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Items: 19

1.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G.

Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

2.

Dynamic compression schemes for graph coloring.

Mustafa H, Schilken I, Karasikov M, Eickhoff C, Rätsch G, Kahles A.

Bioinformatics. 2019 Feb 1;35(3):407-414. doi: 10.1093/bioinformatics/bty632.

3.

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.

Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R.

Genetics. 2017 Apr;205(4):1425-1441. doi: 10.1534/genetics.116.192823. Epub 2017 Feb 7.

4.

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis.

Hartmann L, Drewe-Boß P, Wießner T, Wagner G, Geue S, Lee HC, Obermüller DM, Kahles A, Behr J, Sinz FH, Rätsch G, Wachter A.

Plant Cell. 2016 Nov;28(11):2715-2734. Epub 2016 Nov 1.

5.

AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo.

Kobbe D, Kahles A, Walter M, Klemm T, Mannuss A, Knoll A, Focke M, Puchta H.

Plant J. 2016 Nov;88(4):521-530. doi: 10.1111/tpj.13283. Epub 2016 Sep 17.

6.

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.

Kahles A, Ong CS, Zhong Y, Rätsch G.

Bioinformatics. 2016 Jun 15;32(12):1840-7. doi: 10.1093/bioinformatics/btw076. Epub 2016 Feb 11.

7.

MMR: a tool for read multi-mapper resolution.

Kahles A, Behr J, Rätsch G.

Bioinformatics. 2016 Mar 1;32(5):770-2. doi: 10.1093/bioinformatics/btv624. Epub 2015 Oct 30.

8.

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M.

Elife. 2015 May 5;4:e05255. doi: 10.7554/eLife.05255.

9.

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G.

Pac Symp Biocomput. 2015:44-55.

10.

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G.

Bioinformatics. 2014 May 1;30(9):1300-1. doi: 10.1093/bioinformatics/btt731. Epub 2014 Jan 11.

11.

Excap: maximization of haplotypic diversity of linked markers.

Kahles A, Sarqume F, Savolainen P, Arvestad L.

PLoS One. 2013 Nov 7;8(11):e79012. doi: 10.1371/journal.pone.0079012. eCollection 2013.

12.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium.

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

13.

Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome.

Drechsel G, Kahles A, Kesarwani AK, Stauffer E, Behr J, Drewe P, Rätsch G, Wachter A.

Plant Cell. 2013 Oct;25(10):3726-42. doi: 10.1105/tpc.113.115485. Epub 2013 Oct 25.

14.

MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G.

Bioinformatics. 2013 Oct 15;29(20):2529-38. doi: 10.1093/bioinformatics/btt442. Epub 2013 Aug 25.

15.

Accurate detection of differential RNA processing.

Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G.

Nucleic Acids Res. 2013 May 1;41(10):5189-98. doi: 10.1093/nar/gkt211. Epub 2013 Apr 12.

16.

Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes.

Rühl C, Stauffer E, Kahles A, Wagner G, Drechsel G, Rätsch G, Wachter A.

Plant Cell. 2012 Nov;24(11):4360-75. doi: 10.1105/tpc.112.103622. Epub 2012 Nov 27.

17.

Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes.

Smith LM, Hartmann L, Drewe P, Bohnert R, Kahles A, Lanz C, Rätsch G.

RNA Biol. 2012 May;9(5):596-609. doi: 10.4161/rna.19683. Epub 2012 May 1.

PMID:
22614838
18.

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.

Nature. 2011 Aug 28;477(7365):419-23. doi: 10.1038/nature10414.

19.

RNA-Seq read alignments with PALMapper.

Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.6. doi: 10.1002/0471250953.bi1106s32.

PMID:
21154708

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