Works by Hofacker, Ivo L.

Results: 76

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs.

Published in:

Human Mutation, 2013, v. 34, n. 6, p. 925, doi. 10.1002/humu.22323

By:

Sabarinathan, Radhakrishnan;
Tafer, Hakim;
Seemann, Stefan E.;
Hofacker, Ivo L.;
Stadler, Peter F.;
Gorodkin, Jan

Publication type:

Article

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs.

Published in:

Human Mutation, 2013, v. 34, n. 4, p. 546, doi. 10.1002/humu.22273

By:

Sabarinathan, Radhakrishnan;
Tafer, Hakim;
Seemann, Stefan E.;
Hofacker, Ivo L.;
Stadler, Peter F.;
Gorodkin, Jan

Publication type:

Article

Computational design of RNAs with complex energy landscapes.

Published in:

Biopolymers, 2013, v. 99, n. 12, p. 1124, doi. 10.1002/bip.22337

By:

Höner zu Siederdissen, Christian;
Hammer, Stefan;
Abfalter, Ingrid;
Hofacker, Ivo L.;
Flamm, Christoph;
Stadler, Peter F.

Publication type:

Article

RNAblueprint: flexible multiple target nucleic acid sequence design.

Published in:

Bioinformatics, 2017, v. 33, n. 18, p. 2850, doi. 10.1093/bioinformatics/btx263

By:

Hammer, Stefan;
Tschiatschek, Birgit;
Flamm, Christoph;
Hofacker, Ivo L.;
Findeiß, Sven

Publication type:

Article

Pseudoknots in RNA folding landscapes.

Published in:

Bioinformatics, 2016, v. 32, n. 2, p. 187, doi. 10.1093/bioinformatics/btv572

By:

Kucharík, Marcel;
Hofacker, Ivo L.;
Stadler, Peter F.;
Jing Qin

Publication type:

Article

SHAPE directed RNA folding.

Published in:

Bioinformatics, 2016, v. 32, n. 1, p. 145, doi. 10.1093/bioinformatics/btv523

By:

Lorenz, Ronny;
Luntzer, Dominik;
Hofacker, Ivo L.;
Stadler, Peter F.;
Wolfinger, Michael T.

Publication type:

Article

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3377, doi. 10.1093/bioinformatics/btv372

By:

Kerpedjiev, Peter;
Hammer, Stefan;
Hofacker, Ivo L.

Publication type:

Article

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.

Published in:

Bioinformatics, 2014, v. 30, n. 14, p. 2009

By:

Kucharík, Marcel;
Hofacker, Ivo L.;
Stadler, Peter F.;
Qin, Jing

Publication type:

Article

Challenges in RNA virus bioinformatics.

Published in:

Bioinformatics, 2014, v. 30, n. 13, p. 1793, doi. 10.1093/bioinformatics/btu105

By:

Marz, Manja;
Beerenwinkel, Niko;
Drosten, Christian;
Fricke, Markus;
Frishman, Dmitrij;
Hofacker, Ivo L.;
Hoffmann, Dieter;
Middendorf, Martin;
Rattei, Thomas;
Stadler, Peter F.;
Töpfer, Armin

Publication type:

Article

Folding RNA/DNA hybrid duplexes.

Published in:

Bioinformatics, 2012, v. 28, n. 19, p. 2530, doi. 10.1093/bioinformatics/bts466

By:

Lorenz, Ronny;
Hofacker, Ivo L.;
Bernhart, Stephan H.

Publication type:

Article

Fast accessibility-based prediction of RNA–RNA interactions.

Published in:

Bioinformatics, 2011, v. 27, n. 14, p. 1934, doi. 10.1093/bioinformatics/btr281

By:

Tafer, Hakim;
Amman, Fabian;
Eggenhofer, Florian;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

A folding algorithm for extended RNA secondary structures.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. i129, doi. 10.1093/bioinformatics/btr220

By:

zu Siederdissen, Christian Höner;
Bernhart, Stephan H.;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

Discriminatory power of RNA family models.

Published in:

Bioinformatics, 2010, v. 26, n. 18, p. i453, doi. 10.1093/bioinformatics/btq370

By:

Siederdissen, Christian Höner zu;
Hofacker, Ivo L.

Publication type:

Article

RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Published in:

Bioinformatics, 2010, v. 26, n. 5, p. 610, doi. 10.1093/bioinformatics/btp680

By:

Tafer, Hakim;
Kehr, Stephanie;
Hertel, Jana;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

RNAplex: a fast tool for RNA-RNA interaction search.

Published in:

Bioinformatics, 2008, v. 24, n. 22, p. 2657, doi. 10.1093/bioinformatics/btn193

By:

Hakim Tafer;
Ivo L. Hofacker

Publication type:

Article

SnoReport: computational identification of snoRNAs with unknown targets.

Published in:

Bioinformatics, 2008, v. 24, n. 2, p. 158, doi. 10.1093/bioinformatics/btm464

By:

Jana Hertel;
Ivo L. Hofacker;
Peter F. Stadler

Publication type:

Article

Thermodynamics of RNA–RNA binding.

Published in:

Bioinformatics, 2006, v. 22, n. 10, p. 1177, doi. 10.1093/bioinformatics/btl024

By:

Ulrike Mückstein;
Hakim Tafer;
Jörg Hackermüller;
Stephan H. Bernhart;
Peter F. Stadler;
Ivo L. Hofacker

Publication type:

Article

Memory efficient folding algorithms for circular RNA secondary structures.

Published in:

Bioinformatics, 2006, v. 22, n. 10, p. 1172, doi. 10.1093/bioinformatics/btl023

By:

Ivo L. Hofacker;
Peter F. Stadler

Publication type:

Article

Local RNA base pairing probabilities in large sequences.

Published in:

Bioinformatics, 2006, v. 22, n. 5, p. 614, doi. 10.1093/bioinformatics/btk014

By:

Stephan H. Bernhart;
Ivo L. Hofacker;
Peter F. Stadler

Publication type:

Article

Evolution of metabolic networks: a computational frame-work.

Published in:

Journal of Systems Chemistry, 2010, v. 1, n. 1, p. 1, doi. 10.1186/1759-2208-1-4

By:

Flamm, Christoph;
Ullrich, Alexander;
Ekker, Heinz;
Mann, Martin;
Högerl, Daniel;
Rohrschneider, Markus;
Sauer, Sebastian;
Scheuermann, Gerik;
Klemm, Konstantin;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.

Published in:

Genes, 2018, v. 9, n. 8, p. 392, doi. 10.3390/genes9080392

By:

Thiel, Bernhard C.;
Ochsenreiter, Roman;
Gadekar, Veerendra P.;
Tanzer, Andrea;
Hofacker, Ivo L.

Publication type:

Article

How microRNAs choose their targets.

Published in:

Nature Genetics, 2007, v. 39, n. 10, p. 1191, doi. 10.1038/ng1007-1191

By:

Hofacker, Ivo L.

Publication type:

Article

Bcheck: a wrapper tool for detecting RNase P RNA genes.

Published in:

BMC Genomics, 2010, v. 11, p. 432, doi. 10.1186/1471-2164-11-432

By:

Yusuf, Dilmurat;
Marz, Manja;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

Complete suboptimal folding of RNA and the stability of secondary structures.

Published in:

Biopolymers, 1999, v. 49, n. 2, p. 145, doi. 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G

By:

Wuchty, Stefan;
Fontana, Walter;
Hofacker, Ivo L.;
Schuster, Peter

Publication type:

Article

Alignment of RNA base pairing probability matrices.

Published in:

Bioinformatics, 2004, v. 20, n. 14, p. 2222, doi. 10.1093/bioinformatics/bth229

By:

Ivo L. Hofacker;
Stephan H. F. Bernhart;
Peter F. Stadler

Publication type:

Article

The Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications for the Emergence of Deletions.

Published in:

Intervirology, 2000, v. 43, n. 3, p. 154, doi. 10.1159/000025041

By:

Kidd-Ljunggren, Karin;
Zuker, Michael;
Hofacker, Ivo L.;
Kidd, Alistair H.

Publication type:

Article

RNA In Silico The Computational Biology of RNA Secondary Structures.

Published in:

Advances in Complex Systems, 1999, v. 2, n. 1, p. 65, doi. 10.1142/S0219525999000059

By:

Flamm, Chirstoph;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 4, p. e65, doi. 10.1371/journal.pcbi.0030065

By:

Will, Sebastian;
Reiche, Kristin;
Hofacker, Ivo L.;
Stadler, Peter F.;
Backofen, Rolf

Publication type:

Article

From consensus structure prediction to RNA gene finding.

Published in:

Briefings in Functional Genomics & Proteomics, 2009, v. 8, n. 6, p. 461, doi. 10.1093/bfgp/elp043

By:

Bernhart, Stephan H.;
Hofacker, Ivo L.

Publication type:

Article

The impact of target site accessibility on the design of effective siRNAs.

Published in:

Nature Biotechnology, 2008, v. 26, n. 5, p. 578, doi. 10.1038/nbt1404

By:

Tafer, Hakim;
Ameres, Stefan L;
Obernosterer, Gregor;
Gebeshuber, Christoph A;
Schroeder, Renée;
Martinez, Javier;
Hofacker, Ivo L

Publication type:

Article

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.

Published in:

Nature Biotechnology, 2005, v. 23, n. 11, p. 1383, doi. 10.1038/nbt1144

By:

Washietl, Stefan;
Hofacker, Ivo L.;
Lukasser, Melanie;
Hüttenhofer, Alexander;
Stadler, Peter F.

Publication type:

Article

Evolutionary patterns of non-coding RNAs

Published in:

Theory in Biosciences, 2005, v. 123, n. 4, p. 301, doi. 10.1016/j.thbio.2005.01.002

By:

Bompfünewerer, Athanasius F.;
Flamm, Christoph;
Fried, Claudia;
Fritzsch, Guido;
Hofacker, Ivo L.;
Lehmann, Jörg;
Missal, Kristin;
Mosig, Axel;
Müller, Bettina;
Prohaska, Sonja J.;
Stadler, Bärbel M.R.;
Stadler, Peter F.;
Tanzer, Andrea;
Washietl, Stefan;
Witwer, Christina

Publication type:

Article

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004126

By:

Lavender, Christopher A.;
Lorenz, Ronny;
Zhang, Ge;
Tamayo, Rita;
Hofacker, Ivo L.;
Weeks, Kevin M.

Publication type:

Article

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 8, p. 1, doi. 10.1371/journal.pcbi.1002100

By:

Gorodkin, Jan;
Hofacker, Ivo L.

Publication type:

Article

Algorithm independent properties of RNA secondary structure predictions.

Published in:

European Biophysics Journal, 1996, v. 25, n. 2, p. 115, doi. 10.1007/s002490050023

By:

Tacker, Manfred;
Stadler, Peter F.;
Bornberg-Bauer, Erich G.;
Hofacker, Ivo L.;
Schuster, P.

Publication type:

Article

tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 17, p. 10575, doi. 10.1093/nar/gkae595

By:

Rappol, Tom;
Waldl, Maria;
Chugunova, Anastasia;
Hofacker, Ivo L;
Pauli, Andrea;
Vilardo, Elisa

Publication type:

Article

Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 16, p. e73, doi. 10.1093/nar/gkae602

By:

Thiel, Bernhard C;
Bussi, Giovanni;
Poblete, Simón;
Hofacker, Ivo L

Publication type:

Article

Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture.

Published in:

Viruses (1999-4915), 2019, v. 11, n. 9, p. 798, doi. 10.3390/v11090798

By:

de Bernardi Schneider, Adriano;
Ochsenreiter, Roman;
Hostager, Reilly;
Hofacker, Ivo L.;
Janies, Daniel;
Wolfinger, Michael T.

Publication type:

Article

Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses.

Published in:

Viruses (1999-4915), 2019, v. 11, n. 3, p. 298, doi. 10.3390/v11030298

By:

Ochsenreiter, Roman;
Hofacker, Ivo L.;
Wolfinger, Michael T.

Publication type:

Article

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure.

Published in:

PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0139900

By:

Theis, Corinna;
Zirbel, Craig L.;
zu Siederdissen, Christian Höner;
Anthon, Christian;
Hofacker, Ivo L.;
Nielsen, Henrik;
Gorodkin, Jan

Publication type:

Article

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site.

Published in:

RNA Biology, 2022, v. 19, n. 1, p. 496, doi. 10.1080/15476286.2022.2058818

By:

Gosavi, Devadatta;
Wower, Iwona;
Beckmann, Irene K.;
Hofacker, Ivo L.;
Wower, Jacek;
Wolfinger, Michael T.;
Sztuba-Solinska, Joanna

Publication type:

Article

Animal snoRNAs and scaRNAs with exceptional structures.

Published in:

RNA Biology, 2011, v. 8, n. 6, p. 1, doi. 10.4161/rna.8.6.16603

By:

Marz, Manja;
Gruber, Andreas R.;
Siederdissen, Christian Höner zu;
Amman, Fabian;
Badelt, Stefan;
Bartschat, Sebastian;
Bernhart, Stephan H.;
Beyer, Wolfgang;
Kehr, Stephanie;
Lorenz, Ronny;
Tanzer, Andrea;
Yusuf, Dilmurat;
Tafer, Hakim;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.

Published in:

Algorithms for Molecular Biology, 2023, v. 18, n. 1, p. 1, doi. 10.1186/s13015-023-00236-0

By:

Yao, Hua-Ting;
Lorenz, Ronny;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

RNA folding with hard and soft constraints.

Published in:

Algorithms for Molecular Biology, 2016, v. 11, p. 1, doi. 10.1186/s13015-016-0070-z

By:

Lorenz, Ronny;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

RNA Accessibility in cubic time.

Published in:

Algorithms for Molecular Biology, 2011, v. 6, n. 1, p. 3, doi. 10.1186/1748-7188-6-3

By:

Bernhart, Stephan H.;
Mückstein, Ullrike;
Hofacker, Ivo L.

Publication type:

Article

Partition function and base pairing probabilities of RNA heterodimers.

Published in:

Algorithms for Molecular Biology, 2006, v. 1, p. 3, doi. 10.1186/1748-7188-1-3

By:

Bernhart, Stephan H.;
Tafer, Hakim;
Mückstein, Ulrike;
Flamm, Christoph;
Stadler, Peter F.;
Hofacker, Ivo L.

Publication type:

Article

Vienna RNA secondary structure server.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3429, doi. 10.1093/nar/gkg599

By:

Hofacker, Ivo L.

Publication type:

Article

Conserved RNA secondary structures in Picornaviridae genomes.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 24, p. 5079, doi. 10.1093/nar/29.24.5079

By:

Witwer, Christina;
Rauscher, Susanne;
Hofacker, Ivo L.;
Stadler, Peter F.

Publication type:

Article

Automatic detection of conserved RNA structure elements in complete RNA virus genomes.

Published in:

Nucleic Acids Research, 1998, v. 26, n. 16, p. 3825, doi. 10.1093/nar/26.16.3825

By:

Hofacker, Ivo L.;
Fekete, Martin;
Flamm, Christoph;
Huynen, Martijn A.;
Rauscher, Susanne;
Stolorz, Paul E.;
Stadler, Peter F.

Publication type:

Article

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-13942-4

By:

Kim, Doo Nam;
Thiel, Bernhard C.;
Mrozowich, Tyler;
Hennelly, Scott P.;
Hofacker, Ivo L.;
Patel, Trushar R.;
Sanbonmatsu, Karissa Y.

Publication type:

Article