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Ivo 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
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