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Ivo L. Hofacker
2010 – today
- 2012
[j37]Ronny Lorenz, Ivo L. Hofacker, Stephan H. F. Bernhart: Folding RNA/DNA hybrid duplexes. Bioinformatics 28(19): 2530-2531 (2012)- [j36]Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler: Symmetric circular matchings and RNA folding. Discrete Mathematics 312(1): 100-112 (2012)
- [c18]Ronny Lorenz, Stephan H. F. 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
- [j35]Stephan H. F. Bernhart, Ulrike Mückstein, Ivo L. Hofacker: RNA Accessibility in cubic time. Algorithms for Molecular Biology 6: 3 (2011)
- [j34]Ronny Lorenz, Stephan H. F. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker: ViennaRNA Package 2.0. Algorithms for Molecular Biology 6: 26 (2011)
- [j33]Christian Höner zu Siederdissen, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: A folding algorithm for extended RNA secondary structures. Bioinformatics [ISMB/ECCB] 27(13): 129-136 (2011)
- [j32]Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker: Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics 27(14): 1934-1940 (2011)
- [j31]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 Research 39(Database-Issue): 66-69 (2011)
- [j30]Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker: RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Research 39(Web-Server-Issue): 149-154 (2011)
- [j29]Jan Gorodkin, Ivo L. Hofacker: From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Computational Biology 7(8) (2011)
- 2010
- [j28]Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler: RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics 26(5): 610-616 (2010)
- [j27]Christian Höner zu Siederdissen, Ivo L. Hofacker: Discriminatory power of RNA family models. Bioinformatics 26(18) (2010)
- [j26]Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, David P. Kreil: Hybridization thermodynamics of NimbleGen Microarrays. BMC Bioinformatics 11: 35 (2010)
- [c17]Andreas R. Gruber, Stephan H. F. 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
- [j25]Jana Hertel, Ivo L. Hofacker, Peter F. Stadler: SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24(2): 158-164 (2008)
- [j24]Hakim Tafer, Ivo L. Hofacker: RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 24(22): 2657-2663 (2008)
- [j23]Stephan H. F. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler: RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9 (2008)
- [j22]Andreas R. Gruber, Stephan H. F. Bernhart, Ivo L. Hofacker, Stefan Washietl: Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics 9 (2008)
- [j21]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. Computer Methods and Programs in Biomedicine 90(1): 89-94 (2008)
- [j20]Andreas R. Gruber, Ronny Lorenz, Stephan H. F. Bernhart, Richard Neuböck, Ivo L. Hofacker: The Vienna RNA Websuite. Nucleic Acids Research 36(Web-Server-Issue): 70-74 (2008)
- [c13]Ulrike Mückstein, Hakim Tafer, Stephan H. F. 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
- 2007
- [j19]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 Research 35(Web-Server-Issue): 335-338 (2007)
- [j18]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 Computational Biology 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
- [j17]Stephan H. F. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker: Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology 1 (2006)
- [j16]Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler: Local RNA base pairing probabilities in large sequences. Bioinformatics 22(5): 614-615 (2006)
- [j15]Ivo L. Hofacker, Peter F. Stadler: Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22(10): 1172-1176 (2006)
- [j14]Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: Thermodynamics of RNA-RNA binding. Bioinformatics 22(10): 1177-1182 (2006)
- [j13]Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler: Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 7: 67 (2006)
- [j12]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 Research 34(Database-Issue): 135-139 (2006)
- [j11]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
- [j10]Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler: Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinformatics 6: 160 (2005)
- [j9]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 in Biosciences 123(4): 301-369 (2005)
- [c10]Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. 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
- [j8]Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler: Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20(2): 186-190 (2004)
- [j7]Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits: Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics 20(10): 1495-1499 (2004)
- [j6]Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler: Alignment of RNA base pairing probability matrices. Bioinformatics 20(14): 2222-2227 (2004)
- [j5]Christina Witwer, Ivo L. Hofacker, Peter F. Stadler: Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE/ACM Trans. Comput. Biology 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
- [j4]Ivo L. Hofacker: Vienna RNA secondary structure server. Nucleic Acids Research 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
- [j3]Martin Fekete, Ivo L. Hofacker, Peter F. Stadler: Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. Journal of Computational Biology 7(1-2): 171-182 (2000)
1990 – 1999
- 1999
- [j2]Ivo L. Hofacker, Peter F. Stadler: Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Computers & Chemistry 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. Discrete Applied Mathematics 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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last updated on 2013-03-08 22:09 CET by the dblp team