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ORCIDIvo L. Hofacker
Person information
- affiliation: University of Vienna, Institute for Theoretical Chemistry, Austria
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2020 – today
- 2024
[j65]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): 549-563 (2024)- 2023
- [j64]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): 8 (2023) - [j63]Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker:
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. Bioinform. 39(1) (2023) - [j62]Yuliia Varenyk, Thomas Spicher, Ivo L. Hofacker, Ronny Lorenz:
Modified RNAs and predictions with the ViennaRNA Package. Bioinform. 39(11) (2023) - [j61]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): 2350016:1-2350016:19 (2023) - [c25]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: 267-279 - 2022
- [j60]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) - 2021
- [j59]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): 2126-2133 (2021) - 2020
- [j58]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): i242-i250 (2020) - [c24]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS 2020: 23-31 - [c23]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) 2020: 193-214
2010 – 2019
- 2019
- [j57]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): 1940009:1-1940009:16 (2019) - [c22]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: 131-140 - [c21]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: 159-170 - [i1]Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker:
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Research 8: 287 (2019) - 2018
- [j56]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): 2676-2678 (2018) - 2017
- [j55]Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß:
RNAblueprint: flexible multiple target nucleic acid sequence design. Bioinform. 33(18): 2850-2858 (2017) - 2016
- [j54]Stefan Badelt, Christoph Flamm, Ivo L. Hofacker:
Computational Design of a Circular RNA with Prionlike Behavior. Artif. Life 22(2): 172-184 (2016) - [j53]Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler:
RNA folding with hard and soft constraints. Algorithms Mol. Biol. 11: 8 (2016) - [j52]Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger:
SHAPE directed RNA folding. Bioinform. 32(1): 145-147 (2016) - [j51]Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Pseudoknots in RNA folding landscapes. Bioinform. 32(2): 187-194 (2016) - [j50]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): 90-95 (2016) - [j49]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): 64-75 (2016) - 2015
- [j48]Peter Kerpedjiev, Stefan Hammer, Ivo L. Hofacker:
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinform. 31(20): 3377-3379 (2015) - [j47]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) - [j46]Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler:
Product Grammars for Alignment and Folding. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 507-519 (2015) - 2014
- [j45]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): 1793-1799 (2014) - [j44]Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. Bioinform. 30(14): 2009-2017 (2014) - [j43]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: 89 (2014) - 2013
- [j42]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): 475-479 (2013) - [j41]Florian Eggenhofer, Ivo L. Hofacker, Christian Höner zu Siederdissen:
CMCompare webserver: comparing RNA families via covariance models. Nucleic Acids Res. 41(Webserver-Issue): 499-503 (2013) - [j40]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): 832-844 (2013) - [c20]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: 1-11 - [c19]Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler:
How to Multiply Dynamic Programming Algorithms. BSB 2013: 82-93 - 2012
- [j39]Ronny Lorenz, Ivo L. Hofacker, Stephan H. Bernhart:
Folding RNA/DNA hybrid duplexes. Bioinform. 28(19): 2530-2531 (2012) - [j38]Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler:
Symmetric circular matchings and RNA folding. Discret. Math. 312(1): 100-112 (2012) - [c18]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: 49-60 - 2011
- [j37]Stephan H. Bernhart, Ulrike Mückstein, Ivo L. Hofacker:
RNA Accessibility in cubic time. Algorithms Mol. Biol. 6: 3 (2011) - [j36]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: 26 (2011) - [j35]Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
A folding algorithm for extended RNA secondary structures. Bioinform. 27(13): 129-136 (2011) - [j34]Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker:
Fast accessibility-based prediction of RNA-RNA interactions. Bioinform. 27(14): 1934-1940 (2011) - [j33]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): 66-69 (2011) - [j32]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): 149-154 (2011) - [j31]Jan Gorodkin, Ivo L. Hofacker:
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Comput. Biol. 7(8) (2011) - 2010
- [j30]Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler:
RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinform. 26(5): 610-616 (2010) - [j29]Christian Höner zu Siederdissen, Ivo L. Hofacker:
Discriminatory power of RNA family models. Bioinform. 26(18) (2010) - [j28]Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil:
Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinform. 11: 35 (2010) - [c17]Andreas R. Gruber, Stephan H. Bernhart, You Zhou, Ivo L. Hofacker:
RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures. GCB 2010: 11-20 - [c16]Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler:
Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56 - [c15]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: 69-79
2000 – 2009
- 2009
- [c14]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker:
2D Projections of RNA Folding Landscapes. GCB 2009: 11-20 - 2008
- [j27]Jana Hertel, Ivo L. Hofacker, Peter F. Stadler:
SnoReport: computational identification of snoRNAs with unknown targets. Bioinform. 24(2): 158-164 (2008) - [j26]Hakim Tafer, Ivo L. Hofacker:
RNAplex: a fast tool for RNA-RNA interaction search. Bioinform. 24(22): 2657-2663 (2008) - [j25]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) - [j24]Andreas R. Gruber, Stephan H. Bernhart, Ivo L. Hofacker, Stefan Washietl:
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinform. 9 (2008) - [j23]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): 89-94 (2008) - [j22]Andreas R. Gruber, Ronny Lorenz, Stephan H. Bernhart, Richard Neuböck, Ivo L. Hofacker:
The Vienna RNA Websuite. Nucleic Acids Res. 36(Web-Server-Issue): 70-74 (2008) - [c13]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: 114-127 - [p1]Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Visualization of Barrier Tree Sequences Revisited. Visualization in Medicine and Life Sciences 2008: 275-290 - 2007
- [j21]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): 335-338 (2007) - [j20]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) - [c12]Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler:
Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA 2007: 194-212 - 2006
- [j19]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) - [j18]Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler:
Local RNA base pairing probabilities in large sequences. Bioinform. 22(5): 614-615 (2006) - [j17]Ivo L. Hofacker, Peter F. Stadler:
Memory efficient folding algorithms for circular RNA secondary structures. Bioinform. 22(10): 1172-1176 (2006) - [j16]Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
Thermodynamics of RNA-RNA binding. Bioinform. 22(10): 1177-1182 (2006) - [j15]Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinform. 7: 67 (2006) - [j14]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): 135-139 (2006) - [j13]Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12(5): 781-788 (2006) - [c11]Axel Mosig, Ivo L. Hofacker, Peter F. Stadler:
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. German Conference on Bioinformatics 2006: 93-102 - 2005
- [j12]Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler:
Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinform. 6: 160 (2005) - [j11]Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler:
Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 102(7): 2454-2459 (2005) - [j10]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): 301-369 (2005) - [c10]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: 3-13 - [c9]Ivo L. Hofacker, Peter F. Stadler:
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics 2005: 15-25 - 2004
- [j9]Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler:
Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinform. 20(2): 186-190 (2004) - [j8]Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits:
Conserved RNA secondary structures in viral genomes: a survey. Bioinform. 20(10): 1495-1499 (2004) - [j7]Ivo L. Hofacker, Stephan H. Bernhart, Peter F. Stadler:
Alignment of RNA base pairing probability matrices. Bioinform. 20(14): 2222-2227 (2004) - [j6]Christina Witwer, Ivo L. Hofacker, Peter F. Stadler:
Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE ACM Trans. Comput. Biol. Bioinform. 1(2): 66-77 (2004) - [c8]C. Thurner, Ivo L. Hofacker, Peter F. Stadler:
Conserved RNA Pseudoknots. German Conference on Bioinformatics 2004: 207-216 - [c7]Ivo L. Hofacker, Peter F. Stadler:
The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science 2004: 728-735 - 2003
- [j5]Ivo L. Hofacker:
Vienna RNA secondary structure server. Nucleic Acids Res. 31(13): 3429-3431 (2003) - [c6]Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits:
Conserved RNA secondary structures in viral genomes: A survey. German Conference on Bioinformatics 2003: 57-62 - 2002
- [c5]Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler:
Stochastic pairwise alignments. ECCB 2002: 153-160 - 2000
- [j4]Martin Fekete, Ivo L. Hofacker, Peter F. Stadler:
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. J. Comput. Biol. 7(1-2): 171-182 (2000)
1990 – 1999
- 1999
- [j3]Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
RNA In Silico The Computational Biology of RNA Secondary Structures. Adv. Complex Syst. 2(1): 65-100 (1999) - [j2]Ivo L. Hofacker, Peter F. Stadler:
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Comput. Chem. 23(3-4): 401-414 (1999) - [c4]Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler:
Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics 1999: 73-79 - [c3]G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler:
An efficient potential for protein sequence design. German Conference on Bioinformatics 1999: 107-112 - 1998
- [j1]Ivo L. Hofacker, Peter Schuster, Peter F. Stadler:
Combinatorics of RNA Secondary Structures. Discret. Appl. Math. 88(1-3): 207-237 (1998) - 1996
- [c2]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: 184-186 - [c1]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: 20-25
Coauthor Index
[j65] [j64] [j61] [c25] [c24] [c23] [c21] [j53] [j52] [j51] [j46] [j45] [j44] [j43] [j42] [j40] [c20] [c19] [j38] [c18] [j36] [j35] [j34] [j32] [j30] [c16] [c15] [j27] [j25] [c13] [p1] [j20] [c12] [j19] [j18] [j17] [j16] [j15] [j14] [j13] [c11] [j12] [j11] [j10] [c10] [c9] [j9] [j8] [j7] [j6] [c8] [c7] [c6] [c5] [j4] [j3] [j2] [c4] [c3] [j1] [c2] [c1]
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