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Medical University of Vienna: Vienna, AT

2023-01-02 to present | Senior Bioinformatician (Institute of Hygiene and applied Immunology)
Employment
Source: Self-asserted source
Fabian Amman

Research Center for Molecular Medicine of the Austrian Academy of Sciences: Vienna, Wien, AT

2021-03-01 to present
Employment
Source: Self-asserted source
Fabian Amman

Works (50 of 57)

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Page 1 of 2

Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023

Eurosurveillance
2024-06-06 | Journal article
DOI: 10.2807/1560-7917.es.2024.29.23.2300542
Part of ISSN: 1560-7917
Contributors: Olga Frank; David Acitores Balboa; Maria Novatchkova; Ezgi Özkan; Marcus Martin Strobl; Ramesh Yelagandula; Tanino Guiseppe Albanese; Lukas Endler; Fabian Amman; Vera Felsenstein et al.
Source: Self-asserted source
Fabian Amman

Breakthrough Infections in SARS-CoV-2-Vaccinated Multiple Myeloma Patients Improve Cross-Protection against Omicron Variants

Vaccines
2024-05-09 | Journal article
DOI: 10.3390/vaccines12050518
Part of ISSN: 2076-393X
Contributors: Angelika Wagner; Erika Garner-Spitzer; Claudia Auer; Pia Gattinger; Ines Zwazl; René Platzer; Maria Orola-Taus; Peter Pichler; Fabian Amman; Andreas Bergthaler et al.
Source: Self-asserted source
Fabian Amman

Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment

Emerging Microbes & Infections
2023-12-31 | Journal article
DOI: 10.1080/22221751.2022.2146536
Contributors: Mariam R. Farman; Denisa Petráčková; Dilip Kumar; Jakub Držmíšek; Argha Saha; Ivana Čurnová; Jan Čapek; Václava Hejnarová; Fabian Amman; Ivo Hofacker et al.
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Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale

Nature Biotechnology
2022-12 | Journal article
DOI: 10.1038/s41587-022-01387-y
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Contributors: Fabian Amman; Rudolf Markt; Lukas Endler; Sebastian Hupfauf; Benedikt Agerer; Anna Schedl; Lukas Richter; Melanie Zechmeister; Martin Bicher; Georg Heiler et al.
Source: Self-asserted source
Fabian Amman

VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples

2022-06-22 | Preprint
DOI: 10.1101/2022.06.21.22276717
Contributors: Askar Gafurov; Andrej Baláž; Fabian Amman; Kristína Boršová; Viktória Čabanová; Boris Klempa; Andreas Bergthaler; Tomáš Vinař; Broňa Brejová
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Emergence of SARS-CoV-2 Alpha lineage and its correlation with quantitative wastewater-based epidemiology data

Water Research
2022-05 | Journal article
DOI: 10.1016/j.watres.2022.118257
Contributors: Elena Radu; Amandine Masseron; Fabian Amman; Anna Schedl; Benedikt Agerer; Lukas Endler; Thomas Penz; Christoph Bock; Andreas Bergthaler; Julia Vierheilig et al.
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Detection and abundance of SARS-CoV-2 in wastewater in Liechtenstein, and the estimation of prevalence and impact of the B.1.1.7 variant

Journal of Water and Health
2022-01-01 | Journal article
DOI: 10.2166/wh.2021.180
Contributors: R. Markt; L. Endler; F. Amman; A. Schedl; T. Penz; M. Büchel-Marxer; D. Grünbacher; M. Mayr; E. Peer; M. Pedrazzini et al.
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Comparative omics analysis of historic and recent isolates of bordetella pertussis and effects of genome rearrangements on evolution

Emerging Infectious Diseases
2021 | Journal article
DOI: 10.3201/eid2701.191541
EID:

2-s2.0-85098491556

Part of ISSN: 10806059 10806040
Contributors: Dienstbier, A.; Amman, F.; Petráčková, D.; Štipl, D.; Čapek, J.; Zavadilová, J.; Fabiánová, K.; Držmíšek, J.; Kumar, D.; Wildung, M. et al.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin

Frontiers in Microbiology
2021 | Journal article
DOI: 10.3389/fmicb.2021.626715
EID:

2-s2.0-85106062441

Part of ISSN: 1664302X
Contributors: Cianciulli Sesso, A.; Lilić, B.; Amman, F.; Wolfinger, M.T.; Sonnleitner, E.; Bläsi, U.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence—An Experimental Study of the Human Voltage-Dependent Anion Channel

Membranes
2021-09-28 | Journal article
DOI: 10.3390/membranes11100741
Contributors: Sonja Zayni; Samar Damiati; Susana Moreno-Flores; Fabian Amman; Ivo Hofacker; David Jin; Eva-Kathrin Ehmoser
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Enhancing the Cell-Free Expression of Native Membrane Proteins by in-Silico Optimisation of the Coding Sequence - An Experimental Study of the Human Voltage-Dependent Anion Channel

2021-07-07 | Other
DOI: 10.20944/preprints202107.0172.v1
Contributors: Sonja Zayni; Samar Damiati; Susana Moreno-Flores; Fabian Amman; Ivo Hofacker; Eva Kathrin Ehmoser
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Adaptor protein RapZ activates endoribonuclease RNase e by protein-protein interaction to cleave a small regulatory RNA

RNA
2020 | Journal article
DOI: 10.1261/RNA.074047.119
EID:

2-s2.0-85089787784

Part of ISSN: 14699001 13558382
Contributors: Durica-Mitic, S.; Göpel, Y.; Amman, F.; Görke, B.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

ADAR-deficiency perturbs the global splicing landscape in mouse tissues

Genome Research
2020-08-29 | Journal article
DOI: 10.1101/gr.256933.119
Contributors: Utkarsh Kapoor; Konstantin Licht; Fabian Amman; Tobias Jakobi; David Martin; Christoph Dieterich; Michael F. Jantsch
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Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B

Nucleic Acids Research
2020-06-19 | Journal article
DOI: 10.1093/nar/gkaa353
Contributors: Elisa Vilardo; Fabian Amman; Ursula Toth; Annika Kotter; Mark Helm; Walter Rossmanith
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Identification of RNA 3´ ends and termination sites in Haloferax volcanii

RNA Biology
2020-05-03 | Journal article
DOI: 10.1080/15476286.2020.1723328
Contributors: Sarah J. Berkemer; Lisa-Katharina Maier; Fabian Amman; Stephan H. Bernhart; Julia Wörtz; Pascal Märkle; Friedhelm Pfeiffer; Peter F. Stadler; Anita Marchfelder
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Transcriptional profiling of human macrophages during infection with Bordetella pertussis

RNA Biology
2020-05-03 | Journal article
DOI: 10.1080/15476286.2020.1727694
Contributors: Denisa Petráčková; Mariam R. Farman; Fabian Amman; Irena Linhartová; Ana Dienstbier; Dilip Kumar; Jakub Držmíšek; Ivo Hofacker; Maria Eugenia Rodriguez; Branislav Večerek
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An internal deletion of ADAR rescued by MAVS deficiency leads to a minute phenotype

Nucleic Acids Research
2020-04-06 | Journal article
DOI: 10.1093/nar/gkaa025
Contributors: Prajakta Bajad; Florian Ebner; Fabian Amman; Brigitta Szabó; Utkarsh Kapoor; Greeshma Manjali; Alwine Hildebrandt; Michael P Janisiw; Michael F Jantsch
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MSF: Modulated Sub-graph Finder

F1000Research
2019 | Journal article
DOI: 10.12688/f1000research.16005.2
EID:

2-s2.0-85065621045

Part of ISSN: 1759796X 20461402
Contributors: Farman, M.R.; Hofacker, I.L.; Amman, F.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

iRAPs curb antisense transcription in E. coli

Nucleic Acids Research
2019-11-18 | Journal article
DOI: 10.1093/nar/gkz791
Contributors: Andrés Magán; Fabian Amman; Fatinah El-Isa; Natascha Hartl; Ilya Shamovsky; Evgeny Nudler; Renée Schroeder; Nadezda Sedlyarova
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A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing

Genome Research
2019-09-19 | Journal article
DOI: 10.1101/gr.242636.118
Contributors: Konstantin Licht; Utkarsh Kapoor; Fabian Amman; Ernesto Picardi; David Martin; Prajakta Bajad; Michael F. Jantsch
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Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions

Molecular Cell
2019-09-05 | Journal article
DOI: 10.1016/j.molcel.2019.07.034
Part of ISSN: 1097-2765
Source: Self-asserted source
Fabian Amman
grade
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Identification of RNA 3’ ends and termination sites in Haloferax volcanii

2019-08-28 | Other
DOI: 10.1101/748780
Contributors: Sarah J. Berkemer; Lisa-Katharina Maier; Fabian Amman; Stephan H. Bernhart; Julia Wörtz; Pascal Märkle; Friedhelm Pfeiffer; Peter F. Stadler; Anita Marchfelder
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Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis

International Journal of Molecular Sciences
2019-06-24 | Journal article
DOI: 10.3390/ijms20123073
Contributors: Ana Dienstbier; Fabian Amman; Daniel Štipl; Denisa Petráčková; Branislav Večerek
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MSF: Modulated Sub-graph Finder

F1000Research
2019-04-14 | Journal article
DOI: 10.12688/f1000research.16005.3
Contributors: Mariam R. Farman; Ivo L. Hofacker; Fabian Amman
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Inosine induces context-dependent recoding and translational stalling

Nucleic Acids Research
2019-01-10 | Journal article
DOI: 10.1093/nar/gky1163
Contributors: Konstantin Licht; Markus Hartl; Fabian Amman; Dorothea Anrather; Michael P Janisiw; Michael F Jantsch
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Corrigendum: Accurate mapping of tRNA reads (Bioinformatics (2017) DOI: 10.1093/bioinformatics/btx756)

Bioinformatics
2018 | Journal article
DOI: 10.1093/bioinformatics/bty118
EID:

2-s2.0-85050821741

Part of ISSN: 14602059 13674803
Contributors: Hoffmann, A.; Fallmann, J.; Vilardo, E.; Mörl, M.; Stadler, P.F.; Amman, F.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

MSF: Modulated Sub-graph Finder

F1000Research
2018 | Journal article
DOI: 10.12688/f1000research.16005.1
EID:

2-s2.0-85064853300

Part of ISSN: 20461402
Contributors: Farman, M.R.; Hofacker, I.L.; Amman, F.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Nascent RNA signaling to yeast RNA Pol II during transcription elongation

PLoS ONE
2018 | Journal article
DOI: 10.1371/journal.pone.0194438
EID:

2-s2.0-85044359321
Contributors: Klopf, E.; Moes, M.; Amman, F.; Zimmermann, B.; Von Pelchrzim, F.; Wagner, C.; Schroeder, R.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

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

RNA
2018 | Journal article
DOI: 10.1261/rna.067306.118
EID:

2-s2.0-85055076945

Part of ISSN: 14699001 13558382
Contributors: Keidel, K.; Amman, F.; Bibova, I.; Drzmisek, J.; Benes, V.; Hot, D.; Vecerek, B.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Negative Control of RpoS Synthesis by the sRNA ReaL in Pseudomonas aeruginosa

Frontiers in Microbiology
2018-10-29 | Journal article
DOI: 10.3389/fmicb.2018.02488
Part of ISSN: 1664-302X
Source: Self-asserted source
Fabian Amman
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Comparative genomics of Czech vaccine strains of Bordetella pertussis

Pathogens and Disease
2018-10-01 | Journal article
DOI: 10.1093/femspd/fty071
Contributors: Ana Dienstbier; Derek Pouchnik; Mark Wildung; Fabian Amman; Ivo L Hofacker; Julian Parkhill; Jana Holubova; Peter Sebo; Branislav Vecerek
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Enhancing the cell-free expression of native membrane proteins by in-silico optimization of the coding sequence – an experimental study of the human voltage-dependent anion channel

[]
2018-09-07 | Other
DOI: 10.1101/411694
Source: Self-asserted source
Fabian Amman
grade
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Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system

RNA Biology
2018-07-03 | Journal article
DOI: 10.1080/15476286.2018.1480252
Contributors: Philipp Czermak; Fabian Amman; Michael F. Jantsch; Laura Cimatti
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Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis

RNA Biology
2018-07-03 | Journal article
DOI: 10.1080/15476286.2018.1462655
Part of ISSN: 1547-6286
Part of ISSN: 1555-8584
Source: Self-asserted source
Fabian Amman
grade
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Accurate mapping of tRNA reads

Bioinformatics
2018-04-01 | Journal article
DOI: 10.1093/bioinformatics/btx756
Contributors: Anne Hoffmann; Jörg Fallmann; Elisa Vilardo; Mario Mörl; Peter F Stadler; Fabian Amman; Cenk Sahinalp
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Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

Molecular Ecology
2017 | Journal article
DOI: 10.1111/mec.14123
EID:

2-s2.0-85018991642
Contributors: Balao, F.; Trucchi, E.; Wolfe, T.M.; Hao, B.-H.; Lorenzo, M.T.; Baar, J.; Sedman, L.; Kosiol, C.; Amman, F.; Chase, M.W. et al.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Scientific reports
2017 | Journal article
DOI: 10.1038/srep39421
EID:

2-s2.0-85076320400

Part of ISSN: 20452322
Contributors: Hölzer, M.; Krähling, V.; Amman, F.; Barth, E.; Bernhart, S.H.; Carmelo, V.A.; Collatz, M.; Doose, G.; Eggenhofer, F.; Ewald, J. et al.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

The anaerobically induced sRNA PaiI affects denitrification in Pseudomonas aeruginosa PA14

Frontiers in Microbiology
2017 | Journal article
DOI: 10.3389/fmicb.2017.02312
EID:

2-s2.0-85035051518
Contributors: Tata, M.; Amman, F.; Pawar, V.; Wolfinger, M.T.; Weiss, S.; Häussler, S.; Bläsi, U.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

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

Nucleic Acids Research
2017 | Journal article
DOI: 10.1093/nar/gkx437
EID:

2-s2.0-85026407800
Contributors: Märtens, B.; Hou, L.; Amman, F.; Wolfinger, M.T.; Evguenieva-Hackenberg, E.; Bläsi, U.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Scientific Reports
2016 | Journal article
DOI: 10.1038/srep34589
EID:

2-s2.0-84991066577
Contributors: Hölzer, M.; Krähling, V.; Amman, F.; Barth, E.; Bernhart, S.H.; Carmelo, V.A.O.; Collatz, M.; Doose, G.; Eggenhofer, F.; Ewald, J. et al.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

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

Nature
2016 | Journal article
DOI: 10.1038/nature16547
EID:

2-s2.0-84964262313
Contributors: Westermann, A.J.; Förstner, K.U.; Amman, F.; Barquist, L.; Chao, Y.; Schulte, L.N.; Müller, L.; Reinhardt, R.; Stadler, P.F.; Vogel, J.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

RNA<inf>seq</inf> based transcriptional profiling of Pseudomonas aeruginosa PA14 after shortand long-term anoxic cultivation in synthetic cystic fibrosis sputum medium

PLoS ONE
2016 | Journal article
DOI: 10.1371/journal.pone.0147811
EID:

2-s2.0-84958212677
Contributors: Tata, M.; Wolfinger, M.T.; Amman, F.; Roschanski, N.; Dötsch, A.; Sonnleitner, E.; Häussler, S.; Bläsi, U.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Transcriptional profiling of bordetella pertussis reveals requirement of RNA chaperone Hfq for type III secretion system functionality

RNA Biology
2015 | Journal article
DOI: 10.1080/15476286.2015.1017237
EID:

2-s2.0-84928239614
Contributors: Bibova, I.; Hot, D.; Keidel, K.; Amman, F.; Slupek, S.; Cerny, O.; Gross, R.; Vecerek, B.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

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

F1000Research
2015 | Journal article
DOI: 10.12688/f1000research.6157.2
EID:

2-s2.0-84930857559
Contributors: Wolfinger, M.T.; Fallmann, J.; Eggenhofer, F.; Amman, F.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier
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ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

F1000Research
2015-02-20 | Journal article
DOI: 10.12688/f1000research.6157.1
Contributors: Michael T. Wolfinger; Jörg Fallmann; Florian Eggenhofer; Fabian Amman
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Crossref

Bioinformatics of prokaryotic RNAs

RNA Biology
2014 | Journal article
DOI: 10.4161/rna.28647
EID:

2-s2.0-84906346427
Contributors: Backofen, R.; Amman, F.; Costa, F.; Findeib, S.; Richter, A.; Stadler, P.F.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Impact of Hfq on the Bacillus subtilis transcriptome

PLoS ONE
2014 | Journal article
DOI: 10.1371/journal.pone.0098661
EID:

2-s2.0-84903291745
Contributors: Hämmerle, H.; Amman, F.; Večerek, B.; Stülke, J.; Hofacker, I.; Bläsi, U.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

TSSAR: TSS annotation regime for dRNA-seq data

BMC Bioinformatics
2014 | Journal article
DOI: 10.1186/1471-2105-15-89
EID:

2-s2.0-84898923218
Contributors: Amman, F.; Wolfinger, M.T.; Lorenz, R.; Hofacker, I.L.; Stadler, P.F.; Findeiß, S.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

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

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2013 | Journal article
DOI: 10.1109/TCBB.2013.7
EID:

2-s2.0-84884395122
Contributors: Lorenz, R.; Bernhart, S.H.; Qin, J.; Siederdissen, C.H.Z.; Tanzer, A.; Amman, F.; Hofacker, I.L.; Stadler, P.F.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier

Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2

PLoS ONE
2013 | Journal article
DOI: 10.1371/journal.pone.0076569
EID:

2-s2.0-84885059852
Contributors: Märtens, B.; Amman, F.; Manoharadas, S.; Zeichen, L.; Orell, A.; Albers, S.-V.; Hofacker, I.; Bläsi, U.
Source: Self-asserted source
Fabian Amman via Scopus - Elsevier
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