Target prediction and a statistical sampling algorithm for RNA-RNA interaction (2009)
Huang, F. W. D., Qin, J., Reidys, C. M., Stadler, P. F.
It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable...
tRNAdb 2009: Compilation of tRNA sequences and tRNA genes (2009)
Jühling, F., Mörl, M., Hartmann, R.K., Sprinzl, M., Stadler, P.F., Pütz, J.
One of the first specialized collections of nucleic acid sequences in life sciences was the 'compilation of tRNA sequences and sequences of tRNA genes' (http://www.trna.uni-bayreuth.de). Here, an...
A survey of nematode SmY RNAs. Editorial (2009)
Jones, T.A., Otto, W., Marz, M., Eddy, S.R., Stadler, P.F.
SmY RNAs are a family of similar to 70-90 nt small nuclear RNAs found in nematodes. In C elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that...
Structural profiles of human miRNA families from pairwise clustering (2009)
Kaczkowski , B., Torarinsson, E., Reiche, K., Havgaard, J.H., Stadler, P.F., Gorodkin, J.
MicroRNAs (miRNAs) are a group of small, 21 nt long, riboreg-ulators inhibiting gene expression at a post-transcriptional level. Their most distinctive structural feature is the foldback hairpin of...
Non-coding RNA annotation of the genome of Trichoplax adhaerens (2009)
Hertel, J., Jong, D. De, Marz, M., Rose, D., Tafer, H., Tanzer, A., ...
A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax...
Sequence assembly. Review (2009)
Scheibye-Alsing, K., Hoffmann, S., Frankel, A., Jensen, P., Stadler, P.F., Mang, Y., ...
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational...
Approximate graph products (2009)
Hellmuth, M., Imrich, W., Klöckl, W., Stadler, P.F.
The problem of recognizing approximate graph products arises in theoretical biology. This paper presents an algorithm that recognizes a large class of approximate graph products. The main part of...
Solvent exposure imparts similar selective pressures across a range of yeast proteins (2009)
We study how an amino acid residue's solvent exposure influences its propensity for substitution by analyzing multiple alignments of 61 yeast genes for which the crystal structure is known. We find...
Long non-protein coding RNAs in oncogenic pathways (2009)
Hackermüller, J., Brocke-Heidrich, K., Reiche, K., Kretzschmar, A., Schutt, K., Ahnert, P., ...
Transcriptome profiling reveals many novel p53-regulated human non-coding RNAs (2009)
Böhlig, L., Hackermüller, J., Rose, D., Reiche, K., Kretzschmar, A., Stadler, P.F., ...
Discovering cis-regulatory modules by optimizing barbecues (2009)
Mosig, A., Biyikoglu, T., Prohaska, S.J., Stadler, P.F.
Gene expression in eukaryotic cells is regulated by a complex network of interactions, in which transcription factors and their binding sites on the genomic DNA play a determining role. As...
A note on fundamental, non-fundamental, and robust cycle bases (2009)
In many biological systems, robustness is achieved by redundant wiring, and reflected by the presence of cycles in the graphs connecting the systems' components. When analyzing such graphs,...
Evolution of vault RNAs (2009)
Stadler, P.F., Chen, J.J.-L., Hackermüller, J., Hoffmann, S., Horn, F., Khaitovich, P., ...
Vault RNAs (vtRNAs) are small, about 100 nt long, polymerase III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function, they have received...
FRANz: Reconstruction of wild multi-generation pedigrees (2009)
Riester, M., Stadler, P.F., Klemm, K.
We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). If available,...
Hoffmann, S., Otto, C., Kurtz, S., Sharma, C.M., Khaitovich, P., Vogel, J., ...
With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only...
Evidence for human microRNA-offset RNAs in small RNA sequencing data (2009)
Langenberger, D., Bermudez-Santana, C., Hertel, J., Hoffmann, S., Khaitovich, P., Stadler, P.F.
MicroRNA-offset-RNAs (moRNAs) were recently detected as highly abundant class of small RNAs in a basal chordate. Using short read sequencing data, we show here that moRNAs are also produced from...
ABOUT SEQUENCE MOTIFS IN UTRs (2008)
Sequence motifs of DNA or RNA molecules are sequences of any length having important function in gene regulation. Non-specific sequence motifs are often revealed by cross species comparisons as their...
SnoReport: Computational identification of snoRNAs with unknown targets (2008)
Hertel, J., Hofacker, I.L., Stadler, P.F.
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...
Krauss, V., Thummler, C., Georgi, F., Lehmann, J., Stadler, P.F., Eisenhardt, C.
Today, the reconstruction of the organismal evolutionary tree is basedmainly on molecular sequence data. However, sequence data are sometimes insufficient to reliably resolve in particular deep...
Folding kinetics of large RNAs (2008)
Geis, M., Flamm, C., Wolfinger, M.T., Tanzer, A., Hofacker, I.L., Middendorf, M., ...
Evolution of mitochondrial gene orders in echinoderms (2008)
Perseke, M., Fritzsch, G., Ramsch, K., Bernt, M., Merkle, D., Middendorf, M., ...
Jochl, C., Rederstorff, M., Hertel, J., Stadler, P.F., Hofacker, I.L., Schrettl, M., ...
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 amphioxus Hox cluster: Characterization, comparative genomics, and evolution (2008)
Amemiya, C.T., Prohaska, S.J., Hill-Force, A., Cook, A., Wasserscheid, J., Ferrier, D.E.K., ...
The amphioxus Hox cluster is often viewed as "archetypal" for the chordate lineage. Here, we present a descriptive account of the 448 kb region spanning the Hox cluster of the amphioxus Branchiostoma...
NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences (2008)
Rose, D., Hertel, J., Reiche, K., Stadler, P.F., Hackermüller, J.
Genome-wide multiple sequence alignments (MSAs) are a necessary prerequisite for an increasingly diverse collection of comparative genomic approaches. Here we present a versatile method that...
Funnels in energy landscapes (2008)
Klemm, K., Flamm, C., Stadler, P.F.
Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel" that is concisely...
Noisy: Identification of problematic columns in multiple sequence alignments (2008)
Dress, A.W.M., Flamm, C., Fritzsch, G., Grünewald, S., Kruspe, M., Prohaska, S.J., ...
Motivation: Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary...
Gruber, A.R., Kilgus, C., Mosig, A., Hofacker, I.L., Hennig, W., Stadler, P.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....
Hoffmann, S., Cepok, S., Grummel, V., Lehmann-Horn, K., Hackermüller, J., Stadler, P.F., ...
The formation of antibodies to interferon-beta (IFN-beta), a protein-based disease-modifying agent for multiple sclerosis (MS), is a problem in clinical practice. These antibodies may neutralize the...
SynBlast: Assisting the analysis of conserved synteny information (2008)
Lehmann, J., Stadler, P.F., Prohaska, S.J.
Motivation In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene...
RNAalifold. Improved consensus structure prediction for RNA alignments (2008)
Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., Stadler, P.F.
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 is...
RNAalifold. Improved consensus structure prediction for RNA alignments (2008)
Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., Stadler, P.F.
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 is...
Duplicated RNA genes in teleost fish genomes (2008)
Rose, D., Jöris, J., Hackermüller, J., Reiche, K., Li, Q., Stadler, P.F.
Teleost fishes share a duplication of their entire genomes. We report here on a computational survey of structured non-coding RNAs (ncRNAs) in teleost genomes, focusing on the fate of fish-specific...
Sonnleitner, E., Sorger-Domenigg, T., Madej, M.J., Findeiss, S., Hackermüller, J., Hüttenhofer, A., ...
Inactivation of the Pseudomonas aeruginosa (PAO1) hfq gene, encoding the Sm-like Hfq protein, resulted in pleiotropic effects that included an attenuated virulence. As regulation by Hfq often...
Evolution of spliceosomal snRNA genes in metazoan animals (2008)
Marz, M., Kirsten, T., Stadler, P.F.
While studies of the evolutionary histories of protein families are commonplace, little is known on non-coding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary...
RNAs everywhere: Genome-wide annotation of structured RNAs (2007)
Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermüller, J., ...
Starting with the discovery of microRNAs and the advent of genome-wide transcriptomics, non-protein-coding transcripts have moved from a fringe topic to a central field research in molecular biology....
RNA maps reveal new RNA classes and a possible function for pervasive transcription (2007)
Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T., ...
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and...
Structured RNAs in the ENCODE selected regions of the human genome (2007)
Washietl, S., Pedersen, J.S., Korbel, J.O., Stocsits, C., Gruber, A.R., Hackermüller, J., ...
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...
Progressive multiple sequence alignments from triplets (2007)
Background: The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at...
Löffler, D., Brocke-Heidrich, K., Pfeifer, G., Stocsits, C., Hackermüller, J., Kretzschmar, A.K., ...
Signal transducer and activator of transcription 3 (Stat3) is implicated in the pathogenesis of many malignancies and essential for IL-6-dependent survival and growth of multiple myeloma cells. Here,...
Evolution of the vertebrate Y RNA cluster (2007)
Mosig, A., Guofeng, M., Stadler, B.M.R., Stadler, P.F.
Relatively little is known about the evolutionary histories of most classes of non-protein coding RNAs. Here we consider Y RNAs, a relatively rarely studied group of related pol-III transcripts. A...
CREx: inferring genomic rearrangements based on common intervals (2007)
Bernt, M., Merkle, D., Ramsch, K., Fritzsch, G., Perseke, M., Bernhard, D., ...
Summary: We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals...
Computational RNomics of drosophilids (2007)
Rose, D., Hackermüller, J., Washietl, S., Reiche, K., Hertel, J., Findeiß, S., ...
Background: Recent experimental and computational studies have provided overwhelming evidence for a plethora of diverse transcripts that are unrelated to protein-coding genes. One subclass consists...
Induction of microRNA-21 contributes to the oncogenic potential of Stat3 (2007)
Löffler, D., Brocke-Heidrich, K., Pfeifer, G., Stocsits, C., Hackermüller, J., Kretzschmar, A., ...
Thermodynamics of RNA-RNA binding (2006)
Mückstein, U., Tafer, H., Hackermüller, J., Bernhart, S.H., Stadler, P.F., Hofacker, I.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...
Evolutionary Patterns of Non-Coding RNAs (2005)
Bompfünewerer, A.F., Flamm, Ch., Fried, C., Fritzsch, G., Hofacker, I.L., Lehmann, J., ...
Prediction of locally stable RNA secondary structures for genome-wide surveys (2004)
I. L. Hofacker, B. Priwitzer, P. F. Stadler
Motivation: Recently novel classes of functional RNAs, most prominently the miRNAs have been discovered, strongly suggesting that further types of functional RNAs are still hidden in the recently...
Prediction of locally stable RNA secondary structures for genome-wide surveys (2004)
Hofacker, I. L., Priwitzer, B., Stadler, P. F.
Motivation: Recently novel classes of functional RNAs, most prominently the miRNAs have been discovered, strongly suggesting that further types of functional RNAs are still hidden in the recently...
Conserved RNA secondary structures in viral genomes: a survey (2004)
Hofacker, I.L., Stadler, P.F., Stocsits, R.R.
Summary: 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...
BIOINFORMATICS Conserved RNA secondary structures in viral genomes: a survey (2003)
I. L. Hofacker, P. F. Stadler, R. R. Stocsits
Summary: 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...
Evolution in systems of ligation-based replicators (2002)
Stadler, B.M.R., Stadler, P.F., Wills, P.R.
The population dynamics of macromolecules that reproduce by means of template-directed ligation of two fragments are shown to be represented by a replicator equation with a special non-linear...
Stochastic pairwise alignments (2002)
U. Mückstein, I. L. Hofacker, P. 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...
Stochastic pairwise alignments (2002)
Mückstein, U., Hofacker, I.L., Stadler, P.F.
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...
Fractal geometry of spin-glass models (2001)
Fontanari, J. F., Stadler, P. F.
Stability and diversity are two key properties that living entities share with spin glasses, where they are manifested through the breaking of the phase space into many valleys or local minima...
Relevant cycles in chemical reaction network (2001)
Petra M. Gleiss, Peter F. Stadler, Andreas Wagner, David A. Fell, ...
We characterize the distributions of short cycles in a large metabolic network previously shown to have small world characteristics and a power law degree distribution. Compared with three classes of...
Design of multistable RNA molecules (2001)
Flamm, C., Hofacker, I. L., Maurer-Stroh, S., Stadler, P. F., Zehl, M.
Error Propagation in the Hypercycle (1999)
Campos, P. R. A., Fontanari, J. F., Stadler, P. F.
We study analytically the steady-state regime of a network of n error-prone self-replicating templates forming an asymmetric hypercycle and its error tail. We show that the existence of a master...
Prediction Of Rna Base Pairing Probabilities Using Massively Parallel Computers (1999)
M. Fekete, I. L. Hofacker, P. F. Stadler
this document are those of the authors and should not be interpreted as necessarily representing the o#cial policies or endorsements, either expressed or implied, of Phillips Laboratory or the U.S....
An Efficient Potential For Protein Sequence Design (1999)
G. Weberndorfer, I.L. Hofacker, P. F. Stadler
fined by the spatial coordinates of a subset of its atoms, usually the C # - and/or C # -atoms. A series of studies using a variety of di#erent knowledge based potentials by di#erent groups...
Amplitude spectra of fitness landscapes (1998)
Wim Hordijk, W. Hordijk, P. F. Stadler
ABSTRACT. Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying con guration space. The amplitude spectrum...
Amplitude spectra of fitness landscapes (1998)
Wim Hordijk, Peter F. Stadler, W. Hordijk, P. F. Stadler
ABSTRACT. Fitness landscapes can be decomposed into elementary landscapes using a Fourier transform that is determined by the structure of the underlying configuration space. The amplitude spectrum...
The Evolution of Diversity in Replicator Networks (1997)
Robert Happel, Peter F. Stadler, P. F. Stadler
Novel species are introduced into a network of interacting replicators either (i) as mutants of members of the network or (ii) as unrelated immigrants. We consider the meta-population dynamics of...
The Algebraic Theory of Recombination Spaces (1997)
Peter F. Stadler, Günter P. Wagner, G��unter P. Wagner, P. F. Stadler, G. P. Wagner, ...
A new mathematical representation is proposed for the configuration space structure induced by recombination which we called "P-structure". It consists of a mapping of pairs of objects to...
RNA multi-structure landscapes: a study based on temperature dependent partition functions. (1993)
Bonhoeffer, S., McCaskill, J. S., Stadler, P. F., Schuster, P.
RNA folding and combinatory landscapes. (1993)
Fontana, W., Stadler, P. F., Bornbergbauer, E. G., Griesmacher, T., Hofacker, I. L., Tacker, M., ...
Anisotropy in Fitness Landscapes (1993)
Peter F. Stadler, Walter Grüner, Walter Gr Uner, P. F. Stadler
A definition of empirical anisotropy is proposed, which allows for a quantitative measurement. This theory is applied to RNA free energy landscapes. It is shown that the biophysical GCAU landscapes...
Smoothness within ruggedness: the role of neutrality in adaptation.
Huynen, M A, Stadler, P F, Fontana, W
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks, evolving populations split into subpopulations,...
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Hofacker, I L, Fekete, M, Flamm, C, Huynen, M A, Rauscher, S, Stolorz, P E, ...
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...
Rauscher, S, Flamm, C, Mandl, C W, Heinz, F X, Stadler, P F
The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary...
Design of multistable RNA molecules.
Flamm, C, Hofacker, I L, Maurer-Stroh, S, Stadler, P F, Zehl, M
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...
Smoothness within ruggedness: the role of neutrality in adaptation.
Huynen, M A, Stadler, P F, Fontana, W
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks, evolving populations split into subpopulations,...
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Hofacker, I L, Fekete, M, Flamm, C, Huynen, M A, Rauscher, S, Stolorz, P E, ...
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...
Rauscher, S, Flamm, C, Mandl, C W, Heinz, F X, Stadler, P F
The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary...
Design of multistable RNA molecules.
Flamm, C, Hofacker, I L, Maurer-Stroh, S, Stadler, P F, Zehl, M
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...
Conserved RNA Secondary Structures in Picornaviridae Genomes
C. Witwer, S. Rauscher, I. L. Hofacker, P. F. Stadler
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...
Fractal Geometry of Spin-Glass Models
J. F. Fontanari, P. F. Stadler
Stability and diversity are two key properties that living entities share with spin glasses, where they are manifested through the breaking of the phase space into many valleys or local minima...
Error Propagation in the Hypercycle
J. F. Fontanari, P. F. Stadler
We study analytically the steady-state regime of a network of n error-prone self-replicating templates forming an asymmetric hypercycle and its error tail. We show that the existence of a master...
Folding Kinetics of Large RNAs
Geis, M., Flamm, C., Wolfinger, M. T., Hofacker, I. L., Middendorf, M., Mandl, C., ...