Publications by authors named "Ivo Hofacker"

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Experimental identification of preQ-binding RNAs in the pathogenic bacterium .
Malou Hanisch, Laurin Flemmich, Christoph Mitteregger, Ingo Bauer, Cristian A Velandia-Huerto, Ivo Hofacker

RSC Chem Biol· November 2025

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tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.
Tom Rappol, Maria Waldl, Anastasia Chugunova, Ivo L Hofacker, Andrea Pauli

Nucleic Acids Res· September 2024

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Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.
Bernhard C Thiel, Giovanni Bussi, Simón Poblete, Ivo L Hofacker

Nucleic Acids Res· September 2024

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Sequence Design for RNA-RNA Interactions.
Maria Waldl, Hua-Ting Yao, Ivo L Hofacker

Methods Mol Biol· September 2024

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Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction.
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo Hofacker

J Comput Biol· June 2024

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The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.
Bernhard C Thiel, Simón Poblete, Ivo L Hofacker

Methods Mol Biol· May 2024

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Comparative RNA Genomics.
Rolf Backofen, Jan Gorodkin, Ivo L Hofacker, Peter F Stadler

Methods Mol Biol· May 2024

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3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations.
Irene K Beckmann, Maria Waldl, Sebastian Will, Ivo L Hofacker

RNA· January 2024

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Avirulent phenotype promotes adaptation to the intramacrophage environment.
Mariam R Farman, Denisa Petráčková, Dilip Kumar, Jakub Držmíšek, Argha Saha, Ivo Hofacker

Emerg Microbes Infect· December 2023

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Modified RNAs and predictions with the ViennaRNA Package.
Yuliia Varenyk, Thomas Spicher, Ivo L Hofacker, Ronny Lorenz

Bioinformatics· November 2023

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Local RNA folding revisited.
Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K Beckmann, Ivo L Hofacker

J Bioinform Comput Biol· August 2023

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Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.
Hua-Ting Yao, Ronny Lorenz, Ivo L Hofacker, Peter F Stadler

Algorithms Mol Biol· July 2023

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MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing.
Rong Zhai, Kai Ruan, German Farinas Perez, Miroslav Kubat, Jiaqi Liu, Ivo Hofacker

Res Sq· July 2023

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MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing.
Kai Ruan, German Farinas Perez, Jiaqi Liu, Miroslav Kubat, Ivo Hofacker

bioRxiv· June 2023

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Investigating RNA-RNA interactions through computational and biophysical analysis.
Tyler Mrozowich, Sean M Park, Maria Waldl, Amy Henrickson, Scott Tersteeg, Ivo L Hofacker

Nucleic Acids Res· May 2023

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DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.
Stefan Badelt, Ronny Lorenz, Ivo L Hofacker

Bioinformatics· January 2023

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Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction.
Christoph Flamm, Julia Wielach, Michael T Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L Hofacker

Front Bioinform· July 2022

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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

RNA Biol· April 2022

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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.
Sonja Zayni, Samar Damiati, Susana Moreno-Flores, Fabian Amman, Ivo Hofacker

Membranes (Basel)· September 2021

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RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes.
Gregor Entzian, Ivo L Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer

Bioinformatics· August 2021

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The locality dilemma of Sankoff-like RNA alignments.
Teresa Müller, Milad Miladi, Frank Hutter, Ivo Hofacker, Sebastian Will

Bioinformatics· July 2020

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Transcriptional profiling of human macrophages during infection with .
Denisa Petráčková, Mariam R Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Ivo Hofacker

RNA Biol· May 2020

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Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.
Doo Nam Kim, Bernhard C Thiel, Tyler Mrozowich, Scott P Hennelly, Ivo L Hofacker

Nat Commun· January 2020

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IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.
Rick Gelhausen, Sebastian Will, Ivo L Hofacker, Rolf Backofen, Martin Raden

J Bioinform Comput Biol· October 2019

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Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture.
Adriano de Bernardi Schneider, Roman Ochsenreiter, Reilly Hostager, Ivo L Hofacker, Daniel Janies

Viruses· August 2019

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