Stadler P - Search Results

1

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.

Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, Chu Q, Chuang TJ, Dehghannasiri R, Dieterich C, Dong X, Flicek P, Gaffo E, Gu W, He C, Hoffmann S, Izuogu O, Jackson MS, Jakobi T, Lai EC, Nuytens J, Salzman J, Santibanez-Koref M, Stadler P, Thas O, Vanden Eynde E, Verniers K, Wen G, Westholm J, Yang L, Ye CY, Yigit N, Yuan GH, Zhang J, Zhao F, Vandesompele J, Volders PJ. Vromman M, et al. Among authors: stadler p. Nat Methods. 2023 Aug;20(8):1159-1169. doi: 10.1038/s41592-023-01944-6. Epub 2023 Jul 13. Nat Methods. 2023. PMID: 37443337 Free PMC article.

2

Evidence for human microRNA-offset RNAs in small RNA sequencing data.

Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF. Langenberger D, et al. Among authors: stadler pf. Bioinformatics. 2009 Sep 15;25(18):2298-301. doi: 10.1093/bioinformatics/btp419. Epub 2009 Jul 6. Bioinformatics. 2009. PMID: 19584066

3

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. Hoffmann S, et al. Among authors: stadler pf. PLoS Comput Biol. 2009 Sep;5(9):e1000502. doi: 10.1371/journal.pcbi.1000502. Epub 2009 Sep 11. PLoS Comput Biol. 2009. PMID: 19750212 Free PMC article.

4

Identification and classification of small RNAs in transcriptome sequence data.

Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S. Langenberger D, et al. Among authors: stadler pf. Pac Symp Biocomput. 2010:80-7. doi: 10.1142/9789814295291_0010. Pac Symp Biocomput. 2010. PMID: 19908360 Free article.

5

The primary transcriptome of the major human pathogen Helicobacter pylori.

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. Sharma CM, et al. Nature. 2010 Mar 11;464(7286):250-5. doi: 10.1038/nature08756. Epub 2010 Feb 17. Nature. 2010. PMID: 20164839

6

Traces of post-transcriptional RNA modifications in deep sequencing data.

Findeiss S, Langenberger D, Stadler PF, Hoffmann S. Findeiss S, et al. Biol Chem. 2011 Apr;392(4):305-13. doi: 10.1515/BC.2011.043. Epub 2011 Feb 24. Biol Chem. 2011. PMID: 21345160

7

Fast local fragment chaining using sum-of-pair gap costs.

Otto C, Hoffmann S, Gorodkin J, Stadler PF. Otto C, et al. Algorithms Mol Biol. 2011 Mar 18;6:4. doi: 10.1186/1748-7188-6-4. Algorithms Mol Biol. 2011. PMID: 21418573 Free PMC article.

8

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.

Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S. Fasold M, et al. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W112-7. doi: 10.1093/nar/gkr357. Epub 2011 May 27. Nucleic Acids Res. 2011. PMID: 21622957 Free PMC article.

9

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J. Langenberger D, et al. Bioinformatics. 2012 Jan 1;28(1):17-24. doi: 10.1093/bioinformatics/btr598. Epub 2011 Nov 3. Bioinformatics. 2012. PMID: 22053076 Free PMC article.

10

Fast and sensitive mapping of bisulfite-treated sequencing data.

Otto C, Stadler PF, Hoffmann S. Otto C, et al. Bioinformatics. 2012 Jul 1;28(13):1698-704. doi: 10.1093/bioinformatics/bts254. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581174

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