Maria Waldl,
Thomas Spicher, Ronny Lorenz,
Irene K Beckmann, Ivo L Hofacker,
Sarah Von Lohneysen, and Peter F Stadler.
Local RNA folding revisisted.
Journal of Bioinformatics and Computational Biology, 2023.
(doi:10.1142/S0219720023500166)
Tyler Mrozowich,
Sean M. Park, Maria Waldl, Amy
Henrickson, Scott Tersteeg, Corey R. Nelson,
Anneke Deklerk, Borries Demeler,
Ivo L. Hofacker, Michael T. Wolfinger, and
Trushar R. Patel.
Investigating RNA-RNA interactions through computational and biophysical
analysis.
Nucl. Acids Res., 51:4588–4601, 2023.
(doi:10.1093/nar/gkad223)
Stefan Badelt,
Ronny Lorenz, and Ivo L. Hofacker.
Drtransformer: Heuristic cotranscriptional RNA folding using the nearest
neighbor energy model.
Bioinformatics, 39, 2023.
(doi:10.1093/bioinformatics/btad034)
Mariam R Farman,
Denisa Petráčková, Dilip Kumar,
Jakub Držmıšek, Argha Saha,
Ivana Čurnová, Jan Čapek,
Václava Hejnarová, Fabian Amman,
Ivo L. Hofacker, and Branislav Vevcerek.
Avirulent phenotype promotes Bordetella pertussis adaptation to the
intramacrophage environment.
Emerging Microbes & Infections, 12:e2146536, 2023.
(doi:10.1080/22221751.2022.2146536)
2022
Christoph Flamm,
Julia Wielach, Michael T. Wolfinger,
Stefan Badelt, Ronny Lorenz, and
Ivo L. Hofacker.
Caveats to deep learning approaches to RNA secondary structure prediction.
Frontiers in Bioinformatics, 2, 2022.
(doi:10.3389/fbinf.2022.835422)
Devadatta Gosavi,
Iwona Wower, Irene K Beckmann,
Ivo L Hofacker, Jacek Wower,
Michael T Wolfinger, and Joanna
Sztuba-Solinska.
Insights into the secondary and tertiary structure of the Bovine Viral
Diarrhea Virus internal ribosome entry site.
RNA biology, 19:496–506, 2022.
(doi:10.1080/15476286.2022.2058818)
2021
Sonja Zayni,
Samar Damiati, Susana Moreno-Flores,
Fabian Amman, Ivo L. Hofacker,
David Jin, and Eva-Kathrin Ehmoser.
Enhancing the cell-free expression of native membrane proteins by in silico
optimization of the coding sequence – an experimental study of the human
voltage-dependent anion channel.
Membranes, 11:741, 2021.
(doi:10.3390/membranes11100741)
Gregor Entzian,
Ivo L Hofacker, Yann Ponty, Ronny
Lorenz, and Andrea Tanzer.
RNAxplorer: harnessing the power of guiding potentials to sample RNA
landscapes.
Bioinformatics, 37:2126–2133, 2021.
(doi:10.1093/bioinformatics/btab066)
Michael T Wolfinger,
Roman Ochsenreiter, and Ivo L Hofacker.
Functional RNA structures in the 3'UTR of mosquito-borne flaviviruses.
In Virus Bioinformatics, pages 65–100. Chapman and Hall/CRC,
2021.
Ronny Lorenz,
Christoph Flamm, Ivo L. Hofacker, and
Peter F. Stadler.
Efficient computation of base-pairing probabilities in multi-strand RNA
folding.
In Proceedings of the 13th International Joint Conference on Biomedical
Engineering Systems and Technologies, pages 23–31, 2020.
(doi:10.5220/0008916600230031)
Teresa Müller,
Milad Miladi, Frank Hutter,
Ivo L. Hofacker, Sebastian Will, and
Rolf Backofen.
The locality dilemma of Sankoff-like RNA alignments.
Bioinformatics, 36:i242–i250, 2020.
(doi:10.1093/bioinformatics/btaa431)
Denisa
Petráčková, Mariam R Farman,
Fabian Amman, Irena Linhartová,
Ana Dienstbier, Dilip Kumar,
Jakub Držmıšek, Ivo L.
Hofacker, Maria Eugenia Rodriguez, and
Branislav Večerek.
Transcriptional profiling of human macrophages during infection with bordetella
pertussis.
RNA biology, 17:731–742, 2020.
(doi:10.1080/15476286.2020.1727694)
Doo Nam Kim,
Bernhard C Thiel, Tyler Mrozowich,
Scott P Hennelly, Ivo L Hofacker,
Trushar R Patel, and Karissa Y Sanbonmatsu.
Zinc-finger protein CNBP alters the 3D structure of lncRNA braveheart in
solution.
Nature communications, 11:1–13, 2020.
(doi:10.1038/s41467-019-13942-4)
2019
Rick
Gelhausen, Sebastian Will, Ivo L Hofacker,
Rolf Backofen, and Martin Raden.
IntaRNAhelix – composing RNA–RNA interactions from stable inter-molecular
helices boosts bacterial sRNA target prediction.
Journal of Bioinformatics and Computational Biology, 17:1940009,
2019.
(doi:10.1142/S0219720019400092)
Adriano
de Bernardi Schneider, Roman Ochsenreiter,
Reilly Hostager, Ivo L Hofacker,
Daniel Janies, and Michael T Wolfinger.
Updated phylogeny of chikungunya virus suggests lineage-specific RNA
architecture.
Viruses, 11(9):798, 2019.
(doi:10.3390/v11090798)
Maria Waldl,
Sebastian Will, Michael T. Wolfinger,
Hofacker. Ivo L., and Peter F. Stadler.
Bi-alignments as models of incongruent evolution of RNA sequence and
structure.
In CIBB 2019: 16th International Conference on Computational Intelligence
methods for Bioinformatics and Biostatistics, September 2019.
Michael Kiening,
Roman Ochsenreiter, Hans-Jörg Hellinger,
Thomas Rattei, Ivo L. Hofacker, and
Dmitrij Frishman.
Conserved secondary structures in viral mRNAs.
Viruses, 11(5):401, 2019.
(doi:10.3390/v11050401)
Bernhard C Thiel,
Irene K Beckmann, Peter Kerpedjiev, and
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.
(doi:10.12688/f1000research.18458.2)
Roman
Ochsenreiter, Ivo L. Hofacker, and Michael T.
Wolfinger.
Functional RNA structures in the 3'UTR of tick-borne, insect-specific and
no-known-vector flaviviruses.
Viruses, 11, 2019.
(doi:10.3390/v11030298)
Jules Deforges,
Rodrigo S Reis, Philippe Jacquet,
Shaoline Sheppard, Veerendra P Gadekar,
Gene Hart-Smith, Andrea Tanzer,
Ivo L Hofacker, Christian Iseli,
Ioannis Xenarios, and Yves Poirier.
Control of cognate sense mRNA translation by cis-natural antisense RNAs.
Plant physiology, 180:305–322, 2019.
(doi:10.1104/pp.19.00043)
Tanzer Andrea,
Ivo L. Hofacker, and Ronny Lorenz.
RNA modifications in structure prediction - Status quo and future
challenges.
Methods, 159:32–39, 2019.
(doi:10.1016/j.ymeth.2018.10.019)
2018
Ana Dienstbier,
Derek Pouchnik, Mark Wildung,
Fabian Amman, Ivo L Hofacker,
Julian Parkhill, Jana Holubova,
Peter Sebo, and Branislav Vecerek.
Comparative genomics of czech vaccine strains of bordetella pertussis.
Pathogens and disease, 76(7), 2018.
(doi:10.1093/femspd/fty071)
Mariam R Farman,
Ivo L Hofacker, and Fabian Amman.
Msf: Modulated sub-graph finder.
F1000Research, 7:1346, 2018.
(doi:10.12688/f1000research.16005.3)
Bernhard C. Thiel,
Roman Ochsenreiter, Veerendra P. Gadekar,
Andrea Tanzer, and Ivo L. Hofacker.
RNA structure elements conserved between mouse and 59 other vertebrates.
Genes, 9(8), 2018.
(doi:10.3390/genes9080392)
Michael T Wolfinger,
Christoph Flamm, and Ivo L Hofacker.
Efficient computation of co-transcriptional RNA-ligand interaction dynamics.
Methods, 143:70–76, 2018.
(doi:10.1016/j.ymeth.2018.04.036)
Sven Findeiß,
Stefan Hammer, Michael T Wolfinger,
K Felix, Christoph Flamm, and
Ivo L Hofacker.
In silico design of ligand triggered RNA switches.
Methods, 143:90–101, 2018.
(doi:10.1016/j.ymeth.2018.04.003)
Florian Eggenhofer,
Ivo L Hofacker, Rolf Backofen, and
Christian Höner zu Siederdissen.
CMV: Visualization for RNA and protein family models and their comparisons.
Bioinformatics, 34:2676–2678, 2018.
(doi:10.1093/bioinformatics/bty158)
Rolf Backofen,
Jan Gorodkin, Ivo L. Hofacker, and
Peter F. Stadler.
Comparative RNA genomics.
In João C. Setubal, Peter F. Stadler, and
Jens Stoye, editors, Comparative Genomics, volume
1704, pages 363–400. Springer, Heidelberg, 2018.
(doi:10.1007/978-1-4939-7463-4_14)
2017
Bernhard C Thiel,
Christoph Flamm, and Ivo L Hofacker.
RNA structure prediction: from 2D to 3D.
Emerging Topics in Life Sciences, 1(3):275–285, 2017.
(doi:10.1042/ETLS20160027)
Stefan Hammer,
Birgit Tschiatschek, Christoph Flamm,
Ivo L Hofacker, and Sven Findeiß.
RNAblueprint: Flexible multiple target nucleic acid sequence design.
Bioinformatics, 33:2850–2858, 2017.
(doi:10.1093/bioinformatics/btx263)
Gesche K Gerresheim,
Nadia Dünnes, Anika Nieder-Röhrmann,
Lyudmila A Shalamova, Markus Fricke,
Ivo L. Hofacker, Christian Höner
zu Siederdissen, Manja Marz, and Michael
Niepmann.
microRNA-122 target sites in the hepatitis C virus RNA NS5B coding
region and 3' untranslated region: function in replication and influence of
RNA secondary structure.
Cellular and Molecular Life Sciences, 74:747–760, 2017.
(doi:10.1007/s00018-016-2377-9)
Christina Helmling,
Anna Wacker, Michael T Wolfinger,
Ivo L Hofacker, Martin Hengesbach,
Boris Fürtig, and Harald Schwalbe.
NMR structural profiling of transcriptional intermediates reveals riboswitch
regulation by metastable RNA conformations.
Journal of the American Chemical Society, 139:2647, 2017.
(doi:10.1021/jacs.6b10429)
Ferhat Alkan,
Anne Wenzel, Oana Palasca, Peter
Kerpedjiev, Anders Frost Rudebeck, Peter F
Stadler, Ivo L Hofacker, and Jan Gorodkin.
Risearch2: suffix array-based large-scale prediction of RNA–RNA interactions
and siRNA off-targets.
Nucleic Acids Research, 45:e60, 2017.
(doi:10.1093/nar/gkw1325)
2016
Martin Hölzer,
Verena Krähling, Fabian Amman,
Emanuel Barth, Stephan H Bernhart,
Victor AO Carmelo, Maximilian Collatz,
Gero Doose, Florian Eggenhofer,
Jan Ewald, Jörg Fallmann,
Lasse M Feldhahn, Markus Fricke,
Juliane Gebauer, Andreas J Gruber,
Franziska Hufsky, Henrike Indrischek,
Sabina Kanton, Jörg Linde, Nelly
Mostajo, Roman Ochsenreiter, Konstantin Riege,
Lorena Rivarola-Duarte, Abdullah H Sahyoun,
Sita J Saunders, Stefan E Seemann,
Andrea Tanzer, Bertram Vogel,
Stefanie Wehner, Michael T Wolfinger,
Rolf Backofen, Jan Gorodkin, Ivo
Grosse, Ivo Hofacker, Steve Hoffmann,
Christoph Kaleta, Peter F Stadler,
Stephan Becker, and Manja Marz.
Differential transcriptional responses to ebola and marburg virus infection in
bat and human cells.
Scientific reports, 6, 2016.
(doi:10.1038/srep34589)
Mansoureh Tajaddod,
Andrea Tanzer, Konstantin Licht,
Michael T Wolfinger, Stefan Badelt,
Florian Huber, Oliver Pusch,
Sandy Schopoff, Michael Janisiw,
Ivo L. Hofacker, and Michael F. Jantsch.
Transcriptome-wide effects of inverted SINEs on gene expression and their
impact on RNA polymerase II activity.
Genome biology, 17(1):220, 2016.
(doi:10.1186/s13059-016-1083-0)
Florian Eggenhofer,
Ivo L. Hofacker, and Christian Höner zu
Siederdissen.
RNAlien – unsupervised RNA family model construction.
Nucl. Acids Res., 44:8433–8441, 2016.
(doi:10.1093/nar/gkw558)
Ronny Lorenz,
Michael T. Wolfinger, Andrea Tanzer, and
Ivo L. Hofacker.
Predicting RNA secondary structures from sequence and probing data.
Methods, 103:86–98, 2016.
(doi:10.1016/j.ymeth.2016.04.004)
Vitaly Sedlyarov,
Jörg Fallmann, Florian Ebner,
Jakob Huemer, Lucy Sneezum, Masa
Ivin, Kristina Kreiner, Andrea Tanzer,
Claus Vogl, Ivo L. Hofacker, and
Pavel Kovarik.
Tristetraprolin binding site atlas in the macrophage transcriptome reveals a
switch for inflammation resolution.
Mol Syst Biol, 12(5):868, 2016.
(doi:10.15252/msb.20156628)
Ronny Lorenz,
Ivo L. Hofacker, and Peter F. Stadler.
RNA folding with hard and soft constraints.
Alg. Mol. Biol., 11:8, 2016.
(doi:10.1186/s13015-016-0070-z)
Jörg Fallmann,
Vitaly Sedlyarov, Andrea Tanzer,
Pavel Kovarik, and Ivo L Hofacker.
AREsite2: an enhanced database for the comprehensive investigation of
AU/GU/U-rich elements.
Nucleic Acids Res, 44(D1):D90–D95, 2016.
(doi:10.1093/nar/gkv1238)
Yu-Ting Hsiao,
Wei-Po Lee, Wei Yang, Stefan
Müller, Christoph Flamm, Ivo L. Hofacker,
and Philipp Kugler.
Practical guidelines for incorporating knowledge-based and data-driven
strategies into the inference of gene regulatory networks.
IEEE Trans. Comp. Biol. Bioinf., 13:64–75, 2016.
(doi:10.1109/TCBB.2015.2465954)
Marcel Kucharık,
Ivo L. Hofacker, Peter F. Stadler, and
Jing Qin.
Pseudoknots in RNA folding landscapes.
Bioinformatics, 32:187–194, 2016.
(doi:10.1093/bioinformatics/btv572)
Ronny Lorenz,
Dominik Luntzer, Ivo L. Hofacker,
Peter F. Stadler, and Michael T. Wolfinger.
SHAPE directed RNA folding.
Bioinformatics, 32:145–147, 2016.
(doi:10.1093/bioinformatics/btv523)
Stefan Badelt,
Christoph Flamm, and Ivo L. Hofacker.
Computational design of a circular RNA with prion-like behavior.
Artificial Life, 22:172–184, 2016.
(doi:10.1162/ARTL_a_00197)
2015
Corinna Theis,
Craig .L. Zirbel, Christian Höner zu
Siederdissen, Christian. Anthon, Ivo .L.
Hofacker, Henrik Nielsen, and Jan Gorodkin.
RNA 3D modules in genome-wide predictions of RNA 2D structure.
PLoS ONE, 10(10):e0139900, 2015.
(doi:10.1371/journal.pone.0139900)
Sarah J. Berkemer,
Christian Höner zu Siederdissen, Fabian
Amman, Axel Wintsche, Sebastian Will,
Ivo L. Hofacker, Sonja J. Prohaska, and
Peter F. Stadler.
Processed small RNAs in Archaea and BHB elements.
Genomics Comp. Biol., 1:e18, 2015.
(doi:10.18547/gcb.2015.vol1.iss1.e18)
Peter Kerpedjiev,
Stefan Hammer, and Ivo L. Hofacker.
forna (force-directed RNA): Simple and effective online RNA secondary
structure diagrams.
Bioinformatics, 31:3377–3379, 2015.
(doi:10.1093/bioinformatics/btv372)
Nikolai Hecker,
Mikkel Christensen-Dalsgaard, Stefan E Seemann,
Jakob H Havgaard, Peter F Stadler,
Ivo L Hofacker, Henrik Nielsen, and
Jan Gorodkin.
Optimizing RNA structures by sequence extensions using RNAcop.
Nucleic acids research, 43(17):8135–8145, 2015.
(doi:10.1093/nar/gkv813)
Sonja Petkovic,
Stefan Badelt, Stephan Block,
Christoph Flamm, Mihaela Delcea,
Ivo L. Hofacker, and Sabine Müller.
Sequence-controlled RNA self-processing: computational design, biochemical
analysis, and visualization by AFM.
RNA, 21:1249â1260, 2015.
(doi:10.1261/rna.047670.114)
Peter Kerpedjiev,
Christian Höner zu Siederdissen, and Ivo L.
Hofacker.
Predicting RNA 3D structure using a coarse-grain helix-centered model.
RNA, 21:1110–1121, 2015.
(doi:10.1261/rna.047522.114)
Christopher A.
Lavender, Ronny Lorenz, Ge Zhang,
Rita Tamayo, Ivo L. Hofacker, and
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:e1004126, 05 2015.
(doi:10.1371/journal.pcbi.1004126)
Stefan Badelt,
Stefan Hammer, Christoph Flamm, and
Ivo L. Hofacker.
Thermodynamic and kinetic folding of riboswitches.
In Shi-Jie Chen and Donald H. Burke-Aguero,
editors, Computational Methods for Understanding Riboswitches,
volume 553 of Methods in Enzymology, pages 193–213. Elsevier,
2015.
(doi:10.1016/bs.mie.2014.10.060)
Christian Höner zu
Siederdissen, Ivo L. Hofacker, and Peter F.
Stadler.
Product grammars for alignment and folding.
IEEE Trans. Comp. Biol. Bioinf., 12:507–519, 2015.
(doi:10.1109/TCBB.2014.2326155)
2014
H. Hämmerle,
F. Amman, VeÄerek B., I.L.
Stülke, J.and Hofacker, and U. Bläsi.
Impact of Hfq on the bacillus subtilis transcriptome.
PLoS One, 9:e98661, 2014.
(doi:10.1371/journal.pone.0098661)
Stefan Badelt,
Christoph Flamm, and Ivo L. Hofacker.
Computational design of a circular RNA with prion-like behavior.
In H. Sayama, J. Rieffel, S. Risi,
R. Doursat, and H. Lipson, editors,
Artificial Life 14, pages 565–568. MIT Press, 2014.
(doi:10.7551/978-0-262-32621-6-ch091)
Marcel Kucharık,
Ivo L. Hofacker, Peter F. Stadler, and
Jing Qin.
Basin hopping graph: A computational framework to characterize RNA folding
landscapes.
Bioinformatics, 30:2009–2017, 2014.
(doi:10.1093/bioinformatics/btu156)
Manja Marz,
Niko Beerenwinkel, Christian Drosten,
Markus Fricke, Dmitrij Frishman,
Ivo L. Hofacker, Dieter Hoffmann,
Martin Middendorf, Thomas Rattei,
Peter F. Stadler, and Armin Töpfer.
Challenges in RNA virus bioinformatics.
Bioinformatics, 30:1793–1799, 2014.
(doi:10.1093/bioinformatics/btu105)
Fabian Amman,
Michael T Wolfinger, Ronny Lorenz,
Ivo L Hofacker, Peter F Stadler, and
S. Findeiß.
TSSAR: TSS annotation regime for dRNA-seq data.
BMC Bioinformatics, 15:89, 2014.
(doi:10.1186/1471-2105-15-89)
Ivo L. Hofacker and
Ronny Lorenz.
Predicting RNA structure: Advances and limitations.
In Christina Waldsich, editor, RNA Folding,
volume 1086 of Methods in Molecular Biology, pages 1–19. Humana
Press, 2014.
(doi:10.1007/978-1-62703-667-2_1)
Ivo L. Hofacker.
Energy directed RNA structure prediction.
In Jan Gorodkin and Larry Ruzzo, editors,
RNA Sequence, Structure, and Function: Computational and
Bioinformatic Methods, volume 1097 of Meth. Mol. Biol.,
pages 71–84. Humana Press, New York, 2014.
(doi:10.1007/978-1-62703-709-9_4)
Jan Gorodkin,
Larry Ruzzo, and Ivo L. Hofacker.
Concepts and introduction to RNA bioinformatics.
In Jan Gorodkin and Larry Ruzzo, editors,
RNA Sequence, Structure, and Function: Computational and
Bioinformatic Methods, volume 1097 of Meth. Mol. Biol.,
pages 1–31. Humana Press, New York, 2014.
(doi:10.1007/978-1-62703-709-9_1)
2013
Christian Höner zu
Siederdissen, Ivo L Hofacker, and Peter F
Stadler.
How to multiply dynamic programming algorithms.
In João C. Setubal and Nalvo F. Almeida,
editors, Advances in Bioinformatics and Computational Biology,
volume 8213 of Lecture Notes in Computer Science, pages 82–93.
Springer International Publishing, 2013.
(doi:10.1007/978-3-319-02624-4_8)
Fabian Amman,
Stephan H Bernhart, Gero Doose,
Ivo L Hofacker, Jing Qin, Peter F
Stadler, and Sebastian Will.
The trouble with long-range base pairs in RNA folding.
In João C. Setubal and Nalvo F. Almeida,
editors, Advances in Bioinformatics and Computational Biology,
volume 8213 of Lecture Notes in Computer Science, pages 1–11.
Springer International Publishing, 2013.
(doi:10.1007/978-3-319-02624-4_1)
Christian Höner zu
Siederdissen, Stefan Hammer, Ingrid Abfalter,
Ivo L. Hofacker, Christoph Flamm, and
Peter F. Stadler.
Computational design of RNAs with complex energy landscapes.
Biopolymers, 99:1124–1136, 2013.
(doi:10.1002/bip.22337)
Corinna Theis,
Christian Höner zu Siederdissen, Ivo L
Hofacker, and Jan Gorodkin.
Automated identification of RNA 3D modules with discriminative power in
RNA structural alignments.
Nucleic acids research, 41:9999–10009, 2013.
(doi:10.1093/nar/gkt795)
Birgit Märtens,
Fabian Amman, Salim Manoharadas,
Lukas Zeichen, Alvaro Orell,
Sonja-Verena Albers, Ivo L. Hofacker, and
Udo Bläsi.
Alterations of the transcriptome of sulfolobus acidocaldarius by
exoribonuclease aCPSF2.
PloS one, 8(10):e76569, 2013.
(doi:10.1371/journal.pone.0076569)
Stephan A. Müller,
Sven Findeiß, Sandy R. Pernitzsch,
Dirk K. Wissenbach, Peter F. Stadler,
Ivo L. Hofacker, Martin von Bergen, and
Stefan Kalkhof.
Identification of new protein coding sequences and signal peptidase cleavage
sites of Helicobacter pylori strain 26695 by proteogenomics.
J. Proteomics, 86:27–42, 2013.
(doi:10.1016/j.jprot.2013.04.036)
Ronny Lorenz,
Stephan H. Bernhart, Jing Qin,
Christian Höner zu Siederdissen, Andrea
Tanzer, Fabian Amman, Ivo L. Hofacker, and
Peter F. Stadler.
2D meets 4G: G-quadruplexes in RNA secondary structure prediction.
IEEE Trans. Comp. Biol. Bioinf., 10:832–844, 2013.
(doi:10.1109/TCBB.2013.7)
Florian Eggenhofer,
Ivo L. Hofacker, and Christian Höner zu
Siederdissen.
CMCompare webserver: Comparing RNA families via covariance models.
Nucleic Acids Res., 41:W499–W503, 2013.
(doi:10.1093/nar/gkt329)
Radhakrishnan
Sabarinathan, Hakim Tafer, Stefan Seemann,
Ivo L. Hofacker, Peter F. Stadler, and
Jan Gorodkin.
The RNAsnp Web Server: Predicting SNP effects on local RNA secondary
structure.
Nucleic Acids Res., 41:W475–W479, 2013.
(doi:10.1093/nar/gkt291)
Radhakrishnan
Sabarinathan, Hakim Tafer, Stefan E. Seemann,
Ivo L. Hofacker, Peter F. Stadler, and
Jan Gorodkin.
RNAsnp: Efficient detection of local RNA secondary structure changes
induced by SNPs.
Human Mutation, 34:546–556, 2013.
(doi:10.1002/humu.22273)
2012
Fabian Amman,
Christoph Flamm, and Ivo L. Hofacker.
Modelling translation initiation under the influence of sRNA.
Int. J. Mol. Sci., 13:16223–16240, 2012.
(doi:10.3390/ijms131216223)
Ronny Lorenz,
Ivo .L. Hofacker, and Stephan H. Bernhart.
Folding RNA/DNA hybrid duplexes.
Bioinformatics, 28:2530–2531, 2012.
(doi:10.1093/bioinformatics/bts466)
Ronny Lorenz,
Stephan H. Bernhart, Fabian Externbrink,
Jing Qin, Christian Höner zu Siederdissen,
Fabian Amman, Ivo L. Hofacker, and
Peter F. Stadler.
RNA folding algorithms with G-quadruplexes.
In M. C. P. de Souto and M. G. Kann, editors,
BSB 2012, volume 7409 of Lect. Notes Bioinf., pages
49–60, Heidelberg, 2012. Springer.
(doi:10.1007/978-3-642-31927-3_5)
Sebastian Will,
Tejal Joshi, Ivo L. Hofacker,
Peter F. Stadler, and Rolf Backofen.
LocARNA-P: Accurate boundary prediction and improved detection of structured
RNAs.
RNA, 18:900–914, 2012.
(doi:10.1261/rna.029041.111)
Stefan Washietl,
Ivo L. Hofacker, Peter F. Stadler, and
Manolis Kellis.
RNA folding with soft constraints: Reconciliation of probing data and
thermodynamic secondary structure prediction.
Nucleic Acids Res., 40:4261–4272, 2012.
(doi:10.1093/nar/gks009)
Ivo L. Hofacker,
Christian M. Reidys, and Peter F. Stadler.
Symmetric circular matchings and RNA folding.
Discr. Math., 312:100–112, 2012.
(doi:10.1016/j.disc.2011.06.004)
2011
F Kratochvill,
C Machacek, C Vogl, F Ebner,
V Sedlyarov, A R Gruber,
H Hartweger, R Vielnascher,
M Karaghiosoff, T Rülicke,
M Müller, I L Hofacker,
R Lang, and P Kovarik.
Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA
decay in inflammation.
Mol Syst Biol, 7:560, 2011.
(doi:10.1038/msb.2011.93)
Ronny Lorenz,
Stephan H Bernhart, Christian Höner zu
Siederdissen, Hakim Tafer, Christoph Flamm,
Peter F. Stadler, and Ivo L. Hofacker.
ViennaRNA Package 2.0.
Alg. Mol. Biol., 6:26, 2011.
(doi:10.1186/1748-7188-6-26)
Manja Marz,
Andreas R. Gruber, Christian Höner zu
Siederdissen, Fabian Amman, Stefan Badelt,
Sebastian Bartschat, Stephan H. Bernhart,
Stephanie Beyer, Kehr, Ronny Lorenz,
Andrea Tanzer, Dilmurat Yusuf,
Hakim Tafer, Ivo L. Hofacker, and
Peter F. Stadler.
Animal snoRNAs and scaRNAs with exceptional structures.
RNA Biology, 8:938 – 946, 2011.
(doi:10.4161/rna.8.6.16603)
Jan Gorodkin and
Ivo L Hofacker.
From structure prediction to genomic screens for novel non-coding RNAs.
PLoS computational biology, 7(8):e1002100, 2011.
(doi:10.1371/journal.pcbi.1002100)
Christian Höner zu
Siederdissen, Stephan H. Berhart, Peter F.
Stadler, and Ivo L. Hofacker.
A folding algorithm for extended RNA secondary structures.
Bioinformatics, 27:i129–i136, 2011.
(doi:10.1093/bioinformatics/btr220)
Florian Eggenhofer,
Hakim Tafer, Peter F. Stadler, and
Ivo L. Hofacker.
RNApredator: Fast accessibility-based prediction of sRNA targets.
Nucleic Acids Res., 39:W149–W154, 2011.
(doi:10.1093/nar/gkr467)
Hakim Tafer,
Fabian Amman, Florian Eggenhoffer,
Peter F. Stadler, and Ivo L. Hofacker.
Fast accessibility-based prediction of RNA-RNA interactions.
Bioinformatics, 27:1924–1940, 2011.
(doi:10.1093/bioinformatics/btr281)
Matthias Hackl,
Tobias Jakobi, Jochen Blom,
Daniel Doppmeier, Karina Brinkrolff,
Rafael Sczepanowski, Stephan Bernhart,
Christian Höner zu Siederdissen, Juan
Hernandez-Bort, Matthias Wieser, Renate
Kunert, Simon Jeffs, Ivo L. Hofacker,
Alexander Goesmann, Alfred Pühler,
Nicole Borth, and Johannes Grillari.
Next-generation sequencing of the chinese hamster ovary microRNA
transcriptome: Identification, annotation and profiling of microRNAs as
targets for cellular engineering.
Journal of Biotechnology, 20:62–75, 2011.
(doi:10.1016/j.jbiotec.2011.02.011)
Stefan Washietl,
Sven Findeiß, Stephan Müller,
Stefan Kalkhof, Martin von Bergen,
Ivo L. Hofacker, Peter F. Stadler, and
Nick Goldman.
RNAcode: robust prediction of protein coding regions in comparative genomics
data.
RNA, 17:578–594, 2011.
(doi:10.1261/rna.2536111)
Stephan H Bernhart,
Ulrike Mückstein, and Ivo L Hofacker.
RNA accessibility in cubic time.
Algorithms Mol Biol, 6(1):3, 2011.
(doi:10.1186/1748-7188-6-3)
Andreas R Gruber,
Jörg Fallmann, Franz Kratochvill,
Pavel Kovarik, and Ivo L Hofacker.
AREsite: a database for the comprehensive investigation of AU-rich
elements.
Nucleic Acids Res, 39:D66–69, 2011.
(doi:10.1093/nar/gkq990)
2010
Andreas R. Gruber,
Stephan H. Bernhart, You Zhou, and
Ivo L. Hofacker.
RNALfoldz: Efficient prediction of thermodynamically stable, local secondary
structures.
In German Conference on Bioinformatics 2010, volume 173 of
Lecture Notes in Informatics, pages 12–21, Bonn, 2010.
Gesellschaft f. Informatik.
Christian Höner zu
Siederdissen and Ivo L. Hofacker.
Discriminatory power of RNA family models.
Bioinformatics, 26(18):i453–459, 2010.
(doi:10.1093/bioinformatics/btq370)
Christoph Flamm,
Alexander Ullrich, Heinz Ekker,
Martin Mann, Daniel Högerl,
Markus Rohrschneider, Sebastian Sauer,
Gerik Scheuermann, Konstantin Klemm,
Ivo L. Hofacker, and Peter F. Stadler.
Evolution of metabolic networks: A computational framework.
J. Syst. Chem., 1:4, 2010.
(doi:10.1186/1759-2208-1-4)
Yusuf Dilmurat,
Manja Marz, Peter F. Stadler, and
Ivo L. Hofacker.
Bcheck: a wrapper tool for detecting RNase P RNA genes.
BMC Genomics, 11:432, 2010.
(doi:10.1186/1471-2164-11-432)
Ivo L. Hofacker,
Christoph Flamm, Christian Heine,
Michael T. Wolfinger, Gerik Scheuermann, and
Peter F. Stadler.
BarMap: RNA folding on dynamic energy landscapes.
RNA, 16:1308–1316, 2010.
(doi:10.1261/rna.2093310)
Ilenia Boria,
Andreas R. Gruber, Andrea Tanzer,
Stephan Bernhart, Ronny Lorenz,
Michael M. Mueller, Ivo L. Hofacker, and
Peter F. Stadler.
Nematode sbRNAs: Homologs of vertebrate Y RNAs.
J. Mol. Evol., 70:346–358, 2010.
(doi:10.1007/s00239-010-9332-4)
Mathieu
Rederstorff, Stephan H. Bernhart, Andrea
Tanzer, Marek Zywicki, Kartin Perfler,
Melanie Lukasser, Ivo L. Hofacker, and
Alexander Hüttenhofer.
RNPomics: Defining the ncRNA transcriptome by cDNA library generation
from ribonucleo-protein particles.
Nucleic Acids Res., 38:e113, 2010.
(doi:10.1093/nar/gkq057)
Ulrike
Mückstein, Germán G. Leparc, Alexandra
Posekany, Ivo L. Hofacker, and David P. Kreil.
Hybridization thermodynamics of NimbleGen microarrays.
BMC Bioinformatics, 11:35 [epub], 2010.
(doi:10.1186/1471-2105-11-35)
H. Tafer,
S. Kehr, J. Hertel, Ivo L.
Hofacker, and P. F. Stadler.
RNAsnoop: Efficient target prediction for box H/ACA snoRNAs.
Bioinformatics, 26:610–616, 2010.
(doi:10.1093/bioinformatics/btp680)
Ivo L. Hofacker and
Hakim Tafer.
Designing optimal siRNA based on target site accessibility.
In Wei-Ping Min and Thomas Ichim, editors,
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623 of Methods in Molecular Biology, chapter 9, pages 137–154.
Humana Press, Totowa, NJ, 2010.
(doi:10.1007/978-1-60761-588-0_9)
Stefan Washietl and
Ivo L. Hofacker.
Nucleic acids sequence and structure databases.
In Oliviero Carugo and Frank Eisenhaber, editors,
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Methods in Molecular Biology, chapter 1, pages 3–16. Humana
Press, Totowa, NJ, 2010.
(doi:10.1007/978-1-60327-241-4_1)
Jan Gorodkin,
Ivo L. Hofacker, Elfar Torarinsson,
Zizhen Yao, Jakob H. Havgaard, and
Walter L. Ruzzo.
De novo prediction of structured RNAs from genomic sequences.
Trends in Biotechnology, 28:9–19, 2010.
(doi:10.1016/j.tibtech.2009.09.006)
Andrea Tanzer,
Markus Riester, Jana Hertel,
Clara Isabel Bermudez-Santana, Jan Gorodkin,
Ivo L. Hofacker, and Peter F. Stadler.
Evolutionary genomics of microRNAs and their relatives.
In Gustavo Caetano-Anolles, editor, Evolutionary Genomics
and Systems Biology, pages 295–327. Wiley-Blackwell, Hoboken,
2010.
Rolf Backofen,
Hamid Chitsaz, Ivo L Hofacker,
S Cenk Sahinalp, and Peter F Stadler.
Computational studies of non-coding RNAs.
Pac Symp Biocomput, 15:54–56, 2010.
(doi:10.1142/9789814295291_0007)
Andreas R. Gruber,
Sven Findeiß, Stefan Washietl,
Ivo L. Hofacker, and Peter F. Stadler.
RNAz 2.0: improved noncoding RNA detection.
Proceedings of the Pacific Symposion on Biocomputing, 15:69–79,
2010.
(doi:10.1142/9789814295291_0009)
2009
Stephan H. Bernhart
and Ivo L. Hofacker.
From consensus structure prediction to RNA gene finding.
Brief Funct Genomic Proteomic, 8(6):461–71, 2009.
(doi:10.1093/bfgp/elp043)
Ronny Lorenz,
Christoph Flamm, and Ivo L. Hofacker.
2D projections of RNA folding landscapes.
In I. Grosse, S. Neumann,
S. Posch, F. Schreiber, and P.F.
Stadler, editors, German Conference on Bioinformatics 2009,
volume 157 of Lecture Notes in Informatics, pages 11–20, Bonn,
2009. Gesellschaft f. Informatik.
Ivo L. Hofacker.
RNA secondary structure analysis using the Vienna RNA Package.
In A.D. Baxevanis and D.B. Davison, editors,
Current Protocols in Bioinformatics, volume 1. John Wiley &
Sons, 2009.
(doi:10.1002/0471250953.bi1202s26)
German G. Leparc,
Thomas Tuchler, Gerald Striedner,
Karl Bayer, Peter Sykacek, Ivo L.
Hofacker, and David P. Kreil.
Model-based probe set optimization for high-performance microarrays.
Nucl. Acids Res., 37:e18, 2009.
(doi:10.1093/nar/gkn1001)
Christian Heine,
Gerik Scheuermann, Christoph Flamm,
Ivo L. Hofacker, and Peter F. Stadler.
Visualization of barrier tree sequences revisited.
In L Linsen, H Hagen, and
B Hamann, editors, Visualization in Medicine and Life
Sciences, Mathematics and Visualization, pages 275–290. Springer
Berlin, 2008.
Workshop on Visualization in Medicine and Life Sciences, Rugen, Germany,
2006.
2008
Stephan H. Bernhart,
Ivo L. Hofacker, Sebastian Will,
Andreas R. Gruber, and Peter F. Stadler.
RNAalifold: improved consensus structure prediction for RNA alignments.
BMC Bioinformatics, 9:474, 2008.
(doi:10.1186/1471-2105-9-474)
Andreas R Gruber,
Carsten Kilgus, Axel Mosig, Ivo L
Hofacker, Wolfgang Hennig, and Peter F
Stadler.
Arthropod 7SK RNA.
Mol Biol Evol, 25:1923–1930, 2008.
(doi:10.1093/molbev/msn140)
Hakim Tafer and
Ivo L. Hofacker.
RNAplex: a fast tool for RNA-RNA interaction search.
Bioinformatics, 24(22):2657–2663, 2008.
(doi:10.1093/bioinformatics/btn193)
Ulrike
Mückstein, Hakim Tafer, Stephan H.
Bernhart, Maribel Hernandez-Rosales, Jörg
Vogel, Peter F. Stadler, and Ivo L. Hofacker.
Translational control by RNA-RNA interaction: Improved computation of
RNA-RNA binding thermodynamics.
In M. Elloumi, J. Küng,
M. Linial, R. Murphy,
K. Schneider, and C. Toma, editors,
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114–127. Springer, 2008.
(doi:10.1007/978-3-540-70600-7_9)
Andreas R. Gruber,
Ronny Lorenz, Stephan H Bernhart,
Richard Neuböck, and Ivo L. Hofacker.
The Vienna RNA websuite.
Nucl. Acids Res., 36:W70–W74, 2008.
(doi:10.1093/nar/gkn188)
Hakim Tafer,
Stefan L. Ameres, Gregor Obernosterer,
Christoph A. Gebeshuber, Renée Schroeder,
Javier Martinez, and Ivo L. Hofacker.
The impact of target site accessibility on the design of effective siRNAs.
Nature Biotech., 26:578–583, 2008.
(doi:10.1038/nbt1404)
Michael Geis,
Christoph Flamm, Michael T. Wolfinger,
Andrea Tanzer, Ivo L. Hofacker,
Martin Middendorf, Christian Mandl,
Peter F. Stadler, and Caroline Thurner.
Folding kinetics of large RNAs.
J. Mol. Biol, 379:160–173, 2008.
(doi:10.1016/j.jmb.2008.02.064)
Christoph Jöchl,
Mathieu Rederstorff, Jana Hertel,
Peter F. Stadler, Ivo L. Hofacker,
Markus Schrettl, Hubertus Haas, and
Alexander Hüttenhofer.
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests
a novel mechanism for regulation of protein-synthesis.
Nucleic Acids Res., 36:2677–2689, 2008.
(doi:10.1093/nar/gkn123)
Christoph Flamm and
Ivo L. Hofacker.
Beyond energy minimization: Approaches to the kinetic folding of RNA.
Monatsh. f. Chemie, 139(4):447–457, 2008.
(doi:10.1007/s00706-008-0895-3)
Andreas R. Gruber,
Dorota Koper-Emde, Manja Marz,
Hakim Tafer, Stephan Bernhart,
Gregor Obernosterer, Axel Mosig,
Ivo L. Hofacker, Peter F. Stadler, and
Bernd-Joachim Benecke.
Invertebrate 7SK snRNAs.
J. Mol. Evol., 66:107–115, 2008.
(doi:10.1007/s00239-007-9052-6)
R S Vareková,
I Bradác, M Plchút,
M Skrdla, M Wacenovsky, H Mahr,
G Mayer, H Tanner, H Brugger,
J Withalm, P Lederer, H Huber,
G Gierlinger, R Graf, H Tafer,
I L Hofacker, P Schuster, and
M Polcík.
www.rnaworkbench.com: A new program for analyzing RNA interference.
Comput Methods Programs Biomed, 90(1):89–94, 2008.
(doi:10.1016/j.cmpb.2007.12.001)
Andreas R. Gruber,
Stefan H. Bernhart, Ivo L. Hofacker, and
Stefan Washietl.
Strategies for measuring evolutionary conservation of RNA secondary
structures.
BMC Bioinformatics, 9:122, 2008.
(doi:10.1186/1471-2105-9-122)
Jana Hertel,
Ivo L. Hofacker, and Peter F. Stadler.
snoReport: Computational identification of snoRNAs with unknown
targets.
Bioinformatics, 24:158–164, 2008.
(doi:10.1093/bioinformatics/btm464)
Athanasius F.
Bompfünewerer, Rolf Backofen, Stephan H.
Bernhart, Jana Hertel, Ivo L. Hofacker,
Peter F. Stadler, and Sebastian Will.
Variations on RNA folding and alignment: Lessons from Benasque.
J. Math. Biol., 56:119–144, 2008.
(doi:10.1007/s00285-007-0107-5)
2007
Ivo L. Hofacker.
How microRNAs choose their targets.
Nature Genetics, 39(10):1191–1192, 2007.
(doi:10.1038/ng1007-1191)
Hakim Tafer and
Ivo L. Hofacker.
RNAplex: a fast and flexible RNA-RNA interaction search tool.
In C. Falter, A. Schliep,
J. Selbig, M. Vingron, and
D. Walther, editors, German Conference on Bioinformatics
(GCB 2007), Lecture Notes in Informatics, pages 56–67, 2007.
Stefan Washietl and
Ivo L. Hofacker.
Identifying structural non-coding RNAs using RNAz.
In A.D. Baxevanis and D.B. Davison, editors,
Current Protocols in Bioinformatics, volume 1. John Wiley &
Sons, 2007.
(doi:10.1002/0471250953.bi1207s19)
Stefan E. Seemann,
Michael J. Gilchrist, Ivo L. Hofacker,
Peter F. Stadler, and Jan Gorodkin.
Detection of RNA structures in porcine EST data and related mammals.
BMC Genomics, 8:316, 2007.
(doi:10.1186/1471-2164-8-316)
The ENCODE Consortium.
Identification and analysis of functional elements in 1% of the human genome
by the ENCODE pilot project.
Nature, 447:799–816, 2007.
(doi:10.1038/nature05874)
Ivo L. Hofacker.
RNA consensus structure prediction with RNAalifold.
In Nicholas Bergman, editor, Comparative Genomics,
volume 1 of Methods in Molecular Biology, chapter 33, pages
527–544. Humana Press, Totowa, NJ, 2007.
Stefan Washietl,
Jakob S. Pedersen, Jan O. Korbel,
Andreas Gruber, Jörg Hackermüller,
Jana Hertel, Manja Lindemeyer,
Kristin Reiche, Claudia Stocsits,
Andrea Tanzer, Catherine Ucla,
Carine Wyss, Stylianos E. Antonarakis,
France Denoeud, Julien Lagarde,
Jorg Drenkow, Philipp Kapranov,
Thomas R. Gingeras, Roderic Guigó,
Michael Snyder, Mark B. Gerstein,
Alexandre Reymond, Ivo L. Hofacker, and
Peter F. Stadler.
Structured RNAs in the ENCODE selected regions of the human genome.
Genome Res., 17:852–864, 2007.
(doi:10.1101/gr.5650707)
Andreas R. Gruber,
Richard Neuböck, Ivo L. Hofacker, and
Stefan Washietl.
The RNAz web server: prediction of thermodynamically stable and
evolutionarily conserved RNA structures.
Nucl. Acids Res., 35:W335–W338, 2007.
(doi:10.1093/nar/gkm222)
Philipp Kapranov,
Jill Cheng, Sujit Dike, David A.
Nix, Radharani Duttagupta, Aarron T.
Willingham, Peter F. Stadler, Jana Hertel,
Jörg Hackermüller, Ivo L. Hofacker,
Ian Bell, Evelyn Cheung, Jorg
Drenkow, Erica Dumais, Sandeeep Patel,
Gregg Helt, Ganesh Madhavan,
Srinka Gosh, Antonio Piccolboni,
Victor Sementchenko, Hari Tammana, and
Tom R. Gingeras.
RNA maps reveal new RNA classes and a possible function for pervasive
transcription.
Science, 316:1484–1488, 2007.
(doi:10.1126/science.1138341)
Christoph Flamm,
Ivo L. Hofacker, Bärbel M. R. Stadler, and
Peter F. Stadler.
Saddles and barrier in landscapes of generalized search operators.
In C. R. Stephens, M. Toussaint,
D. Whitley, and P. F. Stadler, editors,
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Lecture Notes Comp. Sci., pages 194–212, Berlin, Heidelberg,
2007. Springer.
9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11,
2007.
Sebastian Will,
Kristin Reiche, Ivo L. Hofacker,
Peter F. Stadler, and Rolf Backofen.
Inferring non-coding RNA families and classes by means of genome-scale
structure-based clustering.
PLoS Comp. Biol., 3:e65, 2007.
(doi:10.1371/journal.pcbi.0030065)
Ivo L. Hofacker and
Peter F. Stadler.
RNA secondary structures.
In Thomas Lengauer, editor, Bioinformatics: From Genomes
to Therapies, volume 1, pages 439–489. Wiley-VCH, Weinheim, Germany,
2007.
The Athanasius
F. Bompfünewerer RNA Consortium:, Rolf Backofen,
Christoph Flamm, Claudia Fried,
Guido Fritzsch, Jörg Hackermüller,
Jana Hertel, Ivo L. Hofacker,
Kristin Missal, Axel Mosig,
Sonja J. Prohaska, Domininc Rose,
Peter F. Stadler, Andrea Tanzer,
Stefan Washietl, and Will Sebastian.
RNAs everywhere: Genome-wide annotation of structured RNAs.
J. Exp. Zool. B: Mol. Dev. Evol., 308B:1–25, 2007.
(doi:10.1002/jez.b.21130)
2006
Ivo L. Hofacker.
RNAs everywhere: Genome-wide annotation of structured RNAs.
volume 17 of Genome Informatics, pages 281–282. Universal Academy
Press, Tokyo, 2006.
Axel Mosig,
Ivo L. Hofacker, and Peter F. Stadler.
Comparative analysis of cyclic sequences: Viroids and other small circular
RNAs.
In Robert Giegerich and Jens Stoye, editors,
Proceedings GCB 2006, volume P-83 of Lecture Notes in
Informatics, pages 93–102, 2006.
Christian Heine,
Gerik Scheuermann, Christoph Flamm,
Ivo L. Hofacker, and Peter F. Stadler.
Visualization of barrier tree sequences.
IEEE Trans. Vis. Comp. Graphics, 12:781–788, 2006.
(doi:10.1109/TVCG.2006.196)
Jord H.A. Nagel,
Christph Flamm, Ivo L. Hofacker,
Kai Franke, Maarten H. de Smit,
Peter Schuster, and Cornelis W.A. Pleij.
Structural parameters affecting the kinetics of RNA hairpin formation.
Nucl. Acids Res., 34:3568–3576, 2006.
(doi:10.1093/nar/gkl445)
Michael T.
Wolfinger, Sebastian Will, Ivo L. Hofacker,
Rolf Backofen, and Peter F. Stadler.
Exploring the lower part of discrete polymer model energy landscapes.
Europhys. Lett., 74:726–732, 2006.
(doi:10.1209/epl/i2005-10577-0)
Stephan H. Bernhart,
Hakim Tafer, Ulrike Mückstein,
Christoph Flamm, Peter F. Stadler, and
Ivo L. Hofacker.
Partition function and base pairing probabilities of RNA heterodimers.
Algorithms Mol. Biol., 1:3 [epub], 2006.
(doi:10.1186/1748-7188-1-3)
Ivo L. Hofacker and
Peter F. Stadler.
Modeling RNA folding.
In Thomas S. Deisboeck and J. Yasha Kresh,
editors, Complex Systems Science in BioMedicine, pages 227–245.
Springer, New York, 2006.
Stephan Bernhart,
Ivo L. Hofacker, and Peter F. Stadler.
Local RNA base pairing probabilities in large sequences.
Bioinformatics, 22:614–615, 2006.
(doi:10.1093/bioinformatics/btk014)
Wei-Che Hsu,
Hsien-Da Huang, Sheng-Da Hsu,
Li-Zen Lin, Ann-Ping Tsou,
Ching-Ping Tseng, Peter F. Stadler,
Stefan Washietl, and Ivo L. Hofacker.
miRNAMap: Genomic maps of microRNA genes and their target genes in
mammalian genomes.
Nucl. Acids Res., 34:D135–D139, 2006.
(doi:10.1093/nar/gkj135)
Christian V. Forst,
Christoph Flamm, Ivo L. Hofacker, and
Peter F. Stadler.
Algebraic comparison of metabolic networks, phylogenetic inference, and
metabolic innovation.
BMC Bioinformatics, 7:67 [epub], 2006.
(doi:10.1186/1471-2105-7-67)
Jana Hertel,
Manuela Lindemeyer, Kristin Missal,
Claudia Fried, Andrea Tanzer,
Christoph Flamm, Ivo L. Hofacker,
Peter F. Stadler, and The Students of
Bioinformatics Computer Labs 2004 and 2005.
The expansion of the metazoan microRNA repertoire.
BMC Genomics, 7:15 [epub], 2006.
(doi:10.1186/1471-2164-7-25)
Ulrike
Mückstein, Hakim Tafer, Jörg
Hackermüller, Stephan H. Bernhart, Peter F.
Stadler, and Ivo L Hofacker.
Thermodynamics of RNA-RNA binding.
Bioinformatics, 22:1177–1182, 2006.
Earlier version in: German Conference on Bioinformatics 2005, Torda,
Andrew and Kurtz, Stefan and Rarey, Matthias (eds.), Lecture Notes in
Informatics P-71, pp 3-13, Gesellschaft f. Informatik, Bonn 2005.
(doi:10.1093/bioinformatics/btl024)
Ivo L. Hofacker and
Peter F. Stadler.
Memory efficient folding algorithms for circular RNA secondary structures.
Bioinformatics, 22:1172–1176, 2006.
Earlier version in: German Conference on Bioinformatics 2005, Torda,
Andrew and Kurtz, Stefan and Rarey, Matthias (eds.), Lecture Notes in
Informatics P-71, pp 3-13, Gesellschaft f. Informatik, Bonn 2005.
(doi:10.1093/bioinformatics/btl023)
2005
Stefan Washietl,
Ivo L. Hofacker, Melanie Lukasser,
Alexander Hüttenhofer, and Peter F.
Stadler.
Mapping of conserved RNA secondary structures predicts thousands of
functional non-coding RNAs in the human genome.
Nature Biotech., 23:1383–1390, 2005.
(doi:10.1038/nbt1144)
Ivo L. Hofacker and
Peter F. Stadler.
RNA secondary structures.
In Robert A. Meyers, editor, Encyclopedia of Molecular
Cell Biology and Molecular Medicine, volume 12, pages 581–603.
Wiley-VCH, Weinheim, 2nd edition, 2005.
Roman R. Stocsits,
Ivo L. Hofacker, Claudia Fried, and
Peter F. Stadler.
Multiple sequence alignments of partially coding nucleic acid sequences.
BMC Bioinformatics, 6:160, 2005.
(doi:10.1186/1471-2105-6-160)
Gudrun
Böhmdorfer, Ivo L. Hofacker, Karin Garber,
Srecko Jelenic, Viktoria Nizhynska,
Hirohiko Hirochika, Peter F. Stadler, and
Andreas Bachmair.
Unorthodox mRNA start site to extend the highly structured leader of
retrotransposon Tto1 mRNA increases transposition rate.
RNA, 11:1181–1191, 2005.
(doi:10.1261/rna.2640105)
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, and Christina Witwer.
Evolutionary patterns of non-coding RNAs.
Th. Biosci., 123:301–369, 2005.
(doi:10.1016/j.thbio.2005.01.002)
Stefan Washietl,
Ivo L. Hofacker, and Peter F. Stadler.
Fast and reliable prediction of noncoding RNAs.
Proc. Natl. Acad. Sci. USA, 102:2454–2459, 2005.
(doi:10.1073/pnas.0409169102)
2004
Hans Binder,
Toralf Kirsten, Ivo L. Hofacker,
Peter F. Stadler, and Markus Löffler.
Interactions in oligonucleotide hybrid duplexes on microarrays.
J. Phys. Chem. B, 108:18015–18025, 2004.
(doi:10.1021/jp049592o)
Christina Witwer,
Ivo L. Hofacker, and Peter F. Stadler.
Prediction of consensus RNA secondary structures including pseudoknots.
IEEE/ACM Trans. Comp. Biol. Bioinf., 1:65–77, 2004.
(doi:10.1109/TCBB.2004.22)
Caroline Thurner,
Ivo L. Hofacker, and Peter F. Stadler.
Conserved RNA pseudoknots.
In Robert Giegerich and Jens Stoye, editors,
Proceedings of the GCB 2004 (Bielefeld), volume P-53 of
GI-Edition: Lecture Notes in Informatics, pages 207–216,
2004.
Stefan Washietl and
Ivo L. Hofacker.
Consensus folding of aligned sequences as a new measure for the detection of
functional RNAs by comparative genomics.
J. Mol. Biol., 342:19–39, 2004.
(doi:10.1016/j.jmb.2004.07.018)
Ivo L. Hofacker,
Stephan H. F. Bernhart, and Peter F. Stadler.
Alignment of RNA base pairing probability matrices.
Bioinformatics, 20:2222–2227, 2004.
(doi:10.1093/bioinformatics/bth229)
Christoph Flamm,
Ivo L. Hofacker, and Peter F. Stadler.
Computational chemistry with RNA secondary structures.
Kemija u industriji, 53:315–322, 2004.
Ivo L. Hofacker,
Roman Stocsits, and Peter F. Stadler.
Conserved RNA secondary structures in viral genomes: A survey.
Bioinformatics, 20:1495–1499, 2004.
Earlier version in: Proceedings of the German Conference on
Bioinformatics. GCB 2003, Mewes, H.-W., Heun, V., and Frishman, D., and
Kramer, S. (eds.), pp 57–62, belleville Verlag Michael Farin, München
2003.
(doi:10.1093/bioinformatics/bth108)
Christoph Flamm,
Ivo L. Hofacker, and Peter F. Stadler.
RNA folding in silico.
In Susanne Brakmann and Andreas Schwienhost,
editors, Evolutionary Methods in Biotechnology, pages 177–190.
Wiley-VCH, Weinheim, Germany, 2004.
Ivo L. Hofacker and
Peter F. Stadler.
The partition function variant of Sankoff's algorithm.
In M. Bubak, G.D. van Albada,
P.M. A. Sloot, and J.J. Dongarra, editors,
Computational Science - ICCS 2004, volume 3039 of Lecture
Notes in Computer Science, pages 728–735, 2004.
Kraków, June 6-9, 2004.
(doi:10.1007/b98005)
Caroline Thurner,
Christine Witwer, Ivo Hofacker, and
Peter F. Stadler.
Conserved RNA secondary structures in Flaviviridae genomes.
J. Gen. Virol., 85:1113–1124, 2004.
(doi:10.1099/vir.0.19462-0)
Michael T.
Wolfinger, W. Andreas Svrcek-Seiler, Christoph
Flamm, Ivo L. Hofacker, and Peter F. Stadler.
Efficient computation of RNA folding dynamics.
J. Phys. A: Math. Gen., 37:4731–4741, 2004.
(doi:10.1088/0305-4470/37/17/005)
Claudia S. Copeland,
Oliver Heyers, Bernd H. Kalinna,
Andreas Bachmair, Peter F. Stadler,
Ivo L. Hofacker, and Paul J. Brindley.
Structural and evolutionary analysis of the transcribed sequence of
Boudicca, a Schistosoma mansoni retrotransposon.
Gene, 329:103–104, 2004.
(doi:10.1016/j.gene.2003.12.023)
Ivo L. Hofacker,
Barbara Priwitzer, and Peter F. Stadler.
Prediction of locally stable RNA secondary structures for genome-wide
surveys.
Bioinformatics, 20:186–190, 2004.
(doi:10.1093/bioinformatics/btg388)
2003
Ivo L. Hofacker.
The Vienna RNA secondary structure server.
Nucl. Acids Res., 31:3429–3431, 2003.
(doi:10.1093/nar/gkg599)
Ivo L. Hofacker.
RNA secondary structure prediction.
In David Cooper, editor, Encyclopedia of the Human
Genome. Nature publishing group, London, 2003.
(doi:10.1038/npg.els.0005274)
Günter
Weberndorfer, Ivo L. Hofacker, and Peter F.
Stadler.
On the evolution of primitive genetic codes.
Origins Life Evol. Biosph., 33:491–514, 2003.
(doi:10.1023/A:1025753712110)
2002
Ulrike
Mückstein, Ivo L. Hofacker, and Peter F.
Stadler.
Stochastic pairwise alignments.
Bioinformatics, 18:S153–S160, 2002.
(doi:10.1093/bioinformatics/18.suppl_2.S153)
Ivo L. Hofacker,
Martin Fekete, and Peter F. Stadler.
Secondary structure prediction for aligned RNA sequences.
J. Mol. Biol., 319:1059–1066, 2002.
(doi:10.1016/S0022-2836(02)00308-X)
Christoph Flamm,
Ivo L. Hofacker, Peter F. Stadler, and
Michael T. Wolfinger.
Barrier trees of degenerate landscapes.
Z. Phys. Chem., 216:155–173, 2002.
(doi:10.1524/zpch.2002.216.2.155)
2001
Christina Witwer,
Susanne Rauscher, Ivo L. Hofacker, and
Peter F. Stadler.
Conserved RNA secondary structures in picornaviridae genomes.
Nucl. Acids Res., 29:5079–5089, 2001.
(doi:10.1093/nar/29.24.5079)
Aderonke Babajide,
Robert Farber, Ivo L. Hofacker,
Jeff Inman, Alan S. Lapedes, ,
and Peter F. Stadler.
Exploring protein sequence space using knowledge based potentials.
J. Theor. Biol., 212:35–46, 2001.
(doi:10.1006/jtbi.2001.2343)
Christoph Flamm,
Ivo L. Hofacker, Sebastian Maurer-Stroh,
Peter F. Stadler, and Martin Zehl.
Design of multi-stable RNA molecules.
RNA, 7:254–265, 2001.
(doi:10.1017/S1355838201000863)
2000
Karin Kidd-Ljunggren,
Michael Zuker, Ivo L. Hofacker, and
Alistair H. Kidd.
The Hepatitis B virus pregenome: Prediction of RNA structure and
implications for the emergence of deletions.
Intervirology, 43:154–164, 2000.
(doi:10.1159/000025041)
Martin Fekete,
Ivo L. Hofacker, and Peter F. Stadler.
Prediction of RNA base pairing probabilities using massively parallel
computers.
J. Comp. Biol., 7:171–182, 2000.
(doi:10.1089/10665270050081441)
Jaromir Konecny,
Michael Schöniger, Ivo L. Hofacker,
Marc-Denis Weitze, and G. Ludwig Hofacker.
Concurrent neutral evolution of mRNA secondary structures and encoded
proteins.
J. Mol. Evol., 50:238–242, 2000.
(doi:10.1007/s002399910027)
Christoph Flamm,
Walter Fontana, Ivo L. Hofacker, and
Peter Schuster.
RNA folding at elementary step resolution.
RNA, 6:325–338, 2000.
(doi:10.1017/S1355838200992161)
1999
Günter
Weberndorfer, Ivo L. Hofacker, and Peter F.
Stadler.
An efficient potential for protein sequence design.
In Computer Science in Biology, pages 107–112, Bielefeld, D,
1999. Univ. Bielefeld.
Proceedings of the GCB'99, Hannover, D.
Roman Stocsits,
Ivo L. Hofacker, and Peter F. Stadler.
Conserved secondary structures in hepatitis B virus RNA.
In Computer Science in Biology, pages 73–79, Bielefeld, D, 1999.
Univ. Bielefeld.
Proceedings of the GCB'99, Hannover, D.
Christoph Flamm,
Ivo L. Hofacker, and Peter F. Stadler.
RNA in silico: The computational biology of RNA secondary structures.
Adv. Complex Syst., 2:65–90, 1999.
(doi:10.1142/S0219525999000059)
Ivo L. Hofacker and
Peter F. Stadler.
Automatic detection of conserved base pairing patterns in RNA virus genomes.
Comp. & Chem., 23:401–414, 1999.
(doi:10.1016/S0097-8485(99)00013-3)
Ivo L. Hofacker.
RNA secondary structures: A tractable model of biopolymer folding.
In P. Grassberger, W. Nadler, and
G. T. Barkema, editors, Monte Carlo Approach to
Biopolymers and Protein Folding, pages 171–182. World Scientific,
Singapore, 1998.
Ivo L. Hofacker,
Peter Schuster, and Peter F. Stadler.
Combinatorics of RNA secondary structures.
Discr. Appl. Math., 88:207–237, 1998.
(doi:10.1016/S0166-218X(98)00073-0)
Ivo L. Hofacker,
Martin Fekete, Christoph Flamm,
Martijn A. Huynen, Susanne Rauscher,
Paul E. Stolorz, and Peter F. Stadler.
Automatic detection of conserved RNA structure elements in complete RNA
virus genomes.
Nucl. Acids Res., 26:3825–3836, 1998.
(doi:10.1093/nar/26.16.3825)
1997
Aderonke Babajide,
Ivo L. Hofacker, Manfred J. Sippl, and
Peter F. Stadler.
Neutral networks in protein space, a computational study based on
knowledge-based potentials of mean force.
Folding & Design, 2:261–269, 1997.
(doi:10.1016/S1359-0278(97)00037-0)
1996
Jan Cupal,
Ivo L. Hofacker, and Peter F. Stadler.
Dynamic programming algorithm for the density of states of RNA secondary
structures.
In R. Hofstädt, T. Lengauer,
M. Löffler, and D. Schomburg, editors,
Computer Science and Biology 96 (Proceedings of the German Conference
on Bioinformatics), pages 184–186, Leipzig (Germany), 1996.
Univeristät Leipzig.
Ivo L. Hofacker,
Martijn A. Huynen, Peter F. Stadler, and
Paul E. Stolorz.
Knowledge discovery in RNA sequence families of HIV using scalable
computers.
In Proc. 2nd International Conference on Knowledge Discovery and Data
Mining, pages 20–25, Menlo Park, CA, 1996. AAAI Press.
Manfred Tacker,
Peter F. Stadler, Erich G. Bornberg-Bauer,
Ivo L. Hofacker, and Peter Schuster.
Algorithm independent properties of RNA secondary structure predictions.
Eur. Biophys. J., 25:115, 1996.
(doi:10.1007/s002490050023)
Walter Grüner,
Robert Giegerich, Dirk Strothmann,
Christian Reidys, Jacqueline Weber,
Ivo L. Hofacker, Peter F. Stadler, and
Peter Schuster.
Analysis of RNA sequence structure maps by exhaustive enumeration.
II. Structures of neutral networks and shape space covering.
Monatsh. Chem., 127:375–389, 1996.
(doi:10.1007/BF00810882)
Walter Grüner,
Robert Giegerich, Dirk Strothmann,
Christian Reidys, Jacqueline Weber,
Ivo L. Hofacker, Peter F. Stadler, and
Peter Schuster.
Analysis of RNA sequence structure maps by exhaustive enumeration.
I. Neutral networks.
Monatsh. Chem., 127:355–374, 1996.
(doi:10.1007/BF00810881)
1994
Peter Schuster,
Walter Fontana, Peter F. Stadler, and
Ivo L. Hofacker.
From sequences to shapes and back: A case study in RNA secondary structures.
Proc. Roy. Soc. (London) B, 255:279–284, 1994.
(PDF)
Ivo L. Hofacker,
Walter Fontana, Peter F. Stadler,
Sebastian Bonhoeffer, Manfred Tacker, and
Peter Schuster.
Fast folding and comparison of RNA secondary structures (the Vienna RNA
Package).
Monatsh. Chem., 125(2):167–188, 1994.
(doi:10.1007/BF00818163)
1993
Walter Fontana,
Peter F. Stadler, Erich G. Bornberg-Bauer,
Thomas Griesmacher, Ivo L. Hofacker,
Manfred Tacker, Pedro Tarazona,
Edward D. Weinberger, and Peter Schuster.
RNA folding and combinatory landscapes.
Phys. Rev. E, 47(3):2083–2099, 1993.
(doi:10.1103/PhysRevE.47.2083)
1992
Matthias Fuchs,
Ivo Hofacker, and Arnulf Latz.
Primary relaxation in a hard-sphere system.
Phys. Rev. A15, 45(2):898, 1992.
(doi:10.1103/PhysRevA.45.898)
1991
Ivo Hofacker,
Matthias Fuchs, and Arnulf Latz.
The double α-peak phenomenon in polymers.
Berichte der Bunsen-Gesellschaft für physikalische Chemie,
95(9):1046, 1991.
Matthias Fuchs,
Wolfgang Götze, Ivo Hofacker, and
Arnulf Latz.
Comments on the α-peak shapes for relaxation in supercooled liquids.
J. Phys. Cond. Matt., 3(26):5047, 1991.
(doi:10.1088/0953-8984/3/26/022)
1990
Branko Borstnik,
Danilo Pumpernik, Ivo L. Hofacker, and
G. Ludwig Hofacker.
An ESS-analysis for ensembles of prisoner's dilemma strategies.
J. Theor. Biol., 142(2):189, 1990.
(doi:10.1016/S0022-5193(05)80221-8)