Ivo L. Hofacker

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 26

Top Topics

Secondary Structure

Soft Constraints

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

J. Bioinform. Comput. Biol.

Publications

Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. J. Comput. Biol. 31 (6) (2024)
Yuliia Varenyk, Thomas Spicher, Ivo L. Hofacker, Ronny Lorenz
Modified RNAs and predictions with the ViennaRNA Package. Bioinform. 39 (11) (2023)
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms Mol. Biol. 18 (1) (2023)
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. ISBRA (2023)
Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K. Beckmann, Ivo L. Hofacker, Sarah von Löhneysen, Peter F. Stadler
Local RNA folding revisited. J. Bioinform. Comput. Biol. 21 (4) (2023)
Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker
: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. Bioinform. 39 (1) (2023)
Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. Frontiers Bioinform. 2 (2022)
Gregor Entzian, Ivo L. Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. Bioinform. 37 (15) (2021)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) (2020)
Teresa Müller, Milad Miladi, Frank Hutter, Ivo L. Hofacker, Sebastian Will, Rolf Backofen
The locality dilemma of Sankoff-like RNA alignments. Bioinform. 36 (Supplement-1) (2020)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS (2020)
Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
, an RNA Python library centered on secondary structure elements. F1000Research 8 (2019)
Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. J. Bioinform. Comput. Biol. 17 (5) (2019)
Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden
Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction. BIOINFORMATICS (2019)
Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. CIBB (2019)
Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen, Christian Höner zu Siederdissen
CMV: visualization for RNA and protein family models and their comparisons. Bioinform. 34 (15) (2018)
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
RNAblueprint: flexible multiple target nucleic acid sequence design. Bioinform. 33 (18) (2017)
Stefan Badelt, Christoph Flamm, Ivo L. Hofacker
Computational Design of a Circular RNA with Prionlike Behavior. Artif. Life 22 (2) (2016)
Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
RNA folding with hard and soft constraints. Algorithms Mol. Biol. 11 (2016)
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
Pseudoknots in RNA folding landscapes. Bioinform. 32 (2) (2016)
Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L. Hofacker, Philipp Kügler
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (1) (2016)
Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
SHAPE directed RNA folding. Bioinform. 32 (1) (2016)
Jörg Fallmann, Vitaly Sedlyarov, Andrea Tanzer, Pavel Kovarik, Ivo L. Hofacker
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. Nucleic Acids Res. 44 (Database-Issue) (2016)
Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
Product Grammars for Alignment and Folding. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Peter Kerpedjiev, Stefan Hammer, Ivo L. Hofacker
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinform. 31 (20) (2015)
Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, Kevin M. Weeks
Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA. PLoS Comput. Biol. 11 (5) (2015)
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. Bioinform. 30 (14) (2014)
Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer
Challenges in RNA virus bioinformatics. Bioinform. 30 (13) (2014)
Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß
TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinform. 15 (2014)
Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, Sebastian Will
The Trouble with Long-Range Base Pairs in RNA Folding. BSB (2013)
Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
How to Multiply Dynamic Programming Algorithms. BSB (2013)
Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (4) (2013)
Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen
CMCompare webserver: comparing RNA families via covariance models. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler
Symmetric circular matchings and RNA folding. Discret. Math. 312 (1) (2012)
Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
RNA Folding Algorithms with G-Quadruplexes. BSB (2012)
Ronny Lorenz, Ivo L. Hofacker, Stephan H. Bernhart
Folding RNA/DNA hybrid duplexes. Bioinform. 28 (19) (2012)
Jan Gorodkin, Ivo L. Hofacker
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Comput. Biol. 7 (8) (2011)
Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
A folding algorithm for extended RNA secondary structures. Bioinform. 27 (13) (2011)
Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker
RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker
Fast accessibility-based prediction of RNA-RNA interactions. Bioinform. 27 (14) (2011)
Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
ViennaRNA Package 2.0. Algorithms Mol. Biol. 6 (2011)
Stephan H. Bernhart, Ulrike Mückstein, Ivo L. Hofacker
RNA Accessibility in cubic time. Algorithms Mol. Biol. 6 (2011)
Andreas R. Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, Ivo L. Hofacker
AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res. 39 (Database-Issue) (2011)
Andreas R. Gruber, Stephan H. Bernhart, You Zhou, Ivo L. Hofacker
RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures. GCB (2010)
Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
Session Introduction. Pacific Symposium on Biocomputing (2010)
Christian Höner zu Siederdissen, Ivo L. Hofacker
Discriminatory power of RNA family models. Bioinform. 26 (18) (2010)
Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil
Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinform. 11 (2010)
Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
RNAz 2.0: Improved Noncoding RNA Detection. Pacific Symposium on Biocomputing (2010)
Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
: efficient target prediction for H/ACA snoRNAs. Bioinform. 26 (5) (2010)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker
2D Projections of RNA Folding Landscapes. GCB (2009)
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
www.rnaworkbench.com: A new program for analyzing RNA interference. Comput. Methods Programs Biomed. 90 (1) (2008)
Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker
Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. BIRD (2008)
Andreas R. Gruber, Stephan H. Bernhart, Ivo L. Hofacker, Stefan Washietl
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinform. 9 (2008)
Andreas R. Gruber, Ronny Lorenz, Stephan H. Bernhart, Richard Neuböck, Ivo L. Hofacker
The Vienna RNA Websuite. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
SnoReport: computational identification of snoRNAs with unknown targets. Bioinform. 24 (2) (2008)
Hakim Tafer, Ivo L. Hofacker
RNAplex: a fast tool for RNA-RNA interaction search. Bioinform. 24 (22) (2008)
Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinform. 9 (2008)
Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler
Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA (2007)
Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, Stefan Washietl
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. 3 (4) (2007)
Axel Mosig, Ivo L. Hofacker, Peter F. Stadler
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. German Conference on Bioinformatics (2006)
Ivo L. Hofacker, Peter F. Stadler
Memory efficient folding algorithms for circular RNA secondary structures. Bioinform. 22 (10) (2006)
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
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res. 34 (Database-Issue) (2006)
Stephan H. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol. 1 (2006)
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
Thermodynamics of RNA-RNA binding. Bioinform. 22 (10) (2006)
Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler
Local RNA base pairing probabilities in large sequences. Bioinform. 22 (5) (2006)
Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinform. 7 (2006)
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12 (5) (2006)
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinform. 6 (2005)
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 102 (7) (2005)
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
Thermodynamics of RNA-RNA Binding. German Conference on Bioinformatics (2005)
Ivo L. Hofacker, Peter F. Stadler
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics (2005)
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
Evolutionary patterns of non-coding RNAs. Theory Biosci. 123 (4) (2005)
Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (2) (2004)
Ivo L. Hofacker, Stephan H. Bernhart, Peter F. Stadler
Alignment of RNA base pairing probability matrices. Bioinform. 20 (14) (2004)
C. Thurner, Ivo L. Hofacker, Peter F. Stadler
Conserved RNA Pseudoknots. German Conference on Bioinformatics (2004)
Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
Conserved RNA secondary structures in viral genomes: a survey. Bioinform. 20 (10) (2004)
Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinform. 20 (2) (2004)
Ivo L. Hofacker, Peter F. Stadler
The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science (2004)
Ivo L. Hofacker
Vienna RNA secondary structure server. Nucleic Acids Res. 31 (13) (2003)
Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
Conserved RNA secondary structures in viral genomes: A survey. German Conference on Bioinformatics (2003)
Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler
Stochastic pairwise alignments. ECCB (2002)
Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. J. Comput. Biol. 7 (1-2) (2000)
Ivo L. Hofacker, Peter F. Stadler
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Comput. Chem. 23 (3-4) (1999)
G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
An efficient potential for protein sequence design. German Conference on Bioinformatics (1999)
Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler
Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics (1999)
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
The Computational Biology of RNA Secondary Structures. Adv. Complex Syst. 2 (1) (1999)
Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
Combinatorics of RNA Secondary Structures. Discret. Appl. Math. 88 (1-3) (1998)
Jan Cupal, Ivo L. Hofacker, Peter F. Stadler
Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. German Conference on Bioinformatics (1996)
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. KDD (1996)