Publications

For other publications of my group see the TBI working papers list.

You can also find my complete list of publictions (with citations) on Google Scholar, on ReasearcherID, or using my ORCID 0000-0001-7132-0800.

2024

• Tom Rappol, Maria Waldl, Anastasia Chugunova, Ivo L Hofacker, Andrea Pauli, and Elisa Vilardo. tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development. Nucleic Acids Research, 52(17):10575–10594, 07 2024. (doi:10.1093/nar/gkae595)
• Bernhard C Thiel, Giovanni Bussi, Simón Poblete, and Ivo L Hofacker. Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data. Nucleic Acids Research, 52(16):e73–e73, 2024. (doi:10.1093/nar/gkae602)
• Maria Waldl, Hua-Ting Yao, and Ivo L Hofacker. Sequence design for RNA-RNA interactions. In RNA Design: Methods and Protocols, Methods in Molecular Biology, pages 1–16. Springer, 2024. (doi:10.1007/978-1-0716-4079-1_1)
• Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo Hofacker, and Peter F Stadler. Phylogenetic and chemical probing information as soft constraints in RNA secondary structure prediction. Journal of Computational Biology, 31(6):549–563, 2024. (doi:10.1089/cmb.2024.0519)
• Irene K Beckmann, Maria Waldl, Sebastian Will, and Ivo L Hofacker. 3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations. RNA, 30(2):113–123, 2024. (doi:10.1261/rna.079756.123)

2023

• Yuliia Varenyk, Thomas Spicher, Ivo L Hofacker, and Ronny Lorenz. Modified RNAs and predictions with the ViennaRNA package. Bioinformatics, 39(11), 2023. (doi:10.1093/bioinformatics/btad696)
• Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo Hofacker, and Peter F Stadler. Phylogenetic information as soft constraints in RNA secondary structure prediction. In International Symposium on Bioinformatics Research and Applications, pages 267–279, 2023.
• Hua-Ting Yao, Ronny Lorenz, Ivo L Hofacker, and Peter F Stadler. Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms for Molecular Biology, 18(1):8, 2023. (doi:10.1186/s13015-023-00236-0)
• 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, 21:2350016, 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 Petrácková, Dilip Kumar, Jakub Drzmísek, Argha Saha, Ivana Curnová, Jan Capek, 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.

2020

• 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 Petrácková, Mariam R Farman, Fabian Amman, Irena Linhartová, Ana Dienstbier, Dilip Kumar, Jakub Drzmísek, Ivo L. Hofacker, Maria Eugenia Rodriguez, and Branislav Vecerek. 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 Kucharík, 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, 21:1249–1260, 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, Večerek 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 Kucharík, 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)

• 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)

• 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)

• 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, RNA Interference: From Biology to Clinical Applications, volume 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, Data Mining Techniques for the Life Sciences, volume 609 of 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)

• 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.

• 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, Bioinformatics Research and Development, volume 13 of Communications in Computer and Information Science, pages 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)

• 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, Foundations of Genetic Algortithms IX, volume 4436 of 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)

• 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)

• 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)

• 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)

• 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)

• 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)

• 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)

• 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)

• 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)
• S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49:145–165, 1999. (doi:10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G)

• 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 and Klaus Schulten. Oxygen and proton pathways in cytochrome c oxidase. Proteins: Structure, Function and Genetics, 30:100–107, 1998. (doi:10.1002/(SICI)1097-0134(199801)30:1<100::AID-PROT9>3.0.CO;2-S)
• 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)

• 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)

• 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)

• 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)

• 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)

• 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)

• 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)

• 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)