Conserved RNA Secondary Structures in (2009)
Flaviviridae Genomes, Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
Abstract. We report here on a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of...
Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler, Ivo L Hofacker, ...
Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of...
From consensus structure prediction to RNA gene finding (2009)
Bernhart, Stephan H., Hofacker, Ivo L.
Reliable structure prediction is a prerequisite for most types of bioinformatical analysis of RNA. Since the accuracy of structure prediction from single sequences is limited, one often resorts to...
RNAalifold: improved consensus structure prediction for RNA alignments (2008)
Bernhart, Stephan H, Hofacker, Ivo L, Will, Sebastian, Gruber, Andreas R, Stadler, Peter F
Abstract Background The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that...
doi:10.1093/bioinformatics/btl024 (2008)
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
Background: Reliable prediction of RNA–RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA–mRNA binding and antisense interactions. The thermodynamics of such RNA–RNA...
PF: Conserved RNA Pseudoknots (2008)
Caroline Thurner, Ivo L. Hofacker, Peter F. Stadler
Abstract: Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life-cycle....
Visualization of Barrier Tree Sequences (2008)
Christian Heine, Ivo L. Hofacker
The increasing complexity of models explaining the spatial structure of RNA molecules require visualization methods that help to analyze the validity of these models. In this article, we consider the...
Ivo L Hofacker, Peter F Stadler
The Vienna Reaction Network Library Vienna-RNL implements basic set-theoretic operations on chemical reaction networks. It provides basic ANSI C data structures for chemical reactions and their...
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs (2008)
Axel Mosig, Ivo L. Hofacker, Peter F. Stadler
Abstract: The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as...
Chapter 1 MODELING RNA FOLDING (2008)
Ivo L. Hofacker, Peter F. Stadler
Abstract In recent years it has become evident that functional RNAs in living organisms are not just curious remnants from a primoridal RNA world but an ubiquitous phenomenon complementing protein...
Strategies for measuring evolutionary conservation of RNA secondary structures (2008)
Gruber, Andreas R, Bernhart, Stephan H, Hofacker, Ivo L, Washietl, Stefan
Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and...
Conserved RNA Secondary Structures in (2008)
Picornaviridae Genomes, Christina Witwer, Susanne Rauscher, Ivo L. Hofacker, Peter F. Stadler
∗ Address for correspondence The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a...
Copyright © 2000 RNA Society+ RNA folding at elementary step resolution (2008)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
Christoph Flamm, Ivo L. Hofacker, Sebastian Maurer-stroh, Peter F. Stadler, Martin Zehl
We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of...
Copyright © 2000 RNA Society+ RNA folding at elementary step resolution (2008)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more...
Gruber, Andreas R., Kilgus, Carsten, Mosig, Axel, Hofacker, Ivo L., Hennig, Wolfgang, Stadler, Peter F.
Mückstein, Ulrike, Tafer, Hakim, Bernhart, Stephan H., Hernandez-Rosales, Maribel, Vogel, Jörg, Stadler, Peter F., ...
Jöchl, Christoph, Rederstorff, Mathieu, Hertel, Jana, Stadler, Peter F., Hofacker, Ivo L., Schrettl, Markus, ...
Variations on RNA Folding and Alignment: Lessons from Benasque (2008)
Bompfünewerer, Athanasius F., Backofen, Rolf, Bernhart, Stephan H., Hertel, Jana, Hofacker, Ivo L., Stadler, Peter F., ...
Gruber, Andreas R., Kilgus, Carsten, Mosig, Axel, Hofacker, Ivo L., Hennig, Wolfgang, Stadler, Peter F.
The 7SK small nuclear RNA (snRNA) is a key player in the regulation of polymerase (pol) II transcription. The 7SK RNA was long believed to be specific to vertebrates where it is highly conserved....
SnoReport: computational identification of snoRNAs with unknown targets (2008)
Hertel, Jana, Hofacker, Ivo L., Stadler, Peter F.
Summary: Unlike tRNAs and microRNAs, both classes of snoRNAs, which direct two distinct types of chemical modifications of uracil residues, have proved to be surprisingly difficult to find in genomic...
RNAplex: a fast tool for RNA-RNA interaction search (2008)
Tafer, Hakim, Hofacker, Ivo L.
Motivation: Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this...
Jöchl, Christoph, Rederstorff, Mathieu, Hertel, Jana, Stadler, Peter F., Hofacker, Ivo L., Schrettl, Markus, ...
Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the...
The Vienna RNA Websuite (2008)
Gruber, Andreas R., Lorenz, Ronny, Bernhart, Stephan H., Neuböck, Richard, Hofacker, Ivo L.
The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA...
Fast Folding and Comparison of RNA Secondary Structures (2007)
The Vienna, Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, ...
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures...
Neutral Networks in Protein Space (2007)
Computational Study, Aderonke Babajide, Ivo L. Hofacker, Peter F. Stadler
Introduction The prediction of protein conformations from amino acid sequences has remained an unsolved problem in spite of all efforts for a variety of reasons. Notably, existing potential functions...
Ulrike Muckstein, Ivo L. Hofacker, Peter F. Stadler
Motivation: The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and...
Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, ...
c;d, and Peter Schuster a;c;d; a
Conserved RNA Secondary Structures in (2007)
Picornaviridae Genomes, Christina Witwer, Susanne Rauscher, Ivo L. Hofacker, Peter F. Stadler
# Address for correspondence The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single...
Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler
Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that,...
Ivo L. Hofacker, Peter F. Stadler, Roman Stocsits
The genomes of RNA viruses often carry conserved RNA structures that perform vital functions during the life cycle of the virus. Such structures can be detected using a combination of structure...
Flaviviridae Genomes, Caroline Thurner, Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
We report here on a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three...
Detection of RNA structures in porcine EST data and related mammals (2007)
Seemann, Stefan E, Gilchrist, Michael J, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan
Abstract Background Non-coding RNAs (ncRNAs) are involved in a wide spectrum of regulatory functions. Within recent years, there have been increasing reports of observed polyadenylated ncRNAs and...
Gruber, Andreas R., Neuböck, Richard, Hofacker, Ivo L., Washietl, Stefan
Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of...
Structured RNAs in the ENCODE selected regions of the human genome (2007)
Washietl, Stefan, Pedersen, Jakob S., Korbel, Jan O., Stocsits, Claudia, Gruber, Andreas R., Hackermüller, Jörg, ...
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional...
Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional...
Sebastian Will, Kristin Reiche, Ivo L Hofacker, Peter F Stadler, Rolf Backofen
The Rfam database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs, box H/ACA snoRNAs, functional commonalities...
Detection of RNA structures in porcine EST data and related mammals. BMC Genomics 8:316 (2007)
Bmc Genomics, Stefan E Seemann, Michael J Gilchrist, Ivo L Hofacker, Peter F Stadler, Jan Gorodkin, ...
Research article
Visualization of Barrier Tree Sequences Revisited. (2007)
Heine, Christian, Scheuermann, Gerik, Flamm, Christoph, Hofacker, Ivo L., Stadler, Peter
Detection of RNA structures in porcine EST data and related mammals (2007)
Seemann, Stefan E., Gilchrist, Michael J., Hofacker, Ivo L., Stadler, Peter F., Gorodkin, Jan
Inferring Non-Coding RNA Families and Classes by Means of Structure-Based Clustering (2007)
Will, Sebastian, Missal, Kristin, Hofacker, Ivo L., Stadler, Peter F., Backofen, Rolf
Structured RNAs in the ENCODE Selected Regions of the Human Genome (2007)
Washietl, Stefan, Pedersen, Jakob S., Korbel, Jan O., Fried, Claudia, Gruber, Andreas R., Hackermüller, Jörg, ...
RNAs Everywhere: Genome-Wide Annotation of Structured RNAs (2007)
Bompfünewerer, Athanasius F., Backofen, Rolf, Bernhart, Stephan H., Flamm, Christoph, Fried, Claudia, Fritzsch, Guido, ...
Partition function and base pairing probabilities of RNA heterodimers (2006)
Bernhart, Stephan H, Tafer, Hakim, Mückstein, Ulrike, Flamm, Christoph, Stadler, Peter F, Hofacker, Ivo L
Abstract Background RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the...
The expansion of the metazoan microRNA repertoire (2006)
Hertel, Jana, Lindemeyer, Manuela, Missal, Kristin, Fried, Claudia, Tanzer, Andrea, Flamm, Christoph, ...
Abstract Background MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We...
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation (2006)
Forst, Christian V, Flamm, Christoph, Hofacker, Ivo L, Stadler, Peter F
Abstract Background Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are...
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures (2006)
Ivo L. Hofacker, Peter F. Stadler
Abstract: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach...
Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler, Ivo L Hofacker
Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of...
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures (2006)
Ivo L. Hofacker, Peter F. Stadler
Abstract. A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach...
Thermodynamics of RNA-RNA binding (2006)
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
Abstract: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired....
Visualization of Barrier Tree Sequences. (2006)
Heine, Christian, Scheuermann, Gerik, Flamm, Christoph, Hofacker, Ivo L., Stadler, Peter F.
miRNAMap: Genomic Maps of MicroRNA Genes and Their Target Genes in Mammalian Genomes (2006)
Hsu, Wei-Che, Huang, Hsien-Da, Hsu, Sheng-Da, Lin, Li-Zen, Tsou, Ann-Ping, Tseng, Ching-Ping, ...
Exploring the Lower Part of Discrete Polymer Model Energy Landscapes (2006)
Wolfinger, Michael T., Will, Sebastian, Hofacker, Ivo L., Backofen, Rolf, Stadler, Peter F.
Partition Function and Base Pairing Probabilities of RNA Heterodimers (2006)
Bernhart, Stephan, Tafer, Hakim, Mückstein, Ulrike, Flamm, Christoph, Stadler, Peter F., Hofacker, Ivo L.
The Expansion of the Metazoan MicroRNA Repertoire (2006)
Hertel, Jana, Lindemeyer, Manuela, Missal, Kristin, Fried, Claudia, Tanzer, Andrea, Flamm, Christoph, ...
Thermodynamics of RNA-RNA Binding (2006)
Mückstein, Ulrike, Tafer, Hakim, Hackermüller, Jörg, Bernhard, Stephan, Stadler, Peter F., Hofacker, Ivo L.
Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation (2006)
Forst, Christian V., Flamm, Christoph, Hofacker, Ivo L., Stadler, Peter F.
Memory efficient folding algorithms for circular RNA secondary structures (2006)
Hofacker, Ivo L., Stadler, Peter F.
Background: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward...
Thermodynamics of RNA-RNA binding (2006)
Mückstein, Ulrike, Tafer, Hakim, Hackermüller, Jörg, Bernhart, Stephan H., Stadler, Peter F., Hofacker, Ivo L.
Background: Reliable prediction of RNA–RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA–mRNA binding and antisense interactions. The thermodynamics of such RNA–RNA...
Local RNA base pairing probabilities in large sequences (2006)
Bernhart, Stephan H., Hofacker, Ivo L., Stadler, Peter F.
Summary: The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically...
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes (2006)
Hsu, Paul W.C., Huang, Hsien-Da, Hsu, Sheng-Da, Lin, Li-Zen, Tsou, Ann-Ping, Tseng, Ching-Ping, ...
Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap,...
Partition function and base pairing probabilities of RNA heterodimers (2006)
Stephan H Bernhart, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker
Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the...
The expansion of the metazoan microRNA repertoire (2006)
Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Ivo L. Hofacker, ...
MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA...
Multiple sequence alignments of partially coding nucleic acid sequences (2005)
Stocsits, Roman R, Hofacker, Ivo L, Fried, Claudia, Stadler, Peter F
Abstract Background High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however,...
Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler
Summary: The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically...
Bmc Bioinformatics, Roman R Stocsits, Ivo L Hofacker, Claudia Fried, Peter F Stadler, Open Access, ...
Software Multiple sequence alignments of partially coding nucleic acid sequences
Multiple sequence alignments of partially coding nucleic acid sequences (2005)
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler, Peter F. Stadler
Background: High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a...
Böhmdorfer, Gudrun, Hofacker, Ivo L., Garber, Karin, Jelenic, Srecko, Nizhynska, Viktoria, Hirochika, Hirohiko, ...
Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences (2005)
Stocsits, Roman R., Hofacker, Ivo L., Fried, Claudia, Stadler, Peter F.
BÖHMDORFER, GUDRUN, HOFACKER, IVO L., GARBER, KARIN, JELENIC, SRECKO, NIZHYNSKA, VIKTORIA, HIROCHIKA, HIROHIKO, ...
Retroelement RNAs serve as templates for both translation and reverse transcription into extrachromosomal DNA. DNA copies may be inserted into the host genome to multiply element sequences. This...
Local RNA base pairing probabilities in large sequences (2005)
Bernhart, Stephan H., Hofacker, Ivo L., Stadler, Peter F.
Summary: The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically...
Stefan Washietl, Ivo L. Hofacker
Facing the ever-growing list of newly discovered classes of functional RNAs, it can be expected that further types of functional RNAs are still hidden in recently completed genomes. The computational...
Prediction of consensus RNA secondary structures including pseudoknots (2004)
Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here we present a method for computing the consensus structures...
Prediction of consensus RNA secondary structures including pseudoknots. submitted (2004)
Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here we present a method for computing the consensus structures...
Conserved RNA secondary structures in viral genomes: a survey (2004)
Ivo L. Hofacker, Peter F. Stadler, Roman Stocsits
The genomes of RNA viruses often carry conserved RNA structures that perform vital functions during the life cycle of the virus. Such structures can be detected using a combination of structure...
Interactions in oligonucleotide hybrid duplexes on microarrays (2004)
Binder, Hans, Kirsten, Toralf, Hofacker, Ivo L., Loeffler, Markus, Stadler, Peter F.
Exact Folding Dynamics of RNA Secondary Structures (2004)
Wolfinger, Michael T., Flamm, W., Hofacker, Ivo L., Stadler, Peter F., Svrcek, Andreas, Seiler, Christoph
Copeland, Claudia S., Heyers, Oliver, Kalinna, Bernd H., Bachmair, Andreas, Stadler, Peter F., Hofacker, Ivo L., ...
Conserved RNA Secondary Structures in Flaviviridae Genomes (2004)
Thurner, Caroline, Witwer, Christina, Hofacker, Ivo L., Stadler, Peter F.
Alignment of RNA base pairing probability matrices (2004)
Hofacker, Ivo L., Bernhart, Stephan H. F., Stadler, Peter F.
Motivation: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore...
Alignment of RNA base pairing probability matrices (2004)
Hofacker, Ivo L., Bernhart, Stephan H. F., Stadler, Peter F.
Motivation: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore...
The partition function variant of Sankoff’s algorithm (2004)
Ivo L. Hofacker, Peter F. Stadler
Abstract. Many classes of functional RNA molcules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be...
The partition function variant of Sankoff’s algorithm (2004)
Ivo L. Hofacker, Peter F. Stadler
Abstract. Many classes of functional RNA molcules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be...
Computational chemistry with RNA secondary structures. Kemija u industriji (2004)
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Abstract. The secondary structure for nucleic acids provides a level of description that is both abstract enough to allow for efficient algorithms and realistic enough to provide a good approximate...
Alignment of RNA base pairing probability matrices (2004)
Hofacker, Ivo L., Bernhart, Stephan H. F., Stadler, Peter F.
Motivation: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore...
Journal of General Virology (2004), 85, 1113–1124 DOI 10.1099/vir.0.19462-0 Correspondence (2003)
Viral RNA genomes not only code for proteins but in many instances also carry RNA motifs that play a crucial role in the viral life-cycle. Well-known examples are the internal ribosomal entry site...
Vienna RNA secondary structure server (2003)
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently...
On the Evolution of Primitive Genetic Codes (2003)
Günter Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the presentday code came about we...
On the evolution of primitive genetic codes (2003)
Günter Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
Abstract. The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the presentday code came...
Vienna RNA secondary structure server (2003)
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently...
Vienna RNA secondary structure server (2003)
The Vienna RNA secondary structure server provides a webinterface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently...
Vienna RNA secondary structure server (2003)
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently...
Secondary structure prediction for aligned RNA sequences (2002)
Ivo L. Hofacker, Martin Fekete, Peter F. Stadler
RNA secondary structure prediction, conserved substructures, compensatory mutations.
Design of Multi-Stable RNA Molecules (2001)
Christoph Flamm, Peter F. Stadler, Sebastian Maurer-Stroh, Martin Zehl, Ivo L. Hofacker, Ivo L. Hofacker
We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of...
Exploring Protein Sequence Space Using Knowledge Based Potentials (2001)
Aderonke Babajide, Robert Farber, Ivo L. Hofacker, Jeff Inman, Alan S. Lapedes, Peter F. Stadler
Knowledge-Based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequencestructure...
Conserved RNA secondary structures in Picornaviridae genomes (2001)
Witwer, Christina, Rauscher, Susanne, Hofacker, Ivo L., Stadler, Peter F.
The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active...
Concurrent neutral evolution of mRNA secondary structures and encoded proteins (2000)
Jaromir Konecny, Michael Schönonger, Ivo L. Hofacker, Marc-denis Weitze, G. Ludwig Hofacker
Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins. We present a statistical analysis of retroviral mRNA which supports the...
RNA folding at elementary step resolution (2000)
Christoph Flamm Walter, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
RNA Folding at Elementary Step Resolution (2000)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
RNA Folding at Elementary Step Resolution (2000)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
A algorithm based one three classes of elementary steps for folding RNA sequences into secondary structures is presented. It is formulated as a stochastic process on the discrete confomational space...
Automatic detection of conserved base pairing patterns in RNA virus genomes (1999)
Ivo L. Hofacker, Peter F. Stadler
Almost all RNA molecules--- and consequently also almost all subsequences of a large RNA molecule---form secondary structures. The presence of secondary structure in itself therefore does not...
RNA in Silico - The Computational Biology of RNA Secondary Structures (1999)
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
. RNA secondary structures provide a unique computer model for investigating the most important aspects of structural and evolutionary biology. The existence of efficient algorithms for solving the...
Conserved Secondary Structures In Hepatitis B Virus RNA (1999)
Roman Stocsits, Ivo L. Hofacker, Peter F. Stadler
Introduction Almost all RNA molecules form secondary structures. The presence of secondary structure in itself therefore does not indicate any functional significance. Extensive computer simulations...
Exploring Protein Sequence Space Using Knowledge Based Potentials (1999)
Aderonke Babajide, Robert Farber, Ivo L. Hofacker, Jeff Inman, Alan S. Lapedes, Peter F. Stadler
Knowledge-Based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequencestructure...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
this paper we describe a fairly simple algorithm which generates all suboptimal folds of a sequence within a desired energy range from the mfe. The idea underlying the algorithm is straightforward,...
RNA Secondary Structures: A Tractable Model of Biopolymer Folding (1998)
RNA secondary structures provide a suitable model system for studying the thermodynamics and kinetics of biopolymer folding. In contrast to models of protein folding of comparable complexity, the...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
this paper we describe a fairly simple algorithm which generates all suboptimal folds of a sequence within a desired energy range from the mfe. The idea underlying the algorithm is straightforward,...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Aderonke Babajide, Ivo L. Hofacker, Manfred J. Sippl, Peter F. Stadler
Background: Protein space is explored by means of an inverse folding procedure that makes use of knowledge-based potentials of mean force. Results: Computer simulations indicate that amino acid...
Algorithm Independent Properties of RNA Secondary Structure Predictions (1996)
Manfred Tacker, Peter F. Stadler, Ivo L. Hofacker, Peter Schuster
Algorithms predicting RNA secondary structures based on different folding criteria -- minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) -- and different parameter sets are...
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration - I. Neutral Networks (1996)
Walter Grüner, Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, ...
Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU...
Walter Grüner, Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, ...
The relations between RNA sequences and secondary structures are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique of tries is used for economic...
Dynamic Programming Algorithm For The Density Of States Of Rna Secondary Structures (1996)
Jan Cupal, Ivo L. Hofacker, Peter F. Stadler
A dynamic programming algorithm for the computation of the complete density of states of RNA secondary structures is presented. CPU and memory requirements scale as n^3*m^2 and n^2*m, respectively,...
Algorithm Independent Properties of RNA Secondary Structure Predictions (1996)
Manfred Tacker, Peter F. Stadler, Ivo L. Hofacker, Peter Schuster
Algorithms predicting RNA secondary structures based on different folding criteria -- minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) -- and different parameter sets are...
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers (1996)
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more...
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration (1996)
Walter Grüner, Walter Gr Uner, Robert Giegerich, Dirk Strohmann, Christian Reidys, Jacqueline Weber, ...
The mapping from RNA sequences to their secondary structures is investigated by exhaustively folding all GC and AU sequences with chain lengths up to 30. We analyse the distribution of secondary...
Combinatorics Of RNA Secondary Structures (1996)
Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as...
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package) (1994)
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures...
RNA Folding and Combinatory Landscapes (1993)
Walter Fontana, Peter F. Stadler, Thomas Griesmacher, Ivo L. Hofacker, Manfred Tacker, ...
In this paper we view the folding of polynucleotide (RNA) sequences as a map that assigns to each sequence a minimum free energy pattern of base pairings, known as secondary structure. Considering...
Conserved RNA secondary structures in Picornaviridae genomes
Witwer, Christina, Rauscher, Susanne, Hofacker, Ivo L., Stadler, Peter F.
The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of...
Vienna RNA secondary structure server
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently...
Fast and reliable prediction of noncoding RNAs
Washietl, Stefan, Hofacker, Ivo L., Stadler, Peter F.
We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a small...
Multiple sequence alignments of partially coding nucleic acid sequences
Stocsits, Roman R, Hofacker, Ivo L, Fried, Claudia, Stadler, Peter F
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes
Hsu, Paul W.C., Huang, Hsien-Da, Hsu, Sheng-Da, Lin, Li-Zen, Tsou, Ann-Ping, Tseng, Ching-Ping, ...
Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap,...
BÖHMDORFER, GUDRUN, HOFACKER, IVO L., GARBER, KARIN, JELENIC, SRECKO, NIZHYNSKA, VIKTORIA, HIROCHIKA, HIROHIKO, ...
Retroelement RNAs serve as templates for both translation and reverse transcription into extrachromosomal DNA. DNA copies may be inserted into the host genome to multiply element sequences. This...
The expansion of the metazoan microRNA repertoire
Hertel, Jana, Lindemeyer, Manuela, Missal, Kristin, Fried, Claudia, Tanzer, Andrea, Flamm, Christoph, ...
Partition function and base pairing probabilities of RNA heterodimers
Bernhart, Stephan H, Tafer, Hakim, Mückstein, Ulrike, Flamm, Christoph, Stadler, Peter F, Hofacker, Ivo L
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
Forst, Christian V, Flamm, Christoph, Hofacker, Ivo L, Stadler, Peter F
Conserved RNA secondary structures in Picornaviridae genomes
Witwer, Christina, Rauscher, Susanne, Hofacker, Ivo L., Stadler, Peter F.
The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of...
Vienna RNA secondary structure server
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently...
Fast and reliable prediction of noncoding RNAs
Washietl, Stefan, Hofacker, Ivo L., Stadler, Peter F.
We report an efficient method for detecting functional RNAs. The approach, which combines comparative sequence analysis and structure prediction, already has yielded excellent results for a small...
Multiple sequence alignments of partially coding nucleic acid sequences
Stocsits, Roman R, Hofacker, Ivo L, Fried, Claudia, Stadler, Peter F
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes
Hsu, Paul W.C., Huang, Hsien-Da, Hsu, Sheng-Da, Lin, Li-Zen, Tsou, Ann-Ping, Tseng, Ching-Ping, ...
Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap,...
BÖHMDORFER, GUDRUN, HOFACKER, IVO L., GARBER, KARIN, JELENIC, SRECKO, NIZHYNSKA, VIKTORIA, HIROCHIKA, HIROHIKO, ...
Retroelement RNAs serve as templates for both translation and reverse transcription into extrachromosomal DNA. DNA copies may be inserted into the host genome to multiply element sequences. This...
The expansion of the metazoan microRNA repertoire
Hertel, Jana, Lindemeyer, Manuela, Missal, Kristin, Fried, Claudia, Tanzer, Andrea, Flamm, Christoph, ...
Partition function and base pairing probabilities of RNA heterodimers
Bernhart, Stephan H, Tafer, Hakim, Mückstein, Ulrike, Flamm, Christoph, Stadler, Peter F, Hofacker, Ivo L
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
Forst, Christian V, Flamm, Christoph, Hofacker, Ivo L, Stadler, Peter F
Secondary Structure Prediction for Aligned RNA Sequences
Ivo L. Hofacker, Martin Fekete, Peter F. Stadler
Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA...
Barrier Trees of Degenerate Landscapes
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
The heights of energy barriers separating two (macro-)states are useful for estimating transition frequencies. In non-degenerate landscapes the decomposition of a landscape into basins surrounding...
Design of Multi-Stable RNA Molecules
Christophe Flamm, Ivo L. Hofacker, Sebastian Maurer-Stroh, Peter F. Stadler, Martin Zehl
We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of...
RNA Folding at Elementary Step Resolution
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
Exploring Protein Sequence Space Using Knowledge-Based Potentials
Aderonke Babajide, Robert Farber, Ivo L. Hofacker, Jeff Inman, Alan S. Lapedes, Peter F. Stadler
Knowledge-based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequence-structure...
Automatic Detection of of Conserved Base Pairing Patterns in RNA Virus Genomes
Ivo L. Hofacker, Peter F. Stadler
Almost all RNA molecules - and consequently also almost all subsequences of a large RNA molecule - form secondary structures. The presence of secondary structure in itself therefore does not indicate...
Prediction of RNA Base Pairing Probabilities Using Massively Parallel Computers
Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The program can be used to...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm performs particularly well in the...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
Will, Sebastian, Reiche, Kristin, Hofacker, Ivo L, Stadler, Peter F, Backofen, Rolf
The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional...
Neutral Networks in Protein Space
Aderonke Babajide, Ivo L. Hofacker, Manfred J. Sippl, Peter F. Stadler
Background: Protein space is explored by means of an inverse folding procedure that makes use of knowledge-based potentials of mean force. Results: Computer simulations indicate that amino acid...
Gruber, Andreas R., Neuböck, Richard, Hofacker, Ivo L., Washietl, Stefan
Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of...
Detection of RNA structures in porcine EST data and related mammals
Seemann, Stefan E, Gilchrist, Michael J, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan
Structured RNAs in the ENCODE selected regions of the human genome
Washietl, Stefan, Pedersen, Jakob S., Korbel, Jan O., Stocsits, Claudia, Gruber, Andreas R., Hackermüller, Jörg, ...
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional...
Strategies for measuring evolutionary conservation of RNA secondary structures
Gruber, Andreas R, Bernhart, Stephan H, Hofacker, Ivo L, Washietl, Stefan
Jöchl, Christoph, Rederstorff, Mathieu, Hertel, Jana, Stadler, Peter F., Hofacker, Ivo L., Schrettl, Markus, ...
Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the...
Gruber, Andreas R., Lorenz, Ronny, Bernhart, Stephan H., Neuböck, Richard, Hofacker, Ivo L.
The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA...
Algorithmic Independence Properties of RNA Secondary Structure Predictions
Manfred Tacker, Peter F. Stadler, Ivo L. Hofacker, Peter Schuster
Algorithms predicting RNA secondary structures based on different folding criteria---minimum free energy (mfe), kinetic folding (kin), maximum matching (mm)---and different parameter sets are studied...
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
Walter Gruner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, ...
Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU...
RNA Folding on Parallel Computers: The Minimum Free Energy Structures of Complete HIV Genomes
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more...
Combinatorics of RNA Secondary Structures
Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as...
From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures
Peter Schuster, Walter Fontana, Peter F. Stadler, Ivo L. Hofacker
RNA folding is viewed as a map assigning secondary structures to sequences. At fixed chain length the number of sequences exceeds by far the number of structures. Frequencies of structures are highly...
Fast Folding and Comparison of RNA Secondary Structures
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
Computer codes for computation and comparison of RNA secondary structures, the {\tt Vienna RNA package}, are presented, that are based on dynamic programming algorithms and aim at predictions of...
RNAalifold: improved consensus structure prediction for RNA alignments
Bernhart, Stephan H, Hofacker, Ivo L, Will, Sebastian, Gruber, Andreas R, Stadler, Peter F
Model-based probe set optimization for high-performance microarrays
Leparc, Germán Gastón, Tüchler, Thomas, Striedner, Gerald, Bayer, Karl, Sykacek, Peter, Hofacker, Ivo L., ...
A major challenge in microarray design is the selection of highly specific oligonucleotide probes for all targeted genes of interest, while maintaining thermodynamic uniformity at the hybridization...
Gruber, Andreas R., Koper-Emde, Dorota, Marz, Manja, Tafer, Hakim, Bernhart, Stephan, Obernosterer, Gregor, ...
7SK RNA is a highly abundant noncoding RNA in mammalian cells whose function in transcriptional regulation has only recently been elucidated. Despite its highly conserved sequence throughout...