Ivo L. Hofacker

91 papers A* 1A 1B 1C 1Misc 3Journal 64Unranked 19
YearRankTypeTitle / Venue / Authors
2025 B conf
Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances.
RECOMB
Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao
2024 J jnl
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction.
J. Comput. Biol.
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2023 J jnl
Local RNA folding revisited.
J. Bioinform. Comput. Biol.
Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K. Beckmann, Ivo L. Hofacker, Sarah von Löhneysen, Peter F. Stadler
2023 J jnl
Modified RNAs and predictions with the ViennaRNA Package.
Bioinform.
Yuliia Varenyk, Thomas Spicher, Ivo L. Hofacker, Ronny Lorenz
2023 J jnl
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.
Algorithms Mol. Biol.
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2023 — conf
Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction.
ISBRA
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2022 J jnl
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction.
Frontiers Bioinform.
Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker
2021 J jnl
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes.
Bioinform.
Gregor Entzian, Ivo L. Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer
2020 — conf
Efficient Algorithms for Co-folding of Multiple RNAs.
BIOSTEC (Selected Papers)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2020 — conf
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding.
BIOINFORMATICS
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2020 J jnl
The locality dilemma of Sankoff-like RNA alignments.
Bioinform.
Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen
2019 J jnl
3D based on 2D: Calculating helix angles and stacking patterns using
F1000Research
Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
2019 — conf
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure.
CIBB
Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler
2019 — conf
Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction.
BIOINFORMATICS
Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
2019 J jnl
IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.
J. Bioinform. Comput. Biol.
Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
2018 J jnl
CMV: visualization for RNA and protein family models and their comparisons.
Bioinform.
Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen, Christian Höner zu Siederdissen
2017 J jnl
RNAblueprint: flexible multiple target nucleic acid sequence design.
Bioinform.
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
2016 J jnl
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
Nucleic Acids Res.
Jörg Fallmann, Vitaly Sedlyarov, Andrea Tanzer, Pavel Kovarik, Ivo L. Hofacker
2016 J jnl
Computational Design of a Circular RNA with Prionlike Behavior.
Artif. Life
Stefan Badelt, Christoph Flamm, Ivo L. Hofacker
2016 J jnl
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L. Hofacker, Philipp Kügler
2016 J jnl
Pseudoknots in RNA folding landscapes.
Bioinform.
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
2016 J jnl
RNA folding with hard and soft constraints.
Algorithms Mol. Biol.
Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2016 J jnl
SHAPE directed RNA folding.
Bioinform.
Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
2015 J jnl
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.
Bioinform.
Peter Kerpedjiev, Stefan Hammer, Ivo L. Hofacker
2015 J jnl
Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.
PLoS Comput. Biol.
Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, Kevin M. Weeks
2015 J jnl
Product Grammars for Alignment and Folding.
IEEE ACM Trans. Comput. Biol. Bioinform.
Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
2014 J jnl
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
Bioinform.
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
2014 J jnl
Challenges in RNA virus bioinformatics.
Bioinform.
Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer
2014 J jnl
TSSAR: TSS annotation regime for dRNA-seq data.
BMC Bioinform.
Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß
2013 J jnl
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
2013 J jnl
CMCompare webserver: comparing RNA families via covariance models.
Nucleic Acids Res.
Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen
2013 — conf
How to Multiply Dynamic Programming Algorithms.
BSB
Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
2013 J jnl
The RNAsnp web server: predicting SNP effects on local RNA secondary structure.
Nucleic Acids Res.
Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
2013 — conf
The Trouble with Long-Range Base Pairs in RNA Folding.
BSB
Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, Sebastian Will
2012 J jnl
Folding RNA/DNA hybrid duplexes.
Bioinform.
Ronny Lorenz, Ivo L. Hofacker, Stephan H. Bernhart
2012 — conf
RNA Folding Algorithms with G-Quadruplexes.
BSB
Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
2012 J jnl
Symmetric circular matchings and RNA folding.
Discret. Math.
Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler
2011 J jnl
A folding algorithm for extended RNA secondary structures.
Bioinform.
Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
2011 J jnl
AREsite: a database for the comprehensive investigation of AU-rich elements.
Nucleic Acids Res.
Andreas R. Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, Ivo L. Hofacker
2011 J jnl
Fast accessibility-based prediction of RNA-RNA interactions.
Bioinform.
Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker
2011 J jnl
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs.
PLoS Comput. Biol.
Jan Gorodkin, Ivo L. Hofacker
2011 J jnl
RNA Accessibility in cubic time.
Algorithms Mol. Biol.
Stephan H. Bernhart, Ulrike Mückstein, Ivo L. Hofacker
2011 J jnl
RNApredator: fast accessibility-based prediction of sRNA targets.
Nucleic Acids Res.
Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker
2011 J jnl
ViennaRNA Package 2.0.
Algorithms Mol. Biol.
Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
2010 J jnl
Discriminatory power of RNA family models.
Bioinform.
Christian Höner zu Siederdissen, Ivo L. Hofacker
2010 J jnl
Hybridization thermodynamics of NimbleGen Microarrays.
BMC Bioinform.
Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil
2010 — conf
RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures.
GCB
Andreas R. Gruber, Stephan H. Bernhart, You Zhou, Ivo L. Hofacker
2010 Misc conf
RNAz 2.0: Improved Noncoding RNA Detection.
Pacific Symposium on Biocomputing
Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
2010 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
2009 — conf
2D Projections of RNA Folding Landscapes.
GCB
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker
2008 J jnl
RNAalifold: improved consensus structure prediction for RNA alignments.
BMC Bioinform.
Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler
2008 J jnl
RNAplex: a fast tool for RNA-RNA interaction search.
Bioinform.
Hakim Tafer, Ivo L. Hofacker
2008 J jnl
SnoReport: computational identification of snoRNAs with unknown targets.
Bioinform.
Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
2008 J jnl
Strategies for measuring evolutionary conservation of RNA secondary structures.
BMC Bioinform.
Andreas R. Gruber, Stephan H. Bernhart, Ivo L. Hofacker, Stefan Washietl
2008 J jnl
The Vienna RNA Websuite.
Nucleic Acids Res.
Andreas R. Gruber, Ronny Lorenz, Stephan H. Bernhart, Richard Neuböck, Ivo L. Hofacker
2008 — conf
Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics.
BIRD
Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker
2008 — ch.
Visualization of Barrier Tree Sequences Revisited.
Visualization in Medicine and Life Sciences
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2008 J jnl
www.rnaworkbench.com: A new program for analyzing RNA interference.
Comput. Methods Programs Biomed.
Radka Svobodová Vareková, Ivan Bradác, Martin Plchút, Michal Skrdla, Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer, Heinrich J. Huber, Gerhard Gierlinger, Ronald Graf, Hakim Tafer, Ivo L. Hofacker, Peter Schuster, Martin Polcík
2007 J jnl
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering.
PLoS Comput. Biol.
Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
2007 A conf
Saddles and Barrier in Landscapes of Generalized Search Operators.
FOGA
Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler
2007 J jnl
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.
Nucleic Acids Res.
Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, Stefan Washietl
2006 J jnl
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BMC Bioinform.
Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2006 — conf
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs.
German Conference on Bioinformatics
Axel Mosig, Ivo L. Hofacker, Peter F. Stadler
2006 J jnl
Local RNA base pairing probabilities in large sequences.
Bioinform.
Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler
2006 J jnl
Memory efficient folding algorithms for circular RNA secondary structures.
Bioinform.
Ivo L. Hofacker, Peter F. Stadler
2006 J jnl
Partition function and base pairing probabilities of RNA heterodimers.
Algorithms Mol. Biol.
Stephan H. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
2006 J jnl
Thermodynamics of RNA-RNA binding.
Bioinform.
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
2006 J jnl
Visualization of Barrier Tree Sequences.
IEEE Trans. Vis. Comput. Graph.
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2006 J jnl
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Nucleic Acids Res.
Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker
2005 J jnl
Evolutionary patterns of non-coding RNAs.
Theory Biosci.
Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer
2005 J jnl
Fast and reliable prediction of noncoding RNAs.
Proc. Natl. Acad. Sci. USA
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
2005 — conf
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures.
German Conference on Bioinformatics
Ivo L. Hofacker, Peter F. Stadler
2005 J jnl
Multiple sequence alignments of partially coding nucleic acid sequences.
BMC Bioinform.
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
2005 — conf
Thermodynamics of RNA-RNA Binding.
German Conference on Bioinformatics
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
2004 J jnl
Alignment of RNA base pairing probability matrices.
Bioinform.
Ivo L. Hofacker, Stephan H. Bernhart, Peter F. Stadler
2004 — conf
Conserved RNA Pseudoknots.
German Conference on Bioinformatics
C. Thurner, Ivo L. Hofacker, Peter F. Stadler
2004 J jnl
Conserved RNA secondary structures in viral genomes: a survey.
Bioinform.
Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
2004 J jnl
Prediction of Consensus RNA Secondary Structures Including Pseudoknots.
IEEE ACM Trans. Comput. Biol. Bioinform.
Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
2004 J jnl
Prediction of locally stable RNA secondary structures for genome-wide surveys.
Bioinform.
Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
2004 Misc conf
The Partition Function Variant of Sankoff's Algorithm.
International Conference on Computational Science
Ivo L. Hofacker, Peter F. Stadler
2003 — conf
Conserved RNA secondary structures in viral genomes: A survey.
German Conference on Bioinformatics
Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
2003 J jnl
Vienna RNA secondary structure server.
Nucleic Acids Res.
Ivo L. Hofacker
2002 C conf
Stochastic pairwise alignments.
ECCB
Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler
2000 J jnl
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers.
J. Comput. Biol.
Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
1999 — conf
An efficient potential for protein sequence design.
German Conference on Bioinformatics
G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
1999 J jnl
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes.
Comput. Chem.
Ivo L. Hofacker, Peter F. Stadler
1999 — conf
Conserved secondary structures in hepatitis B virus DNA.
German Conference on Bioinformatics
Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler
1999 J jnl
RNA
Adv. Complex Syst.
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
1998 J jnl
Combinatorics of RNA Secondary Structures.
Discret. Appl. Math.
Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
1996 — conf
Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures.
German Conference on Bioinformatics
Jan Cupal, Ivo L. Hofacker, Peter F. Stadler
1996 A* conf
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers.
KDD
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz