Items where Author is "Hofacker, Ivo L."

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Number of items: 93.

Journal Paper

  • 3D Feasibility of 2D RNA-RNA Interaction Paths by stepwise Folding Simulations
    Beckmann, Irene K. and Waldl, Maria and Will, Sebastian and Hofacker, Ivo L. RNA. pp. 113-123 ISSN 1355-8382 (2024)

  • Investigating RNA- RNA interactions through computational and biophysical analysis.
    Mrozowich, Tyler and Park, Sean and Waldl, Maria and Henrickson, Amy and Tersteeg, Scott and Nelson, Corey and De Klerk, Anneke and Demeler, Borries and Hofacker, Ivo L. and Wolfinger, Michael T. and Patel, Trushar R. ISSN 1362-4962 (2023)

  • Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment
    Farman, Mariam R. and Petráčková, Denisa and Kumar, Dilip and Držmíšek, Jakub and Saha, Argha and Čurnová, Ivana and Čapek, Jan and Hejnarová, Václava and Amman, Fabian and Hofacker, Ivo L. and Vecerek, Branislav Emerging Microbes & Infections, 12 (1). e2146536 ISSN 2222-1751 (2023)

  • DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
    Badelt, Stefan and Lorenz, Ronny and Hofacker, Ivo L. Bioinformatics, 39 (1). btad034 ISSN 1367-4803 Oxford University Press (2023)

  • Local RNA folding revisited
    Waldl, Maria and Spicher, Thomas and Lorenz, Ronny and Beckmann, Irene K. and Hofacker, Ivo L. and von Löhneysen, Sarah and Stadler, Peter F. p. 2350016 ISSN 1757-6334 World Scientific (2023)

  • Modified RNAs and predictions with the ViennaRNA Package
    Varenyk, Yuliia and Spicher, Thomas and Hofacker, Ivo L. and Lorenz, Ronny Bioinformatics, 39 (11). ISSN 1367-4803 Oxford University Press (2023)

  • Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
    Yao, Hua-Ting and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. Algorithms for Molecular Biology, 18 (1). p. 8 ISSN 1748-7188 Springer (2023)

  • Caveats to deep learning approaches to RNA secondary structure prediction
    Flamm, Christoph and Wielach, Julia and Wolfinger, Michael T. and Badelt, Stefan and Lorenz, Ronny and Hofacker, Ivo L. ISSN 0000-0000 Frontiers (2022)

  • Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site
    Gosavi, Devadatta and Wower, Iwona and Beckmann, Irene K. and Hofacker, Ivo L. and Wolfinger, Michael T. and Sztuba-Solinska, Joanna pp. 496-506 ISSN 0305-1048 Taylor & Francis (2022)

  • 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
    Zayni, Sonja and Damiati, Samar and Moreno-Flores, Susana and Amman, Fabian and Hofacker, Ivo L. and Jin, David and Ehmoser, Eva-Kathrin Membranes, 11. p. 741 ISSN 2077-0375 mdpi (2021)

  • RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes
    Entzian, Gregor and Hofacker, Ivo L. and Ponty, Yann and Lorenz, Ronny and Tanzer, Andrea Bioinformatics, 37. pp. 2126-2133 ISSN 1367-4803 (2021)

  • Transcriptional profiling of human macrophages during infection with Bordetella pertussis
    Petráčková, Denisa and Farman, Mariam R. and Amman, Fabian and Linhartová, Irena and Dienstbier, Ana and Kumar, Dilip and Držmíšek, Jakub and Hofacker, Ivo L. and Rodriguez, Maria Eugenia and Vecerek, Branislav RNA Biology, 17 (5). pp. 731-742 ISSN 1555-8584 (2020)

  • Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution
    Kim, Doo Nam and Thiel, Bernhard and Mrozowich, Tyler and Henelly, Scatt P. and Hofacker, Ivo L. and Patel, Trushar R. and Sanbonmatsu, Karissa Y. ISSN 2041-1723 (2020)

  • The locality dilemma of Sankoff-like RNA alignments
    Backofen, Rolf and Will, Sebastian and Hofacker, Ivo L. and Hutter, Frank and Miladi, Milad and Müller, Teresa Bioinformatics, 36. i242-i250 ISSN 1367-4803 (2020)

  • Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture
    de Bernardi Schneider, Adriano and Ochsenreiter, Roman and Hostager, Reilly and Hofacker, Ivo L. and Janies, Daniel and Wolfinger, Michael T. p. 798 MDPI (2019)

  • Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses
    Ochsenreiter, Roman and Hofacker, Ivo L. and Wolfinger, Michael T. Viruses, 11 (3). p. 298 ISSN 1999-4915 MDPI (2019)

  • 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
    Thiel, Bernhard and Beckmann, Irene K. and Kerpedjiev, Peter and Hofacker, Ivo L. ISSN 2046-1402 (2019)

  • Conserved secondary structures in viral mRNAs
    Kiening, Michael and Ochsenreiter, Roman and Hellinger, Hans-Jörg and Rattei, Thomas and Hofacker, Ivo L. and Frishman, Dmitrij ISSN 1999-4915 MDPI (2019)

  • Control of cognate sense mRNA translation by cis-natural antisense RNAs
    Deforges, Jules and Reis, Rodrigo and Jacquet, Philippe and Sheppard, Shaoline and Gadekar, Veerendra and Tanzer, Andrea and Hofacker, Ivo L. and Iseli, Christian and Xenarios, Ioannis and Poirier, Yves ISSN 0032-0889 (2019)

  • IntaRNAhelix-composing RNA–RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction
    Gelhausen, Rick and Will, Sebastian and Hofacker, Ivo L. and Backofen, Rolf and Raden, Martin ISSN 1757-6334 (2019)

  • MSF: Modulated Sub-graph Finder
    Farman, Mariam R. and Hofacker, Ivo L. and Amman, Fabian ISSN 2046-1402 (2019)

  • CMV: visualization for RNA and protein family models and their comparisons
    Eggenhofer, Florian and Hofacker, Ivo L. and Backofen, Rolf and Höner zu Siederdissen, Christian Bioinformatics, 34 (15). pp. 2676-2678 ISSN 1367-4803 Oxford University Press (2018)

  • Comparative genomics of Czech vaccine strains of Bordetella pertussis
    Dienstbier, Ana and Pouchnik, Derek and Wildung, Mark and Amman, Fabian and Hofacker, Ivo L. and Parkhill, Julian and Holubova, Jana and Sebo, Peter and Vecerek, Branislav Pathogens and Disease, 76 (7). Oxford University Press (2018)

  • Efficient computation of co-transcriptional RNA-ligand interaction dynamics
    Wolfinger, Michael T. and Flamm, Christoph and Hofacker, Ivo L. Methods, 143. pp. 70-76 Elsevier (2018)

  • In silico design of ligand triggered RNA switches
    Findeiß, Sven and Hammer, Stefan and Wolfinger, Michael T. and Kühnl, Felix and Flamm, Christoph and Hofacker, Ivo L. Methods, 143. pp. 90-101 Elsevier (2018)

  • RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
    Thiel, Bernhard and Ochsenreiter, Roman and Gadekar, Veerendra and Tanzer, Andrea and Hofacker, Ivo L. Genes, 9 (8). p. 392 (2018)

  • RNA modifications in structure prediction – Status quo and future challenges
    Tanzer, Andrea and Hofacker, Ivo L. and Lorenz, Ronny Methods. Elsevier (2018)

  • RNAblueprint: Flexible multiple target nucleic acid sequence design
    Hammer, Stefan and Tschiatschek, Birgit and Flamm, Christoph and Hofacker, Ivo L. and Findeiß, Sven Bioinformatics. ISSN 1367-4803 Oxford University Press (2017)

  • 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
    Gerresheim, Gesche and Dünnes, Nadia and Nieder-Röhrmann, Anika and Shalamova, Lyudmila and Fricke, Markus and Hofacker, Ivo L. and Höner zu Siederdissen, Christian and Marz, Manja and Niepmann, Michael pp. 747-760 ISSN 1420-682X (2017)

  • NMR structural profiling of transcriptional intermediates reveals riboswitch regulation by metastable RNA conformations
    Helmling, Christina and Wacker, Anna and Wolfinger, Michael T. and Hofacker, Ivo L. and Hengesbach, Martin and Fürtig, Boris and Schwalbe, Harald pp. 2647-2656 ISSN 0002-7863 (2017)

  • RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets
    Alkan, Ferhat and Wenzel, Anne and Palasca, Oana and Kerpedjiev, Peter and Rudebeck, Anders Frost and Stadler, Peter F. and Hofacker, Ivo L. and Gorodkin, Jan e60 ISSN 0305-1048 (2017)

  • RNA structure prediction: from 2D to 3D
    Thiel, Bernhard and Flamm, Christoph and Hofacker, Ivo L. pp. 275-285 ISSN 2397-8554 (2017)

  • Predicting RNA secondary structures from sequence and probing data
    Lorenz, Ronny and Wolfinger, Michael T. and Tanzer, Andrea and Hofacker, Ivo L. pp. 86-98 ISSN 1046-2023 (2016)

  • Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution
    Sedlyarov, Vitaly and Fallmann, Jörg and Ebner, Florian and Huemer, Jakob and Sneezum, Lucy and Ivin, Masa and Kreiner, Kristina and Tanzer, Andrea and Vogl, Claus and Hofacker, Ivo L. and Kovarik, Pavel ISSN 1744-4292 (2016)

  • AREsite2: An enhanced database for the comprehensive investigation of AU/GU/U-rich elements
    Fallmann, Jörg and Sedlyarov, Vitaly and Tanzer, Andrea and Kovarik, Pavel and Hofacker, Ivo L. D90-D95 ISSN 0305-1048 (2016)

  • Computational design of a circular RNA with prion-like behavior
    Badelt, Stefan and Flamm, Christoph and Hofacker, Ivo L. pp. 172-184 ISSN 1064-5462 (2016)

  • Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
    Hölzer, Martin and Krähling , Verena and Amman, Fabian and Barth, Emanuel and Bernhart, Stephan H. and Carmelo, Victor and Collatz, Maximilian and Doose, Gero and Eggenhofer, Florian and Ewald, Jan and Fallmann, Jörg and Feldhahn, Lasse and Fricke, Markus and Gebauer, Juliane and Gruber, Andreas R and Hufsky, Franziska and Indrischek, Henrike and Kanton, Sabina and Linde, Jörg and Mostajo, Nelly and Ochsenreiter, Roman and Riege, Konstantin and Rivarola-Duarte, Lorena and Sahyoun, Abdullah and Saunders, Sita and Seemann, Stefan E and Tanzer, Andrea and Vorgel, bertram and Wehner, Stefanie and Wolfinger, Michael T. and Backofen, Rolf and Gorodkin, Jan and Grosse, Ivo and Hoffmann, Steve and Hofacker, Ivo L. and Kaleta, Christoph and Stadler, Peter F. and Becker, Stephan and Marz, Manja ISSN 2045-2322 (2016)

  • Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks
    Hsiao, Yu-Ting and Lee, Wei-Po and Müller, Stefan and Flamm, Christoph and Hofacker, Ivo L. and Kügler, Philipp pp. 64-75 ISSN 1557-9964 (2016)

  • RNA folding with hard and soft constraints
    Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. ISSN 1748-7188 (2016)

  • RNAlien - Unsupervised RNA family model construction
    Eggenhofer, Florian and Höner zu Siederdissen, Christian and Hofacker, Ivo L. pp. 8433-8441 ISSN 0305-1048 (2016)

  • Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity
    Tajaddod, Mansoureh and Tanzer, Andrea and Licht, Konstantin and Wolfinger, Michael T. and Badelt, Stefan and Huber, Florian and Pusch, Oliver and Schopoff, Sandy and Janisiw, Michael and Hofacker, Ivo L. and Jantsch, Michael F. p. 220 ISSN 1474-760X (2016)

  • Pseudoknots in RNA folding landscapes
    Kucharik, Marcel and Hofacker, Ivo L. and Stadler, Peter F. and Qin, Jing Bioinformatics, 32. pp. 187-194 ISSN 1367-4803 (2016)

  • Product grammars for alignment and folding.
    Höner zu Siederdissen, Christian and Hofacker, Ivo L. and Stadler, Peter F. pp. 507-519 ISSN 1557-9964 (2015)

  • Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams
    Kerpedjiev, Peter and Hammer, Stefan and Hofacker, Ivo L. Bioinformatics, 31 (20). pp. 3377-3379 ISSN 1367-4803 Oxford University Press (2015)

  • Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
    Lavender, Christopher A. and Lorenz, Ronny and Zhang, Ge and Tamayo, Rita and Hofacker, Ivo L. and Weeks, Kevin M. PLoS Comput Biol, 11. e1004126 ISSN 1553-734X (2015)

  • Optimizing RNA structures by sequence extensions using RNAcop
    Hecker, Nikolai and Christensen-Dalsgaard, Mikkel and Seemann, Stefan E and Havgaard, Jakob H and Stadler, Peter F and Hofacker, Ivo L. and Nielsen, Henrik and Gorodkin, Jan Nucleic acids research, 43 (17). pp. 8135-8145 ISSN 0305-1048 (2015)

  • Predicting RNA 3D structure using a coarse-grain helix-centered model
    Kerpedjiev, Peter and Höner zu Siederdissen, Christian and Hofacker, Ivo L. RNA, 21. pp. 1110-1121 ISSN 1355-8382 (2015)

  • Processed Small RNAs in Archaea and BHB Elements
    Berkemer, Sarah J. and Höner zu Siederdissen, Christian and Amman, Fabian and Wintsche, Axel and Will, Sebastian and Hofacker, Ivo L. and Prohaska, Sonja J. and Stadler, Peter F. Genomics Comp. Biol., 1. e18 ISSN 2365-7154 (2015)

  • RNA 3D modules in genome-wide predictions of RNA 2D structure
    Theis, Corinna and Zirbel, Craig and Höner zu Siederdissen, Christian and Anthon, Christian and Hofacker, Ivo L. and Nielsen, Henrik and Gorodkin, Jan PLoS ONE, 10 (10). ISSN 1932-6203 (2015)

  • SHAPE directed RNA folding
    Luntzer, Dominik and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. and Wolfinger, Michael T. Bioinformatics, 32. pp. 145-147 ISSN 1367-4803 (2015)

  • Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM
    Petkovic, Sonja and Badelt, Stefan and Block, Stephan and Flamm, Christoph and Delcea, Mihaela and Hofacker, Ivo L. and Müller, Sabine RNA, 21. pp. 1249-1260 ISSN 1355-8382 (2015)

  • Basin Hopping Graph: A computational framework to characterize RNA folding landscapes
    Kucharik, Marcel and Hofacker, Ivo L. and Stadler, Peter F. and Qin, Jing Bioinformatics, 30. pp. 2009-2017 ISSN 1367-4803 (2014)

  • Challenges in RNA Virus Bioinformatics
    Marz, Manja and Beerenwinkel, Niko and Drosten, Christian and Fricke, Markus and Frishman, Dmitrij and Hofacker, Ivo L. and Hoffmann, Dieter and Middendorf, Martin and Rattei, Thomas and Stadler, Peter F. and Töpfer, Armin Bioinformatics, 30. pp. 1793-1799 ISSN 1367-4803 (2014)

  • TSSAR: TSS Annotation Regime for dRNA-seq data
    Amman, Fabian and Wolfinger, Michael T and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F and Findeiß, Sven BMC Bioinformatics, 15. p. 89 ISSN 1471-2105 (2014)

  • Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.
    Müller, Stephan A. and Findeiß, Sven and Pernitzsch, Sandy R. and Wissenbach, Dirk K. and Stadler, Peter F. and Hofacker, Ivo L. and von Bergen, Martin and Kalkhof, Stefan J Proteomics, 86. pp. 27-42 ISSN 1874-3919 (2013)

  • 2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction
    Lorenz, Ronny and Bernhart, Stephan H. and Qin, Jing and Höner zu Siederdissen, Christian and Tanzer, Andrea and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F. IEEE Trans. Comp. Biol. Bioinf., 10. pp. 832-844 ISSN 1557-9964 (2013)

  • Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2
    Märtens, Birgit and Amman, Fabian and Manoharadas, Salim and Zeichen, Lukas and Orell, Alvaro and Albers, Sonja-Verena and Hofacker, Ivo L. and Bläsi, Udo PloS one, 8 (10). e76569 ISSN 1932-6203 (2013)

  • Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
    Theis, Corinna and Höner zu Siederdissen, Christian and Hofacker, Ivo L. and Gorodkin, Jan Nucleic acids research, 41. pp. 9999-10009 ISSN 0305-1048 (2013)

  • CMCompare webserver: Comparing RNA Families via Covariance models
    Eggenhofer, Florian and Hofacker, Ivo L. and Höner zu Siederdissen, Christian Nucleic Acids Res., 41. W499-W503 ISSN 0305-1048 (2013)

  • Computational Design of RNAs with Complex Energy Landscapes
    Höner zu Siederdissen, Christian and Hammer, Stefan and Abfalter, Ingrid and Hofacker, Ivo L. and Flamm, Christoph and Stadler, Peter F. Biopolymers, 99. pp. 1124-1136 ISSN 0006-3525 (2013)

  • The RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure
    Sabarinathan, Radhakrishnan and Tafer, Hakim and Seemann, Stefan and Hofacker, Ivo L. and Stadler, Peter F. and Gorodkin, Jan Nucleic Acids Res., 41. W475-W479 ISSN 0305-1048 (2013)

  • RNAsnp: Efficient detection of local RNA secondary structure changes induced by SNPs
    Sabarinathan, Radhakrishnan and Tafer, Hakim and Seemann, Stefan E. and Hofacker, Ivo L. and Stadler, Peter F. and Gorodkin, Jan Human Mutation, 34. 546-556 ISSN 1059-7794 (2013)

  • Folding RNA/DNA hybrid duplexes
    Lorenz, Ronny and Hofacker, Ivo L. and Bernhart, Stephan H Bioinformatics, 28 (19). pp. 2530-2531 ISSN 1367-4803 (2012)

  • LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
    Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and Stadler, Peter F. and Backofen, Rolf RNA, 18 (5). pp. 900-914 ISSN 1355-8382 (2012)

  • Modelling Translation Initiation under the Influence of sRNA
    Amman, Fabian and Flamm, Christoph and Hofacker, Ivo L. International Journal of Molecular Sciences, 13 (12). pp. 16223-16240 ISSN 1422-0067 (2012)

  • RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction
    Washietl, Stefan and Hofacker, Ivo L. and Stadler, Peter F. and Kellis, Manolis Nucleic Acids Research, 40 (10). pp. 4261-4272 ISSN 0305-1048 (2012)

  • Symmetric Circular Matchings and RNA Folding
    Hofacker, Ivo L. and Reidys, Christian M. and Stadler, Peter F. Discrete Mathematics, 312 (1). 100-112 Elsevier (2012)

  • Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation.
    Kratochvill, Franz and Machacek, Christian and Vogl, Claus and Ebner, Florian and Sedlyarov, Vitaly and Gruber, Andreas R and Hartweger, Hartweger and Vielnascher, Raimund and Karaghiosoff, Marina and Rülicke, Thomas and Müller, Mathias and Hofacker, Ivo L. and Lang, Roland and Kovarik, Pavel Molecular Systems Biology, 7 (560). Nature publishing group (2011)

  • ViennaRNA Package 2.0
    Lorenz, Ronny and Bernhart, Stephan H and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. Algorithms for Molecular Biology, 6 (1). p. 26 Biomed Central (2011)

  • RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
    Washietl, Stefan and Findeiß, Sven and Müller, Stephan A and Kalkhof, Stefan and von Bergen, Martin and Hofacker, Ivo L. and Stadler, Peter F and Goldman, Nick RNA, 17 (4). pp. 578-594 (2011)

  • AREsite: a database for the comprehensive investigation of AU-rich elements.
    Gruber, Andreas R and Fallmann, Jörg and Kratochvill, Franz and Kovarik, Pavel and Hofacker, Ivo L. Nucleic Acids Research, 39. D66-D69 Oxford University Press (2011)

  • Animal snoRNAs and scaRNAs with Exceptional Structures
    Marz, Manja and Gruber, Andreas R. and Höner zu Siederdissen, Christian and Amman, Fabian and Badelt, Stefan and Bartschat, Sebastian and Bernhart, Stephan H. and Beyer, Stephanie and Lorenz, Ronny and Tanzer, Andrea and Yusuf, Dilmurat and Tafer, Hakim and Hofacker, Ivo L. and Stadler, Peter F. RNA Biology, 8 (6). ISSN 1547-6286 Landes Bioscience (2011)

  • Fast Accessibility-Based Prediction of RNA-RNA Interactions
    Tafer, Hakim and Ammann, Fabian and Eggenhoffer, Florian and Stadler, Peter F. and Hofacker, Ivo L. Bioinformatics, 27 (14). pp. 1924-1940 Oxford University Press (2011)

  • A Folding Algorithm for Extended RNA Secondary Structures
    Höner zu Siederdissen, Christian and Berhart, Stephan H. and Stadler, Peter F. and Hofacker, Ivo L. Bioinformatics, 27 ( ). i129-i136 Oxford University Press (2011)

  • Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering
    Hackl, Matthias and Jakobi, Tobias and Blom, Jochen and Doppmeier, Daniel and Brinkrolff, Karina and Sczepanowski, Rafael and Bernhart, Stephan and Höner zu Siederdissen, Christian and Hernandez-Bort, Juan and Wieser, Matthias and Kunert, Renate and Jeffs, Simon and Hofacker, Ivo L. and Goesmann, Alexander and Pühler, Alfred and Borth, Nicole and Grillari, Johannes Journal of Biotechnology, 153 (1-2). pp. 62-75 Elsevier (2011)

  • RNAcode: robust prediction of protein coding regions in comparative genomics data
    Washietl, Stefan and Findeiß, Sven and Müller, Stephan and Kalkhof, Stefan and Bergen, Martin von and Hofacker, Ivo L. and Stadler, Peter F. and Goldman, Nick RNA , 17 (4). pp. 578-594 Cold Spring Harbor Laboratory Press (2011)

  • RNApredator: Fast accessibility-Based Prediction of sRNA targets
    Eggenhofer, Florian and Tafer, Hakim and Stadler, Peter F. and Hofacker, Ivo L. Nucleic Acids Research, 39 (S2). W149-W154 Oxford University Press (2011)

  • The impact of target site accessibility on the design of effective siRNAs
    Tafer, Hakim and Ameres, Stefan L. and Obernosterer, Gregor and Gebeshuber, Christoph A. and Schroeder, Renée and Martinez, Javier and Hofacker, Ivo L. Nature Biotech., 26 (-). pp. 578-583 ISSN 1087-0156 Nature publishing (2008)

    • Paper in Conference Proceedings or in Workshop Proceedings

  • Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
    von Löhneysen, Sarah and Spicher, Thomas and Varenyk, Yuliia and Yao, Hua-Ting and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F. In: International Symposium on Bioinformatics Research and Applications , October 9–12 , Wrocław, Poland (2023)

  • Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding
    Stadler, Peter F. and Hofacker, Ivo L. and Flamm, Christoph and Lorenz, Ronny In: 13th International Joint Conference on Biomedical Engineering Systems and Technologies , 02.2020 , Valletta, Malta (2020)

  • Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure
    Waldl, Maria and Will, Sebastian and Wolfinger, Michael T. and Hofacker, Ivo L. and Stadler, Peter F. In: CIBB 2019: 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics , 4-6 September 2019 , Bergamo. Italy (2019)

  • Computational design of a circular RNA with prion-like behavior
    Badelt, Stefan and Flamm, Christoph and Hofacker, Ivo L. In: Artificial Life 14 , 30.7.2014 - 2.8.2014 , New York, USA (2014)

  • How to Multiply Dynamic Programming Algorithms
    Höner zu Siederdissen, Christian and Hofacker, Ivo L. and Stadler, Peter F. In: Brazilian Symposium on Bioinformatics 2013 , 3-6 Nov 2013 , Recife, Brazil (2013)

  • The Trouble with Long-Range Base Pairs in RNA Folding
    Amman, Fabian and Bernhart, Stephan H. and Doose, Gero and Hofacker, Ivo L. and Qin, Jing and Stadler, Peter F. and Will, Sebastian In: Brazilian Symposium on Bioinformatics 2013 , 3-6 Nov 2013 , Recife, Brazil (2013)

    • Book

  • Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
    Waldl, Maria and Will, Sebastian and Wolfinger, Michael T. and Hofacker, Ivo L. and Stadler, Peter F. Lecture Notes in Computer Science, 12313 Springer, Cham, pp. 159-170 ISBN 978-3-030-63061-4 (2020)

    • Book Section/Chapter

  • Functional RNA Structures in the 3'UTR of Mosquito-Borne Flaviviruses
    Wolfinger, Michael T. and Ochsenreiter, Roman and Hofacker, Ivo L. In: Virus Bioinformatics. Chapman and Hall/CRC Press, Boca Raton, pp. 65-100 ISBN 9781003097679 (2021)

  • Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure
    Waldl, Maria and Will, Sebastian and Wolfinger, Michael T. and Hofacker, Ivo L. and Stadler, Peter F. In: Computational Intelligence Methods for Bioinformatics and Biostatistics. Lecture Notes in Computer Science, 12313 Springer, pp. 159-170 (2020)

  • Comparative RNA Genomics
    Backofen, Rolf and Gorodkin, Jan and Hofacker, Ivo L. and Stadler, Peter F. In: Comparative Genomics. Methods in Molecular Biology, 1704 Humana Press, pp. 363-400 ISBN 978-1-4939-7461-0 (2018)

  • Thermodynamic and Kinetic Folding of Riboswitches
    Badelt, Stefan and Hammer, Stefan and Flamm, Christoph and Hofacker, Ivo L. In: Methods in Enzymology. Computational Methods for Understanding Riboswitches, 553 Academic Press, Waltham, Massachusetts, USA, pp. 193-213 (2015)

  • Concepts and introduction to RNA bioinformatics
    Gorodkin, Jan and Ruzzo, Larry and Hofacker, Ivo L. In: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Meth. Mol. Biol., 1097 Humana Press, New York, pp. 1-31 (2014)

  • Energy Directed RNA Structure Prediction
    Hofacker, Ivo L. In: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Meth. Mol. Biol., 1097 Humana Press, New York, pp. 71-84 (2014)

  • Predicting RNA Structure: Advances and Limitations
    Hofacker, Ivo L. and Lorenz, Ronny In: RNA Folding. Meth. Mol. Biol., 1086 Humana Press, pp. 1-19 (2014)

  • RNA Folding Algorithms with G-Quadruplexes
    Lorenz, Ronny and Bernhart, Stephan H. and Externbrink, Fabian and Qin, Jing and Höner zu Siederdissen, Christian and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F. In: Advances in Bioinformatics and Computational Biology. Lecture Notes in Computer Science , 7409 Springer, pp. 49-60 (2012)

    • This list was generated on Fri Apr 19 08:52:24 2024 CEST.
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