Otto C - Search Results

1

Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.

Nunn A, Otto C, Fasold M, Stadler PF, Langenberger D. Nunn A, et al. Among authors: otto c. BMC Genomics. 2022 Jun 28;23(1):477. doi: 10.1186/s12864-022-08691-6. BMC Genomics. 2022. PMID: 35764934 Free PMC article.

2

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

3

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.

Nunn A, Otto C, Stadler PF, Langenberger D. Nunn A, et al. Among authors: otto c. Brief Bioinform. 2021 Sep 2;22(5):bbab021. doi: 10.1093/bib/bbab021. Brief Bioinform. 2021. PMID: 33624017 Free PMC article.

4

EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

Nunn A, Can SN, Otto C, Fasold M, Díez Rodríguez B, Fernández-Pozo N, Rensing SA, Stadler PF, Langenberger D. Nunn A, et al. Among authors: otto c. NAR Genom Bioinform. 2021 Nov 12;3(4):lqab106. doi: 10.1093/nargab/lqab106. eCollection 2021 Dec. NAR Genom Bioinform. 2021. PMID: 34805989 Free PMC article.

5

Lacking alignments? The next-generation sequencing mapper segemehl revisited.

Otto C, Stadler PF, Hoffmann S. Otto C, et al. Bioinformatics. 2014 Jul 1;30(13):1837-43. doi: 10.1093/bioinformatics/btu146. Epub 2014 Mar 13. Bioinformatics. 2014. PMID: 24626854

6

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods.

Drozdova P, Rivarola-Duarte L, Bedulina D, Axenov-Gribanov D, Schreiber S, Gurkov A, Shatilina Z, Vereshchagina K, Lubyaga Y, Madyarova E, Otto C, Jühling F, Busch W, Jakob L, Lucassen M, Sartoris FJ, Hackermüller J, Hoffmann S, Pörtner HO, Luckenbach T, Timofeyev M, Stadler PF. Drozdova P, et al. Among authors: otto c. BMC Genomics. 2019 Sep 13;20(1):712. doi: 10.1186/s12864-019-6024-3. BMC Genomics. 2019. PMID: 31519144 Free PMC article.

7

Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.

Nunn A, Otto C, Stadler PF, Langenberger D. Nunn A, et al. Among authors: otto c. Brief Bioinform. 2021 Sep 2;22(5):bbab183. doi: 10.1093/bib/bbab183. Brief Bioinform. 2021. PMID: 33899096 Free PMC article. No abstract available.

8

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: otto c. 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.

9

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.

Jühling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S. Jühling F, et al. Among authors: otto c. Genome Res. 2016 Feb;26(2):256-62. doi: 10.1101/gr.196394.115. Epub 2015 Dec 2. Genome Res. 2016. PMID: 26631489 Free PMC article.

10

Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species.

Shatilina Z, Drozdova P, Bedulina D, Rivarola-Duarte L, Schreiber S, Otto C, Jühling F, Aulhorn S, Busch W, Lubyaga Y, Kondrateva E, Pobezhimova T, Jakob L, Lucassen M, Sartoris FJ, Hackermüller J, Pörtner HO, Stadler PF, Luckenbach T, Timofeyev M. Shatilina Z, et al. Among authors: otto c. Comp Biochem Physiol Part D Genomics Proteomics. 2020 Mar;33:100630. doi: 10.1016/j.cbd.2019.100630. Epub 2019 Oct 31. Comp Biochem Physiol Part D Genomics Proteomics. 2020. PMID: 31710888

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