Publications by authors named "Ivo L Hofacker"

100Publications

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

Nat Commun 2020 01 9;11(1):148. Epub 2020 Jan 9.

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

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http://dx.doi.org/10.1038/s41467-019-13942-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952434PMC
January 2020

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.

J Bioinform Comput Biol 2019 10;17(5):1940009

Bioinformatics Group, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.

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http://dx.doi.org/10.1142/S0219720019400092DOI Listing
October 2019

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

Viruses 2019 08 29;11(9). Epub 2019 Aug 29.

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.

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http://dx.doi.org/10.3390/v11090798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784101PMC
August 2019

3D based on 2D: Calculating helix angles and stacking patterns using , an RNA Python library centered on secondary structure elements.

F1000Res 2019 14;8. Epub 2019 Mar 14.

Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria.

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http://dx.doi.org/10.12688/f1000research.18458.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480952PMC
June 2020

MSF: Modulated Sub-graph Finder.

F1000Res 2018 29;7:1346. Epub 2018 Aug 29.

Institute for Theoretical Chemistry,Theoretical Biochemistry Group,, University of Vienna, Vienna, 1090, Austria.

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http://dx.doi.org/10.12688/f1000research.16005.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446500PMC
November 2019

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

Viruses 2019 03 24;11(3). Epub 2019 Mar 24.

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.

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http://dx.doi.org/10.3390/v11030298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466055PMC
March 2019

RNA modifications in structure prediction - Status quo and future challenges.

Methods 2019 03 30;156:32-39. Epub 2018 Oct 30.

Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria.

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183019
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http://dx.doi.org/10.1016/j.ymeth.2018.10.019DOI Listing
March 2019

Comparative genomics of Czech vaccine strains of Bordetella pertussis.

Pathog Dis 2018 10 1;76(7). Epub 2018 Oct 1.

Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.

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https://academic.oup.com/femspd/article/doi/10.1093/femspd/f
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http://dx.doi.org/10.1093/femspd/fty071DOI Listing
October 2018

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.

Genes (Basel) 2018 Aug 1;9(8). Epub 2018 Aug 1.

Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria.

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http://dx.doi.org/10.3390/genes9080392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116022PMC
August 2018

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

Methods 2018 07 4;143:70-76. Epub 2018 May 4.

Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria; Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstr. 29, 1090 Vienna, Austria; Research Network Chemistry Meets Microbiology, University of Vienna, 1090 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2018.04.036DOI Listing
July 2018

In silico design of ligand triggered RNA switches.

Methods 2018 07 13;143:90-101. Epub 2018 Apr 13.

University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria.

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http://dx.doi.org/10.1016/j.ymeth.2018.04.003DOI Listing
July 2018

Comparative RNA Genomics.

Methods Mol Biol 2018 ;1704:363-400

Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://link.springer.com/10.1007/978-1-4939-7463-4_14
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http://dx.doi.org/10.1007/978-1-4939-7463-4_14DOI Listing
December 2018

RNAblueprint: flexible multiple target nucleic acid sequence design.

Bioinformatics 2017 Sep;33(18):2850-2858

Faculty of Chemistry, Department of Theoretical Chemistry.

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http://dx.doi.org/10.1093/bioinformatics/btx263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870862PMC
September 2017

NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.

J Am Chem Soc 2017 02 13;139(7):2647-2656. Epub 2017 Feb 13.

Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany.

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http://dx.doi.org/10.1021/jacs.6b10429DOI Listing
February 2017

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

Nucleic Acids Res 2017 05;45(8):e60

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkw1325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416843PMC
May 2017

RNAlien - Unsupervised RNA family model construction.

Nucleic Acids Res 2016 09 21;44(17):8433-41. Epub 2016 Jun 21.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Leipzig, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041467PMC
http://dx.doi.org/10.1093/nar/gkw558DOI Listing
September 2016

RNA folding with hard and soft constraints.

Algorithms Mol Biol 2016 23;11. Epub 2016 Apr 23.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria ; Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark ; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany ; Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany ; Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany ; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM87501 USA.

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http://dx.doi.org/10.1186/s13015-016-0070-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4842303PMC
April 2016

Predicting RNA secondary structures from sequence and probing data.

Methods 2016 07 5;103:86-98. Epub 2016 Apr 5.

University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.04.004DOI Listing
July 2016

Computational Design of a Circular RNA with Prionlike Behavior.

Artif Life 2016 2;22(2):172-84. Epub 2016 Mar 2.

University of Vienna.

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http://dx.doi.org/10.1162/ARTL_a_00197DOI Listing
October 2018

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.

Nucleic Acids Res 2016 Jan 23;44(D1):D90-5. Epub 2015 Nov 23.

Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkv1238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702876PMC
January 2016

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

PLoS One 2015 28;10(10):e0139900. Epub 2015 Oct 28.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark; Department of Veterinary Clinical and Animal Science, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139900PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624896PMC
June 2016

Pseudoknots in RNA folding landscapes.

Bioinformatics 2016 Jan 1;32(2):187-94. Epub 2015 Oct 1.

Institute for Theoretical Chemistry, RTH, University of Copenhagen, Frederiksberg, Denmark, IMADA, University of Southern Denmark, Campusvej 55, Odense, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btv572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4708108PMC
January 2016

Product Grammars for Alignment and Folding.

IEEE/ACM Trans Comput Biol Bioinform 2015 May-Jun;12(3):507-19

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http://dx.doi.org/10.1109/TCBB.2014.2326155DOI Listing
June 2016

SHAPE directed RNA folding.

Bioinformatics 2016 Jan 9;32(1):145-7. Epub 2015 Sep 9.

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btv523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681990PMC
January 2016

Optimizing RNA structures by sequence extensions using RNAcop.

Nucleic Acids Res 2015 Sep 17;43(17):8135-45. Epub 2015 Aug 17.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark

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http://dx.doi.org/10.1093/nar/gkv813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787817PMC
September 2015

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

Bioinformatics 2015 Oct 22;31(20):3377-9. Epub 2015 Jun 22.

Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währinger Straße 29, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btv372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595900PMC
October 2015

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

PLoS Comput Biol 2015 May 20;11(5):e1004126. Epub 2015 May 20.

Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438973PMC
May 2015

Predicting RNA 3D structure using a coarse-grain helix-centered model.

RNA 2015 Jun 22;21(6):1110-21. Epub 2015 Apr 22.

Institute for Theoretical Chemistry, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, University of Vienna, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1261/rna.047522.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4436664PMC
June 2015

Thermodynamic and kinetic folding of riboswitches.

Methods Enzymol 2015 12;553:193-213. Epub 2015 Feb 12.

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Research Group Bioinformatics and Computational Biology, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1016/bs.mie.2014.10.060DOI Listing
December 2015

TSSAR: TSS annotation regime for dRNA-seq data.

BMC Bioinformatics 2014 Mar 27;15:89. Epub 2014 Mar 27.

Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2105-15-89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098767PMC
March 2014

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

Bioinformatics 2014 Jul 19;30(14):2009-17. Epub 2014 Mar 19.

Institute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btu156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125618PMC
July 2014

Energy-directed RNA structure prediction.

Authors:
Ivo L Hofacker

Methods Mol Biol 2014 ;1097:71-84

Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1007/978-1-62703-709-9_4DOI Listing
November 2014

Concepts and introduction to RNA bioinformatics.

Methods Mol Biol 2014 ;1097:1-31

Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-709-9_1DOI Listing
November 2014

Challenges in RNA virus bioinformatics.

Bioinformatics 2014 Jul 3;30(13):1793-9. Epub 2014 Mar 3.

Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz Center Munich-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, Institut für theoretische Chemie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria, Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 München, Germany, University of Leipzig, Faculty of Mathematics and Computer Science, Institute for Computer Science, Augustusplatz 10, 04109 Leipzig, Germany, Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Universität Wien, Althanstraße 14, 1090 Wien, Austria, Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany and The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USAFriedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz

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http://dx.doi.org/10.1093/bioinformatics/btu105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110044PMC
July 2014

2D meets 4G: G-quadruplexes in RNA secondary structure prediction.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jul-Aug;10(4):832-44

University of Leipzig, Leipzig, Max Planck Institute for Mathematics in the Sciences, Leipzig, Fraunhofer Institute for CellTherapy and Immunology and University of Copenhagen.

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http://dx.doi.org/10.1109/TCBB.2013.7DOI Listing
August 2014

Predicting RNA structure: advances and limitations.

Methods Mol Biol 2014 ;1086:1-19

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1007/978-1-62703-667-2_1DOI Listing
May 2014

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

Nucleic Acids Res 2013 Dec 4;41(22):9999-10009. Epub 2013 Sep 4.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark, Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkt795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905863PMC
December 2013

Computational design of RNAs with complex energy landscapes.

Biopolymers 2013 Dec;99(12):1124-36

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1002/bip.22337DOI Listing
December 2013

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

J Proteomics 2013 Jun 9;86:27-42. Epub 2013 May 9.

Department of Proteomics, UFZ, Helmholtz-Centre for Environmental Research Leipzig, 04318 Leipzig, Germany.

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http://dx.doi.org/10.1016/j.jprot.2013.04.036DOI Listing
June 2013

CMCompare webserver: comparing RNA families via covariance models.

Nucleic Acids Res 2013 Jul 2;41(Web Server issue):W499-503. Epub 2013 May 2.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkt329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692125PMC
July 2013

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

Nucleic Acids Res 2013 Jul 29;41(Web Server issue):W475-9. Epub 2013 Apr 29.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkt291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977658PMC
July 2013

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.

Hum Mutat 2013 Apr;34(4):546-56

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.

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http://dx.doi.org/10.1002/humu.22273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708107PMC
April 2013

Folding RNA/DNA hybrid duplexes.

Bioinformatics 2012 Oct 24;28(19):2530-1. Epub 2012 Jul 24.

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/bts466DOI Listing
October 2012

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.

RNA 2012 May 26;18(5):900-14. Epub 2012 Mar 26.

Chair for Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, D-79110 Freiburg, Germany.

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http://dx.doi.org/10.1261/rna.029041.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334699PMC
May 2012

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.

Nucleic Acids Res 2012 May 28;40(10):4261-72. Epub 2012 Jan 28.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gks009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378861PMC
May 2012

ViennaRNA Package 2.0.

Algorithms Mol Biol 2011 Nov 24;6:26. Epub 2011 Nov 24.

Institute for Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1186/1748-7188-6-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319429PMC
November 2011

From structure prediction to genomic screens for novel non-coding RNAs.

PLoS Comput Biol 2011 Aug 4;7(8):e1002100. Epub 2011 Aug 4.

Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1002100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150283PMC
August 2011

A folding algorithm for extended RNA secondary structures.

Bioinformatics 2011 Jul;27(13):i129-36

Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btr220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117358PMC
July 2011

RNApredator: fast accessibility-based prediction of sRNA targets.

Nucleic Acids Res 2011 Jul 14;39(Web Server issue):W149-54. Epub 2011 Jun 14.

Institute of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkr467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125805PMC
July 2011

Fast accessibility-based prediction of RNA-RNA interactions.

Bioinformatics 2011 Jul 18;27(14):1934-40. Epub 2011 May 18.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr281DOI Listing
July 2011

RNA Accessibility in cubic time.

Algorithms Mol Biol 2011 Mar 9;6(1). Epub 2011 Mar 9.

Theoretical Biochemistry group, Institute for theoretical chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria.

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http://dx.doi.org/10.1186/1748-7188-6-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3063221PMC
March 2011

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

RNA 2011 Apr 28;17(4):578-94. Epub 2011 Feb 28.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB101SD, United Kingdom.

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http://dx.doi.org/10.1261/rna.2536111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062170PMC
April 2011

AREsite: a database for the comprehensive investigation of AU-rich elements.

Nucleic Acids Res 2011 Jan 11;39(Database issue):D66-9. Epub 2010 Nov 11.

Department of Microbiology and Immunobiology, Institute for Theoretical Chemistry, Max F Perutz Laboratories, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkq990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013810PMC
January 2011

Discriminatory power of RNA family models.

Bioinformatics 2010 Sep;26(18):i453-9

Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btq370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935435PMC
September 2010

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

BMC Genomics 2010 Jul 13;11:432. Epub 2010 Jul 13.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1186/1471-2164-11-432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996960PMC
July 2010

BarMap: RNA folding on dynamic energy landscapes.

RNA 2010 Jul 26;16(7):1308-16. Epub 2010 May 26.

Institute for Theoretical Chemistry, University of Vienna, 1090 Wien, Austria.

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http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.2093310
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http://dx.doi.org/10.1261/rna.2093310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885680PMC
July 2010

Nematode sbRNAs: homologs of vertebrate Y RNAs.

J Mol Evol 2010 Apr 27;70(4):346-58. Epub 2010 Mar 27.

Department of Medical Sciences and Interdisciplinary Research Centre for Autoimmune Diseases, Università del Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy.

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http://dx.doi.org/10.1007/s00239-010-9332-4DOI Listing
April 2010

Nucleic acid sequence and structure databases.

Methods Mol Biol 2010 ;609:3-15

Department of Theoretical Chemistry, University of Vienna, Wien, Austria.

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http://dx.doi.org/10.1007/978-1-60327-241-4_1DOI Listing
May 2010

Designing optimal siRNA based on target site accessibility.

Methods Mol Biol 2010 ;623:137-54

Institute for Theoretical Chemistry, University Vienna, Vienna, Austria.

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http://dx.doi.org/10.1007/978-1-60761-588-0_9DOI Listing
May 2010

RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles.

Nucleic Acids Res 2010 Jun 11;38(10):e113. Epub 2010 Feb 11.

Division of Genomics and RNomics, Innsbruck Biocentre, Innsbruck Medical University, Innsbruck and Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkq057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879528PMC
June 2010

RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Bioinformatics 2010 Mar 16;26(5):610-6. Epub 2009 Dec 16.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btp680DOI Listing
March 2010

De novo prediction of structured RNAs from genomic sequences.

Trends Biotechnol 2010 Jan 26;28(1):9-19. Epub 2009 Nov 26.

Section for Genetics and Bioinformatics, IBHV and Center for Applied Bioinformatics, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1016/j.tibtech.2009.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712260PMC
January 2010

RNAz 2.0: improved noncoding RNA detection.

Pac Symp Biocomput 2010 :69-79

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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November 2013

From consensus structure prediction to RNA gene finding.

Brief Funct Genomic Proteomic 2009 Nov;8(6):461-71

Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1093/bfgp/elp043DOI Listing
November 2009

RNA secondary structure analysis using the Vienna RNA package.

Authors:
Ivo L Hofacker

Curr Protoc Bioinformatics 2009 Jun;Chapter 12:Unit12.2

University of Vienna-Institute of Theoretical Chemistry, Vienna, Austria.

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http://dx.doi.org/10.1002/0471250953.bi1202s26DOI Listing
June 2009

Model-based probe set optimization for high-performance microarrays.

Nucleic Acids Res 2009 Feb 22;37(3):e18. Epub 2008 Dec 22.

Institute of Applied Microbiology, Boku University Vienna, Muthgasse 18, 1190 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkn1001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647282PMC
February 2009

RNAalifold: improved consensus structure prediction for RNA alignments.

BMC Bioinformatics 2008 Nov 11;9:474. Epub 2008 Nov 11.

Department of Computer Science, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2105-9-474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621365PMC
November 2008

Arthropod 7SK RNA.

Mol Biol Evol 2008 Sep 19;25(9):1923-30. Epub 2008 Jun 19.

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/molbev/msn140DOI Listing
September 2008

Folding kinetics of large RNAs.

J Mol Biol 2008 May 6;379(1):160-73. Epub 2008 Mar 6.

Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1016/j.jmb.2008.02.064DOI Listing
May 2008

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

Nat Biotechnol 2008 May 27;26(5):578-83. Epub 2008 Apr 27.

Institute of Theoretical Biochemistry (TBI), University of Vienna, Austria.

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http://dx.doi.org/10.1038/nbt1404DOI Listing
May 2008

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

Bioinformatics 2008 Nov 23;24(22):2657-63. Epub 2008 Apr 23.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btn193DOI Listing
November 2008

Identifying structural noncoding RNAs using RNAz.

Curr Protoc Bioinformatics 2007 Sep;Chapter 12:Unit 12.7

University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1002/0471250953.bi1207s19DOI Listing
September 2007

RNA secondary structure analysis using the Vienna RNA package.

Authors:
Ivo L Hofacker

Curr Protoc Bioinformatics 2004 Feb;Chapter 12:Unit 12.2

University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1002/0471250953.bi1202s04DOI Listing
February 2004

The Vienna RNA websuite.

Nucleic Acids Res 2008 Jul 19;36(Web Server issue):W70-4. Epub 2008 Apr 19.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Wien, Austria.

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http://dx.doi.org/10.1093/nar/gkn188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447809PMC
July 2008

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis.

Nucleic Acids Res 2008 May 16;36(8):2677-89. Epub 2008 Mar 16.

Innsbruck Biocenter, Division of Genomics and RNomics - Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria.

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http://dx.doi.org/10.1093/nar/gkn123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377427PMC
May 2008

Strategies for measuring evolutionary conservation of RNA secondary structures.

BMC Bioinformatics 2008 Feb 26;9:122. Epub 2008 Feb 26.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Wien, Austria.

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http://dx.doi.org/10.1186/1471-2105-9-122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335298PMC
February 2008

Evolutionary patterns of non-coding RNAs.

Theory Biosci 2005 Apr;123(4):301-69

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Wien, Austria.

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http://dx.doi.org/10.1016/j.thbio.2005.01.002DOI Listing
April 2005

Invertebrate 7SK snRNAs.

J Mol Evol 2008 Feb 12;66(2):107-15. Epub 2008 Jan 12.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1007/s00239-007-9052-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755741PMC
February 2008

RNA consensus structure prediction with RNAalifold.

Authors:
Ivo L Hofacker

Methods Mol Biol 2007 ;395:527-44

Department of Theoretical Chemistry, University of Vienna.

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http://dx.doi.org/10.1007/978-1-59745-514-5_33DOI Listing
March 2008

How microRNAs choose their targets.

Authors:
Ivo L Hofacker

Nat Genet 2007 Oct;39(10):1191-2

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http://dx.doi.org/10.1038/ng1007-1191DOI Listing
October 2007

SnoReport: computational identification of snoRNAs with unknown targets.

Bioinformatics 2008 Jan 25;24(2):158-64. Epub 2007 Sep 25.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btm464DOI Listing
January 2008

Detection of RNA structures in porcine EST data and related mammals.

BMC Genomics 2007 Sep 10;8:316. Epub 2007 Sep 10.

Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark.

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http://dx.doi.org/10.1186/1471-2164-8-316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2072958PMC
September 2007

Variations on RNA folding and alignment: lessons from Benasque.

J Math Biol 2008 Jan 5;56(1-2):129-44. Epub 2007 Jul 5.

Zentralfriedhof Wien, 3. Tor Simmeringer Haupstrasse, Wien, Austria.

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http://dx.doi.org/10.1007/s00285-007-0107-5DOI Listing
January 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

RNAs everywhere: genome-wide annotation of structured RNAs.

Authors:
Ivo L Hofacker

Genome Inform 2006 ;17(2):281-2

Institute for Theoretical Chemistry, University of Vienna, Austria.

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June 2007

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W335-8. Epub 2007 Apr 22.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkm222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933143PMC
July 2007

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.

PLoS Comput Biol 2007 Apr 22;3(4):e65. Epub 2007 Feb 22.

Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.0030065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851984PMC
April 2007

RNAs everywhere: genome-wide annotation of structured RNAs.

J Exp Zool B Mol Dev Evol 2007 Jan;308(1):1-25

Bioinformatics Group, Department of Computer Science, University of Freiburg, D-79110 Freiburg, Germany.

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http://dx.doi.org/10.1002/jez.b.21130DOI Listing
January 2007

Visualization of barrier tree sequences.

IEEE Trans Vis Comput Graph 2006 Sep-Oct;12(5):781-8

Image and Signal Processing Group, Department of Computer Science, University of Leipzig.

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http://dx.doi.org/10.1109/TVCG.2006.196DOI Listing
January 2007

Prediction of consensus RNA secondary structures including pseudoknots.

IEEE/ACM Trans Comput Biol Bioinform 2004 Apr-Jun;1(2):66-77

Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Wahringerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1109/TCBB.2004.22DOI Listing
November 2006

Partition function and base pairing probabilities of RNA heterodimers.

Algorithms Mol Biol 2006 Mar 16;1(1). Epub 2006 Mar 16.

Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria.

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http://dx.doi.org/10.1186/1748-7188-1-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459172PMC
March 2006

The expansion of the metazoan microRNA repertoire.

BMC Genomics 2006 Feb 15;7:25. Epub 2006 Feb 15.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2164-7-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1388199PMC
February 2006

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.

BMC Bioinformatics 2006 Feb 14;7:67. Epub 2006 Feb 14.

Bioscience Division, Los Alamos National Laboratory, Mailstop M888, PO Box 1663, Los Alamos, NM 87545, USA.

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http://dx.doi.org/10.1186/1471-2105-7-67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475643PMC
February 2006

Memory efficient folding algorithms for circular RNA secondary structures.

Bioinformatics 2006 May 1;22(10):1172-6. Epub 2006 Feb 1.

Institute for Theoretical Chemistry, University of Vienna Währingerstr. 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btl023DOI Listing
May 2006