Fabian Amman

Fabian Amman

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Fabian Amman

Fabian Amman

Publications by authors named "Fabian Amman"

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Transcriptional profiling of human macrophages during infection with .

RNA Biol 2020 Feb 19:1-12. Epub 2020 Feb 19.

Institute of Microbiology of the Czech Academy of Sciences, Laboratory of Post-transcriptional Control of Gene Expression, Prague, Czech Republic.

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http://dx.doi.org/10.1080/15476286.2020.1727694DOI Listing
February 2020

An internal deletion of ADAR rescued by MAVS deficiency leads to a minute phenotype.

Nucleic Acids Res 2020 Jan 20. Epub 2020 Jan 20.

Department of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkaa025DOI Listing
January 2020

MSF: Modulated Sub-graph Finder.

F1000Res 2018 29;7:1346. Epub 2018 Aug 29.

Institute for Theoretical Chemistry,Theoretical Biochemistry Group,, University of Vienna, Vienna, 1090, Austria.

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http://dx.doi.org/10.12688/f1000research.16005.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446500.3PMC
November 2019

iRAPs curb antisense transcription in E. coli.

Nucleic Acids Res 2019 Nov;47(20):10894-10905

Department of Biochemistry and Cell biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria.

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http://dx.doi.org/10.1093/nar/gkz791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6847712PMC
November 2019

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.

Genome Res 2019 09 19;29(9):1453-1463. Epub 2019 Aug 19.

Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1101/gr.242636.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724681PMC
September 2019

Comparative Integrated Omics Analysis of the Hfq Regulon in .

Int J Mol Sci 2019 Jun 24;20(12). Epub 2019 Jun 24.

Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.

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https://www.mdpi.com/1422-0067/20/12/3073
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http://dx.doi.org/10.3390/ijms20123073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627887PMC
June 2019

Inosine induces context-dependent recoding and translational stalling.

Nucleic Acids Res 2019 01;47(1):3-14

Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gky1163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326813PMC
January 2019

Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system.

RNA Biol 2018 31;15(7):877-885. Epub 2018 Jul 31.

a Center of Anatomy and Cell Biology, Division of Cell Biology , Medical University of Vienna , Vienna , Austria.

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http://dx.doi.org/10.1080/15476286.2018.1480252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161736PMC
December 2018

Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen .

RNA 2018 11 10;24(11):1530-1541. Epub 2018 Aug 10.

Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.

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http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.067306.11
Publisher Site
http://dx.doi.org/10.1261/rna.067306.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191719PMC
November 2018

Comparative genomics of Czech vaccine strains of Bordetella pertussis.

Pathog Dis 2018 10 1;76(7). Epub 2018 Oct 1.

Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.

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https://academic.oup.com/femspd/article/doi/10.1093/femspd/f
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http://dx.doi.org/10.1093/femspd/fty071DOI Listing
October 2018

Negative Control of RpoS Synthesis by the sRNA ReaL in .

Front Microbiol 2018 29;9:2488. Epub 2018 Oct 29.

Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna - Vienna Biocenter, Vienna, Austria.

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https://www.frontiersin.org/article/10.3389/fmicb.2018.02488
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http://dx.doi.org/10.3389/fmicb.2018.02488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6215814PMC
October 2018

Accurate mapping of tRNA reads.

Bioinformatics 2018 04;34(7):1116-1124

Department of Theoretical Chemistry of the University of Vienna, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btx756DOI Listing
April 2018

The Anaerobically Induced sRNA PaiI Affects Denitrification in PA14.

Front Microbiol 2017 23;8:2312. Epub 2017 Nov 23.

Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.3389/fmicb.2017.02312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703892PMC
November 2017

The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts.

Nucleic Acids Res 2017 Jul;45(13):7938-7949

Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkx437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570065PMC
July 2017

RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.

PLoS One 2016 28;11(1):e0147811. Epub 2016 Jan 28.

Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147811PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731081PMC
July 2016

Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.

Nature 2016 Jan 20;529(7587):496-501. Epub 2016 Jan 20.

University of Würzburg, RNA Biology Group, Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.

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http://dx.doi.org/10.1038/nature16547DOI Listing
January 2016

Impact of Hfq on the Bacillus subtilis transcriptome.

PLoS One 2014 16;9(6):e98661. Epub 2014 Jun 16.

Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Centre of Molecular Biology, University of Vienna, Vienna, Austria.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098661PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059632PMC
October 2015

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines.

F1000Res 2015 20;4:50. Epub 2015 Feb 20.

Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria ; Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.

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http://dx.doi.org/10.12688/f1000research.6157.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513691PMC
August 2015

Bioinformatics of prokaryotic RNAs.

RNA Biol 2014 2;11(5):470-83. Epub 2014 Apr 2.

Institute for Theoretical Chemistry; University of Vienna; Währingerstraße 17; A-1090 Wien, Austria; Bioinformatics Group; Department of Computer Science, and Interdisciplinary Center for Bioinformatics; University of Leipzig; Härtelstraße 16-18; D-04107 Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences; Inselstraße 22; D-04103 Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology - IZI; Perlickstraße 1; D-04103 Leipzig, Germany; Center for non-coding RNA in Technology and Health; University of Copenhagen; Grønnegårdsvej 3; DK-1870 Frederiksberg C, Denmark; Santa Fe Institute; Santa Fe, NM USA.

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http://dx.doi.org/10.4161/rna.28647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152356PMC
March 2015

Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2.

PLoS One 2013 7;8(10):e76569. Epub 2013 Oct 7.

Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076569PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792030PMC
August 2014

2D meets 4G: G-quadruplexes in RNA secondary structure prediction.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jul-Aug;10(4):832-44

University of Leipzig, Leipzig, Max Planck Institute for Mathematics in the Sciences, Leipzig, Fraunhofer Institute for CellTherapy and Immunology and University of Copenhagen.

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http://dx.doi.org/10.1109/TCBB.2013.7DOI Listing
August 2014

TSSAR: TSS annotation regime for dRNA-seq data.

BMC Bioinformatics 2014 Mar 27;15:89. Epub 2014 Mar 27.

Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2105-15-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098767PMC
March 2014

Archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in Sulfolobus acidocaldarius.

Mol Cell Proteomics 2013 Dec 27;12(12):3908-23. Epub 2013 Sep 27.

Molecular Biology of Archaea, Max Planck Institute for terrestrial Microbiology, Karl-von-Frisch Straβe 10, 35043 Marburg, Germany;

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http://dx.doi.org/10.1074/mcp.M113.027375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861733PMC
December 2013

Modelling translation initiation under the influence of sRNA.

Int J Mol Sci 2012 Nov 30;13(12):16223-40. Epub 2012 Nov 30.

Institute for Theoretical Chemistry, University Vienna, Währingerstraße 17, 1090 Vienna, Austria.

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http://dx.doi.org/10.3390/ijms131216223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546686PMC
November 2012

Fast accessibility-based prediction of RNA-RNA interactions.

Bioinformatics 2011 Jul 18;27(14):1934-40. Epub 2011 May 18.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr281DOI Listing
July 2011