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Building an international consortium for tracking coronavirus health status.
Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen WE, Alquaddoomi F, Altae-Tran H, Anders S, Balicer R, Bauman T, Bonilla X, Booman G, Chan AT, Cohen O, Coletti S, Davidson N, Dor Y, Drew DA, Elemento O, Evans G, Ewels P, Gale J, Gavrieli A, Geiger B, Grad YH, Greene CS, Hajirasouliha I, Jerala R, Kahles A, Kallioniemi O, Keshet A, Kocarev L, Landua G, Meir T, Muller A, Nguyen LH, Oresic M, Ovchinnikova S, Peterson H, Prodanova J, Rajagopal J, Rätsch G, Rossman H, Rung J, Sboner A, Sigaras A, Spector T, Steinherz R, Stevens I, Vilo J, Wilmes P. Segal E, et al. Among authors: kahles a. Nat Med. 2020 Aug;26(8):1161-1165. doi: 10.1038/s41591-020-0929-x. Nat Med. 2020. PMID: 32488218 No abstract available.
RNA-Seq read alignments with PALMapper.
Jean G, Kahles A, Sreedharan VT, De Bona F, Rätsch G. Jean G, et al. Among authors: kahles a. Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.6. doi: 10.1002/0471250953.bi1106s32. Curr Protoc Bioinformatics. 2010. PMID: 21154708
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. Engström PG, et al. Among authors: kahles a. Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. Nat Methods. 2013. PMID: 24185836 Free PMC article.
Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F; RGASP Consortium; Hubbard TJ, Guigó R, Harrow J, Bertone P. Steijger T, et al. Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3. Nat Methods. 2013. PMID: 24185837 Free PMC article.
MMR: a tool for read multi-mapper resolution.
Kahles A, Behr J, Rätsch G. Kahles A, et al. Bioinformatics. 2016 Mar 1;32(5):770-2. doi: 10.1093/bioinformatics/btv624. Epub 2015 Oct 30. Bioinformatics. 2016. PMID: 26519503 Free PMC article.
Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase but also has significant impact on the results of downstream analyses. ...In addition, MMR decreases the alignment file sizes by more than 50%, and this leads to …
Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase but also has signific …
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data.
Kahles A, Ong CS, Zhong Y, Rätsch G. Kahles A, et al. Bioinformatics. 2016 Jun 15;32(12):1840-7. doi: 10.1093/bioinformatics/btw076. Epub 2016 Feb 11. Bioinformatics. 2016. PMID: 26873928 Free PMC article.
Whereas an identification of complete transcripts is technically challenging and computationally expensive, focusing on single splicing events as a proxy for transcriptome characteristics is fruitful and sufficient for a wide range of analyses. ...AVAILABILITY: Sour …
Whereas an identification of complete transcripts is technically challenging and computationally expensive, focusing on single splicing even …
Dynamic compression schemes for graph coloring.
Mustafa H, Schilken I, Karasikov M, Eickhoff C, Rätsch G, Kahles A. Mustafa H, et al. Among authors: kahles a. Bioinformatics. 2019 Feb 1;35(3):407-414. doi: 10.1093/bioinformatics/bty632. Bioinformatics. 2019. PMID: 30020403 Free PMC article.
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. Kahles A, et al. Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2. Cancer Cell. 2018. PMID: 30078747 Free PMC article.
Sparse Binary Relation Representations for Genome Graph Annotation.
Karasikov M, Mustafa H, Joudaki A, Javadzadeh-No S, Rätsch G, Kahles A. Karasikov M, et al. Among authors: kahles a. J Comput Biol. 2020 Apr;27(4):626-639. doi: 10.1089/cmb.2019.0324. Epub 2019 Dec 20. J Comput Biol. 2020. PMID: 31891531 Free PMC article.
99 results