Publications

This is a list of bioinformatics-related publications. To see all publication please click here.

2010

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana
Ossowski, S, Schneeberger, K, Lucas-Lledo, JI, Warthmann, N, Clark, RM, Shaw, RG, Weigel, D, Lynch, M
Science 1 January 2010
Related Links: PubMed

2009

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 10: R98
Related Links: PubMed GenomeMapper project site
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 6: 550-551
Related Links: PubMed SHOREmap project site
Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii
Molnar, A, Bassett, A, Thuenemann, E, Schwach, F, Karkare, S, Ossowski, S, Weigel, D, and Baulcombe, D
Plant J. 2009 Jan 17.
Related Links: PubMed
KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences
Schultheiss, SJ, Busch, W, Lohmann, JU, Kohlbacher, O, and Ratsch, G
Bioinformatics, doi:10.1093/bioinformatics/btp278
Related Links: PubMed
Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays
Zeller, G, Henz, SR, Widmer, CK, Sachsenberg, T, Ratsch, G, Weigel, D, and Laubinger, S
Plant J. 2009 Mar 9. [Epub ahead of print]
Related Links: PubMed At-TAX Project Page

2008

Evolution of Arabidopsis thaliana microRNAs from random sequences
de Felippes, FF, Schneeberger, K, Dezulian, T, Huson, DH, and Weigel, D
RNA, 14(12):2455-9.
Related Links: PubMed
Sequencing of natural strains of Arabidopsis thaliana with short reads
Ossowski S, Schneeberger K, Clark RM et al.
Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
Related Links: PubMed 1001 Genomes
Optimal spliced alignments of short sequence reads
De Bona F, Ossowski S, Schneeberger K and Rätsch G
Bioinformatics. 2008 Aug 15;24(16):i174-80.
Related Links: PubMed
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., Schölkopf B., Rätsch G., and Weigel D.
Genome Biol. 2008, Jul 9:9(8):R112
Related Links: PubMed At-TAX GBrowse tileViz At-TAX Project Page
Gene silencing in plants using artificial microRNAs and other small RNAs
Ossowski S, Schwab R, Weigel D.
Plant Journal 53, 674-690.
Related Links: PubMed
Highly specific gene silencing by artificial miRNAs in rice
Warthmann N, Chen H, Ossowski S, Weigel D, and Hervé P.
PLoS ONE 3:e1829.
Related Links: PubMed
Transcript normalization and segmentation of tiling array data
Zeller G, Henz SR, Laubinger S, Weigel D, Rätsch G
Pacific Symposium on Biocomputing 12, 527-538.
Related Links: PubMed
Detecting polymorphic regions in the Arabidopsis thaliana genome with resequencing microarrays
Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D, Rätsch G.
Genome Research, DOI: 10.1101/gr.070169.107; Published online before print March 6, 2008
Related Links: PubMed

2007

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana
Clark RM, Schweikert G, Ossowski S, Zeller G, Shinn P, Rätsch G, Warthmann N, Fu G, Hinds D, Chen H-M, Frazer K, Toomajian C, Hu T, Huson DH, Schölkopf B, Nordborg M, Ecker JR, Weigel D.
Science 317, 338-342.
Related Links: PubMed Data download POLYMORPH web tool
Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis
Henz SR, Cumbie JS, Kasschau KD, Lohmann JU, Carrington JC, Weigel D and Schmid M
Plant Physiology 144(3):1247-1255.
Related Links: PubMed
MSQT for choosing SNP assays from multiple DNA alignments
Warthmann N, Fitz J and Weigel D.
Bioinformatics 2007 23(20):2784-2787; doi:10.1093/bioinformatics/btm428.
Related Links: Project Website Supplementary Data PubMed
ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata
Dreyer C, Hoffmann M, Lanz C, Willing E-M, Riester M, Warthmann N, Sprecher A, Tripathi N, Henz SR, Weigel D.
BMC Genomics 8, 269
Related Links: Guppy Databases PubMed
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs
Dezulian T, Schaefer M, Wiese R, Weigel D, Huson D.
Nucleic Acids Research 34 Web Server Issue, W400-W404.
Related Links: CrossLink PubMed

2006


The 100 Most-Frequently
Read Articles in Plant Cell
Ranked 4th (Mar, 2008)
Highly specific gene silencing by artificial microRNAs in Arabidopsis
Schwab R, Ossowski, S, Riester M, Warthmann N, Weigel D.
Plant Cell 2006 May;18(5):1121-33. Epub 2006 Mar 10.
Related Links: WMD PubMed
Identification of plant microRNA homologs
Dezulian T, Remmert M, Palatnik J, Weigel D, Huson D.
Bioinformatics 2006 22(3):359-360; doi:10.1093/bioinformatics/bti802
Related Links: PubMed

2005

A gene expression map of Arabidopsis thaliana development
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU.
Nature Genetics - 37, 501 - 506 (2005)
Related Links: AtGeneExpress Visualization Tool Supplementary Data PubMed

2003

Large-scale identification of single-feature polymorphisms in complex genomes
Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J.
Genome Research 13, 513-523
Related Links: PubMed