage for improved genome-wide association studies, but also revealed a much more fine-grained picture of the evolutionary past of the species. Because few computational tools were available when we started to use short read sequencing, we produced the SHORE pipeline for the analysis of such data. While the early focus was on re-sequencing, we are now focusing on assembling genomes de novo using both short and long-read technologies. This work is complemented by assembling high-quality genomes of related species for pan-genome analyses, as well as studies of spontaneous mutation rates and of epigenomic variation.

  • Intra- and interspecific genome and methylome variation
  • Graph-based methods for comparative sequence analyses
  • Resource and tool development for genomics

Collaboration Partners



1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

1001 Genomes Consortium
(2016), 166(2) 481-91.

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.

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), Jan 13.

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.

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.
(2014), 30(22) 3264-5.

Accurate indel prediction using paired-end short reads

Grimm D., Hagmann J., Koenig D., Weigel D. and Borgwardt K.
BMC Genomics
(2013), 14 132.

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.

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.

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.
(2012), 151(4) 859-70.

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.

Fast-forward genetics enabled by new sequencing technologies

Schneeberger K. and Weigel D.
Trends Plant Sci
(2011), 16(5) 282-8.

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.
(2011), 27(16) 2187-93.

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.

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K. and Weigel D.
(2011), 480(7376) 245-9.

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.

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.

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.

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.
(2010), 327(5961) 92-4.

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.

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.

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.

The 1001 genomes project for Arabidopsis thaliana

Weigel D. and Mott R.
Genome Biol
(2009), 10(5) 107.

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.

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.

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.

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.

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.
(2007), 317(5836) 338-42.

MSQT for choosing SNP assays from multiple DNA alignments

Warthmann N., Fitz J. and Weigel D.
(2007), 23(20) 2784-7.

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.