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Preprints

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
Devadatta Gosavi, Iwona Wower, Irene K Beckmann, Ivo L Hofacker, Jacek Wower, Michael T Wolfinger, Joanna Sztuba-Solinska
bioRxiv 2021.05.13.444024 | doi:10.1101/2021.05.13.444024 | Preprint PDF

Peer-reviewed journal articles and book chapters

2021

Functional RNA Structures in the 3’UTR of Mosquito-Borne Flaviviruses
Michael T. Wolfinger, Roman Ochsenreiter, Ivo L. Hofacker
In Virus Bioinformatics, edited by Dmitrij Frishman and Manja Marz, pp65–100. Chapman and Hall/CRC Press (2021) | doi:10.1201/9781003097679-5 | Preprint PDF

Gene Expression Profiling of Pseudomonas Aeruginosa Upon Exposure to Colistin and Tobramycin
Anastasia Cianciulli Sesso, Branislav Lilić, Fabian Amman, Michael T. Wolfinger, Elisabeth Sonnleitner, Udo Bläsi
Front. Microbiol. 12:937 (2021) | doi:10.3389/fmicb.2021.626715 | PDF

An African Tick Flavivirus Forming an Independent Clade Exhibits Unique Exoribonuclease-Resistant RNA Structures in the Genomic 3’-Untranslated Region
Hayato Harima, Yasuko Orba, Shiho Torii, Yongjin Qiu, Masahiro Kajihara, Yoshiki Eto, Naoya Matsuta, Bernard M. Hang’ombe, Yuki Eshita, Kentaro Uemura, Keita Matsuno, Michihito Sasaki, Kentaro Yoshii, Ryo Nakao, William W. Hall, Ayato Takada, Takashi Abe, Michael T. Wolfinger, Martin Simuunza, Hirofumi Sawa
Sci. Rep. 11:4883 (2021) | doi: 10.1038/s41598-021-84365-9 | PDF

Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
Genes 12 (2):239 (2021) | doi:10.3390/genes12020239 | PDF

2020

Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler
In Computational Intelligence Methods for Bioinformatics and Biostatistics, pp159–70. Springer International Publishing (2020) | doi:10.1007/978-3-030-63061-4_15 | Preprint PDF

Genomic Epidemiology of Superspreading Events in Austria Reveals Mutational Dynamics and Transmission Properties of SARS-CoV-2
Alexandra Popa, Jakob-Wendelin Genger, Michael D. Nicholson, Thomas Penz, Daniela Schmid, Stephan W Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique Colaco, Mark Smyth, Michael Schuster, Miguel L. Grau, Francisco Martínez-Jiménez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Mar- tin Senekowitsch, Jan Laine, Judith H Aberle, Monika Redlberger-Fritz, Mario Karolyi, Alexander Zoufaly, Sabine Maritschnik, Martin Borkovec, Peter Hufnagl, Manfred Nairz, Günter Weiss, Michael T. Wolfinger, Dorothee von Laer, Giulio Superti-Furga, Nuria Lopez-Bigas, Elisabeth Puchhammer-Stöckl, Franz Allerberger, Franziska Michor, Christoph Bock, Andreas Bergthaler
Sci. Transl. Med. 12 (573):eabe2555 (2020) | doi:10.1126/scitranslmed.abe2555

Discoveries of Exoribonuclease-Resistant Structures of Insect-Specific Flaviviruses Isolated in Zambia
Christida E. Wastika, Hayato Harima, Michihito Sasakai, Bernard M. Hang’ombe, Yuki Eshita, Qiu Yongjin, William W. Hall, Michael T. Wolfinger, Hirofumi Sawa, Yasuko Orba
Viruses 12:1017 (2020)| doi:10.3390/v12091017 | PDF

Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas Aeruginosa by Hfq
Elisabeth Sonnleitner, Petra Pusic, Michael T. Wolfinger, Udo Bläsi
Front. Microbiol. 11:1001 (2020) | doi:10.3389/fmicb.2020.01001 | PDF

2019

Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture
Adriano de Bernardi Schneider, Roman Ochsenreiter, Reilly Hostager, Ivo L. Hofacker, Daniel Janies, Michael T. Wolfinger
Viruses 11:798 (2019) | doi:10.3390/v11090798 | PDF

Musashi Binding Elements in Zika and Related Flavivirus 3’UTRs: A Comparative Study in Silico
Adriano de Bernardi Schneider, Michael T. Wolfinger
Sci. Rep. 9(1):6911 (2019) | doi:10.1038/s41598-019-43390-5 | PDF

Indications for a Moonlighting Function of Translation Factor aIF5A in the Crenarchaeum Sulfolobus Solfataricus
Flavia Bassani, Isabelle Anna Zink, Thomas Pribasnig, Michael T. Wolfinger, Alice Romagnoli, Armin Resch, Christa Schleper, Udo Bläsi, Anna La Teana
RNA Biol. 16 (5):675–85 (2019) | doi:10.1080/15476286.2019.1582953 | PDF

Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No Known Vector Flaviviruses
Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger
Viruses 11:298 (2019) | doi:10.3390/v11030298 | PDF

2018

Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas Aeruginosa
Petra Pusic, Elisabeth Sonnleitner, Beatrice Krennmayr, Dorothea Agnes Heitzinger, Michael T. Wolfinger, Armin Resch, Udo Bläsi
Front. Microbiol. 9:2709 (2018) | doi:10.3389/fmicb.2018.02709 | PDF

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
Maria Waldl, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João Victor de Araujo Oliveira, Maria Emília M.T. Walter, Michael T. Wolfinger, Peter F. Stadler
Genes 9 (8), 372 (2018) | doi:10.3390/genes9080372 | PDF

Efficient Computation of Cotranscriptional RNA-Ligand Interaction Dynamics
Michael T. Wolfinger, Christoph Flamm, Ivo L. Hofacker
Methods 143:70–76 (2018) | doi:10.1016/j.ymeth.2018.04.036 | Preprint PDF

In Silico Design of Ligand Triggered RNA Switches
Sven Findeiß, Stefan Hammer, Michael T. Wolfinger, Felix Kühnl, Christoph Flamm, Ivo L. Hofacker
Methods 143:90–101 (2018) | doi:10.1016/j.ymeth.2018.04.003

Interplay Between the Catabolite Repression Control Protein Crc, Hfq and RNA in Hfq-Dependent Translational Regulation in Pseudomonas Aeruginosa
Elisabeth Sonnleitner, Alexander Wulf, Sébastien Campagne, Xue-Yuan Pei, Michael T. Wolfinger, Giada Forlani, Konstantin Prindl, Laetitia Abdou, Armin Resch, Frederic Allain, Ben Luisi, Henning Urlaub, Udo Bläsi
Nucleic Acids Res. 46:1470–85 (2018) | doi:10.1093/nar/gkx1245 | PDF

2017

The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas Aeruginosa PA14
Muralidhar Tata, Fabian Amman, Vinay Pawar, Michael T. Wolfinger, Siegfried Weiss, Susanne Häussler, Udo Bläsi
Front. Microbiol. 8:2312 (2017) | doi:10.3389/fmicb.2017.02312 | PDF

The SmAP1/2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Interact with the Exosome and Stimulate A-Rich Tailing of Transcripts
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T. Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
Nucleic Acids Res. 45: 7938–49 (2017) | doi:10.1093/nar/gkx437 | PDF

NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations
Christina Helmling, Anna Wacker, Michael T. Wolfinger, Ivo L. Hofacker, Martin Hengsbach, Boris Fürtig, Harald Schwalbe
J. Am. Chem. Soc. 139 (7):2647–56 (2017) | doi:10.1021/jacs.6b10429

2016

Cross-Regulation by CrcZ RNA Controls Anoxic Biofilm Formation in Pseudomonas Aeruginosa
Petra Pusic, Muralidhar Tata, Michael T. Wolfinger, Elisabeth Sonnleitner, Susanne Häussler, Udo Bläsi
Sci. Rep. 6 (39621) (2016) | doi:10.1038/srep39621 | PDF

Transcriptome-Wide Effects of Inverted SINEs on Gene Expression and Their Impact on RNA Polymerase II Activity
Mansoured Tajadodd, Andrea Tanzer, Konstantin Licht, Michael T. Wolfinger, Stefan Badelt, Florian Huber, Oliver Pusch, Sandy Schopoff, Ivo L. Hofacker, Michael F. Jantsch
Genome Biol. 17:220 (2016) | doi:10.1186/s13059-016-1083-0 | PDF

Differential Transcriptional Responses to Ebola and Marburg Virus Infection in Bat and Human Cells
Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H. Bernhart, Victor Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M. Feldhahn, Markus Fricke, Juliane Gebauer, Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jörg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Stefanie Wehner, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo L. Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, Manja Marz
Sci. Rep. 6 (34589) (2016) | doi:10.1038/srep34589 | PDF

The MazF-Regulon: A Toolbox for the Post-Transcriptional Stress Response in Escherichia Coli
Martina Sauert, Michael T. Wolfinger, Oliver Vesper, Christian Müller, Konstantin Byrgazov, Isabella Moll
Nucleic Acids Res. 44 (14):6660–75 (2016) | doi:10.1093/nar/gkw115 | PDF

Predicting RNA Structures from Sequence and Probing Data
Ronny Lorenz, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker
Methods 103:86–98 (2016) | doi:10.1016/j.ymeth.2016.04.004 | Preprint PDF

RNA-Seq Based Transcriptional Profiling of Pseudomonas Aeruginosa Pa14 After Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium
Muralidhar Tata, Michael T. Wolfinger, Fabian Amman, Nicole Roschanski, Andreas Dötsch, Elisabeth Sonnleitner, Susanne Häussler, Udo Bläsi
PLoS ONE 11 (1): e0147811 (2016) | doi:10.1371/journal.pone.0147811 | PDF

SHAPE Directed RNA Folding
Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
Bioinformatics 32: 145–47 (2016) | doi:10.1093/bioinformatics/btv523 | PDF

2015

General and miRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells
Sanja Antic, Michael T. Wolfinger, Anna Skucha, Stefanie Hosiner, Silke Dorner
Mol. Cell. Biol. MCB–01346 (2015) | doi:10.1128/MCB.01346-14 | PDF

ViennaNGS: A Toolbox for Building Efficient Next-Generation Sequencing Analysis Pipelines
Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
F1000Research 4:50 (2015) | doi:10.12688/f1000research.6157.2 | PDF

2014

Memory Efficient RNA Energy Landscape Exploration
Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger
Bioinformatics 30: 2584–91 (2014) | doi:10.1093/bioinformatics/btu337 | PDF

TSSAR: TSS Annotation Regime for dRNA-Seq Data
Fabian Amman, Michael T. Wolfinger, Ronny. Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß
BMC Bioinformatics 15 (1) (2014) | doi:10.1186/1471-2105-15-89 | PDF

2010

BarMap: RNA Folding on Dynamic Energy Landscapes
Ivo L. Hofacker, Christoph Flamm, Michael Heine, Michael T. Wolfinger, Gerik Scheuermann, Peter F. Stadler
RNA 16:1308–16 (2010) | doi:10.1261/rna.2093310 | PDF

2008

Folding Kinetics of Large RNAs
Michael Geis, Christoph Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler, Caroline Thurner
J. Mol. Biol. 379 (1): 160–73 (2008) | doi:10.1016/j.jmb.2008.02.064 | Preprint PDF

2006

Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler
Europhys. Lett. 74(4): 726–32 (2006) | doi:10.1209/epl/i2005-10577-0 | Preprint PDF

Visualization of Lattice-Based Protein Folding Simulations
Sebastian Pötzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm
In IV '06 Proceedings of the Conference on Information Visualization, pp89–94. Washington, DC, USA: IEEE Computer Society (2006) | doi:10.1109/IV.2006.127

2004

Efficient Computation of RNA Folding Dynamics
Michael T. Wolfinger, W. Andreas Svrcek-Seiler, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
J. Phys. A: Math. Gen. 37(17): 4731–41 (2004) | doi:10.1088/0305-4470/37/17/005 | PDF

2002

Barrier Trees of Degenerate Landscapes
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
Z. Phys. Chem. 216: 155–73 (2002) | doi:10.1524/zpch.2002.216.2.155 | Preprint PDF



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