Copeland, Claudia C, Marz, Manja, Rose, Dominic, Hertel, Jana, Brindley, Paul J, Santana, Clara, ...
Abstract Background Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality....
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...
Christoph Flamm C, Claudia Fried A, Guido Fritzsch B, Jörg Lehmann A, ...
A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple...
Katharina Wimmer, Markus Eckart, Peter F. Stadler, Helga Rehder, Christa Fonatsch
Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder affecting one in 3,500 individuals. The mutation rate in the NF1 gene is one of the highest known for human genes. Compared to...
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...
CelloS: a Multi-level Approach to Evolutionary Dynamics (2009)
Peter F. Stadler, Christoph Flamm
Abstract. We study the evolution of simple cells that are equipped with a genome, a rudimentary gene regulation network at transcription level and two classes of functional genes: motion effectors...
CelloS: a Multi-level Approach to Evolutionary Dynamics (2009)
Peter F. Stadler, Christoph Flamm
Abstract. We study the evolution of simple cells that are equipped with a genome, a rudimentary gene regulation network at transcription level and two classes of functional genes: motion effectors...
EPJ manuscript No. (will be inserted by the editor) Funnels in Energy Landscapes (2009)
Konstantin Klemm, Christoph Flamm, Peter F. Stadler
Abstract. 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 ”...
RNA-RNA interaction prediction: partition function and base pair pairing probabilities (2009)
Huang, Fenix W. D., Qin, Jing, Reidys, Christian M., Stadler, Peter F.
In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan {\it et al.} (Alkan {\it et al.}, J. Comput. Biol., Vol:267--282, 2006). Our...
A survey of nematode SmY RNAs (2009)
Jones, Thomas A., Otto, Wolfgang, Marz, Manja, Eddy, Sean R., Stadler, Peter F.
Hox cluster duplications in the basal teleost Hiodon alosoides (Osteoglossomorpha) (2009)
Chambers, Karen E., McDaniell, Ryan, Raincrow, Jeremy F., Deshmukh, Maya, Stadler, Peter F, Chiu, Chi-hua
Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens (2009)
Hertel, Jana, Jong, Danielle De, Marz, Manja, Rose, Dominic, Tafer, Hakim, Tanzer, Andrea, ...
tRNAdb 2009: compilation of tRNA sequences and tRNA genes (2009)
Jühling, Frank, Mörl, Mario, Hartmann, Roland K., Sprinzl, Mathias, Stadler, Peter F., Pütz, Joern
A Topological Approach to Chemical Organization (2009)
Benkö, Gil, Centler, Florian, Dittrich, Peter, Flamm, Christoph, Stadler, Bärbel M. R., Stadler, Peter F.
Discovering cis-regulatory modules by optimizing barbecues (2009)
Mosig, Axel, Biyikoglu, Türker, Prohaska, Sonja J., Stadler, Peter F.
Evolution of Vault RNAs (2009)
Stadler, Peter F., Chen, Julian J.-L., Hackermüller, Jörg, Hoffmann, Steve, Horn, Friedemann, Khaitovich, Phillip, ...
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...
Conserved introns reveal novel transcripts in Drosophila melanogaster (2009)
Hiller, Michael, Findeiß, Sven, Lein, Sandro, Marz, Manja, Nickel, Claudia, Rose, Dominic, ...
Noncoding RNAs that are—like mRNAs—spliced, capped, and polyadenylated have important functions in cellular processes. The inventory of these mRNA-like noncoding RNAs (mlncRNAs), however, is...
Non-coding RNA annotation of the genome of Trichoplax adhaerens (2009)
Hertel, Jana, De Jong, Danielle, Marz, Manja, Rose, Dominic, Tafer, Hakim, Tanzer, Andrea, ...
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...
tRNAdb 2009: compilation of tRNA sequences and tRNA genes (2009)
Jühling, Frank, Mörl, Mario, Hartmann, Roland K., Sprinzl, Mathias, Stadler, Peter F., Pütz, Joern
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...
Solvent Exposure Imparts Similar Selective Pressures across a Range of Yeast Proteins (2009)
Conant, Gavin C., Stadler, Peter F.
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...
Structural profiles of human miRNA families from pairwise clustering (2009)
Kaczkowski, Bogumil, Torarinsson, Elfar, Reiche, Kristin, Havgaard, Jakob Hull, Stadler, Peter F., Gorodkin, Jan
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...
FRANz: reconstruction of wild multi-generation pedigrees (2009)
Riester, Markus, Stadler, Peter F., Klemm, Konstantin
Summary: 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...
Customized strategies for discovering distant ncRNA homologs (2009)
Mosig, Axel, Zhu, Liang, Stadler, Peter F.
A large fraction of non-coding RNAs is short and/or poorly conserved in sequence. Most of the longer examples, furthermore, consist of a collection of conserved structural motifs rather than a...
Accurate and efficient reconstruction of deep phylogenies from structured RNAs (2009)
Stocsits, Roman R., Letsch, Harald, Hertel, Jana, Misof, Bernhard, Stadler, Peter F.
Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly...
Combinatorial vector fields and the valley structure of fitness landscapes (2009)
Stadler, Bärbel M. R., Stadler, Peter F.
Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis,...
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...
SynBlast: Assisting the analysis of conserved synteny information (2008)
Lehmann, Jörg, Stadler, Peter F, Prohaska, Sonja J
Abstract 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...
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...
Noisy: Identification of problematic columns in multiple sequence alignments (2008)
Dress, Andreas WM, Flamm, Christoph, Fritzsch, Guido, Grünewald, Stefan, Kruspe, Matthias, Prohaska, Sonja J, ...
Abstract Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large...
Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, ...
Summary: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful...
BIOINFORMATICS Genes and Genomes Non-coding RNAs in Ciona intestinalis (2008)
Kristin Missal, Dominic Rose, Peter F. Stadler
Motivation: The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes are...
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....
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...
The footprint sorting problem (2008)
Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler
Phylogenetic footprints are short pieces of non-coding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints...
NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES (2008)
RNA molecules interact by forming inter-molecular base pairs that compete with the intramolecular base pairs of their secondary structures. Here we investigate the patterns of neutral mutations in...
user-defined constraints @ GOBICS (2008)
Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, ...
Multiple sequence alignment with
∗ Corresponding author: (2008)
Christoph Flamm C, Claudia Fried A, Guido Fritzsch B, Jörg Lehmann A, ...
A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple...
Consensus Arrangements of Mitochondrial Genomes (2008)
Guido Fritzsch, Martin Schlegel, Peter F. Stadler
The overwhelming part of the literature in molecular phylogenetics is based upon the analysis of nucleic acid and/or amino acid sequences of individual genes or groups of genes. With the advent of...
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...
Stephan Steigele, Wolfgang Huber, Claudia Fried, Peter F. Stadler, Kay Nieselt
Background: Non-coding RNAs (ncRNAs) are in emerging focus for both computational analysis and experimental research resulting in a growing number of novel, non-protein coding transcripts with often...
Homology Search with Fragmented Nucleic Acid Sequence Patterns (2008)
Abstract. The comprehensive annotation of non-coding RNAs in newly sequenced genomes is still a largely unsolved problem because many functional RNAs exhibit not only poorly conserved sequences but...
Basic Properties of Closure Spaces (2008)
∗ Address for corresponce Abstract. This technical report summarized facts from the basic theory of generalized closure spaces and gives detailed proofs for them. Many of the results collected here...
Counterexamples in chemical ring perception (2008)
Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler
∗ Address for correspondence Abstract. Ring information is a large part of the structural topology used to identify and characterize molecular structures. It is hence of crucial importance to...
Independent Hox-Cluster Duplications in (2008)
Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
Abstract. The analysis of the publicly available Hox gene sequences from the sea lamprey Petromyzon marinus provides evidence that the Hox clusters in lampreys and other vertebrate species arose from...
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...
Peter F. Stadler, Peter F. Stadler
Version of (28/Aug/2002) Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics...
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...
Sesame: A Generic Architecture for Storing and Querying (2008)
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...
Basic properties of filter convergence spaces (2008)
∗ Address for corresponce Abstract. This technical report summarized facts from the basic theory of filter convergence spaces and gives detailed proofs for them. Many of the results collected here...
Peter F. Stadler, Max Shpak, Günter P. Wagner
The topological features of genotype spaces given a genetic operator have a substantial impact on the course of evolution. We explore the structure of the recombination spaces arising from four...
Quasi-independence, homology and the unity of type: A topological theory of characters (2008)
Günter P. Wagner, Peter F. Stadler
Abstract. In this paper Lewontin’s notion of “quasi-independence ” of characters is formalized as the assumption that a region of the phenotype space can be represented by a product space of...
Andreas Schwienhorst, Andreas Schober, Rolf Günther, Peter F. Stadler
Synthesis of random libraries of polynucleotide sequences has become a standard procedure in biotechnology; in combination with amplification methods such as the polymerase chain reaction (PCR) [1]...
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...
Peter F. Stadler, Jean-marc Luck
Our model of shaken sand, presented in earlier work, has been extended to include a more realistic ‘glassy ’ state, i.e., when the sandbox is shaken at very low intensities of vibration. We...
Graph Laplacians, nodal domains, and hyperplane arrangements (2008)
Wim Hordijk, Josef Leydold, Peter F. Stadler
Abstract. Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the...
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...
RNA Multi-Structure Landscapes - A Study Based on Temperature Dependent Partition Functions (2008)
Sebastian Bonhoeffer, John S. McCaskill, Peter F. Stadler, Peter Schuster
Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill, 1990) are investigated in detail. The pair correlation of free energies as a function of the...
A Note on Minimum Path Bases (2008)
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
Given an undirected graph G(V, E) and a vertex subset U V the U-space is the vector space over GF(2) spanned by the paths with end-points in U and the cycles in G(V, E). We extend Vismara's...
Quasi-Independence, Homology and the Unity of Type: A Topological Theory of Characters (2008)
Günter P. Wagner, Peter F. Stadler
In this paper Lewontin's notion of "quasi-independence" of characters is formalized as the assumption that a region of the phenotype space can be represented by a product space of...
Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns (2008)
Heffel, Andreas, Stadler, Peter F., Prohaska, Sonja J., Kauer, Gerhard, Kuska, Jens-Peer
Structural profiles of miRNA families from pairwise clustering (2008)
Kaczkowski, Bogumil, Torarinsson, Elfar, Reiche, Kristin, Havgaard, Jakob Hull, Stadler, Peter F., Gorodkin, Jan
Approximate Graph Products (2008)
Hellmuth, Marc, Imrich, Wilfried, Klöckl, Werner, Stadler, Peter F.
Hoffmann, Steve, Cepok, Sabine, Grummel, Verena, Lehmann-Horn, Klaus, Hackermüller, Jörg, Stadler, Peter F., ...
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, ...
The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and Evolution (2008)
Amemiya, Chris T., Prohaska, Sonja J., Hill-Force, Alicia, Cooke, April, Wasserscheid, Jessica, Ferrier, David E. K., ...
Size Variation and Structural Conservation of Vertebrate Telomerase RNA (2008)
Xie, Mingyi, Mosig, Axel, Qi, Xiaodong, Li, Yang, Stadler, Peter F., Chen, Julian J.-L.
Duplicated RNA Genes in Teleost Fish Genomes (2008)
Rose, Dominic, Jöris, Julian, Hackermüller, Jörg, Reiche, Kristin, LI, Qiang, Stadler, Peter F.
Krauss, Veiko, Thümmler, Christian, Georgi, Franziska, Lehmann, Jörg, Stadler, Peter F., Eisenhardt, Carina
Invertebrate 7SK snRNAs (2008)
Gruber, Andreas R., Koper-Emde, Dorota, Marz, Manja, Tafer, Hakim, Bernhart, Stephan, Obernosterer, Gregor, ...
PCR Survey of Xenoturbella bocki Hox Genes (2008)
Fritzsch, Guido, Böhme, Manja U., Thorndyke, Mike, Nakano, Hiroaki, Israelson, Olle, Stach, Thomas, ...
NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences (2008)
Rose, Dominic, Hertel, Jana, Reiche, Kristin, Hackermüller, Jörg, Stadler, Peter F.
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...
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...
Krauss, Veiko, Thümmler, Christian, Georgi, Franziska, Lehmann, Jörg, Stadler, Peter F., Eisenhardt, Carina
Today, the reconstruction of the organismal evolutionary tree is based mainly on molecular sequence data. However, sequence data are sometimes insufficient to reliably resolve in particular deep...
Bogumił Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin, ...
Structural profiles of human miRNA families from pairwise clustering
Cycles in Secondary Structure Graphs (2007)
Secondary structure graphs are a class of outer-planar graphs that are used in molecular biology as representations of the spatial structure of nucleic acid molecules. The elementary cycles of...
Peter F. Stadler, Walter Fontana
The topology of the possible: Formal spaces underlying patterns of evolutionary change B arbel M. R. Stadler
Oliver Bastert, Dan Rockmore, Peter F. Stadler, Gottfried Tinhofer, Zentrum Mathematik, Tu Munchen
c,d, and
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...
Generic Properties Of The Sequence-Structure Relations Of Biopolymers (2007)
ntaining all ff n possible genotypes of given chain length n, where ff denotes the size of the polynucleotide or amino acid alphabet. Distances in sequence space are expressed by the minimum number...
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...
Landscapes and E#ective Fitness (2007)
Peter F. Stadler, Christopher R. Stephens
# Address for correspondence Abstract. The concept of a fitness landscape arose in theoretical biology, while that of e#ective fitness has its origin in evolutionary computation. Both have emerged as...
The search spaces in combinatorial chemistry as well as the sequence spaces underlying (molecular) evolution are conventionally thought of as graphs. Recombination, however, implies a non-graphical...
Graph Laplacians, nodal domains, and hyperplane arrangements (2007)
Wim Hordijk, Josef Leydold, Peter F. Stadler
Abstract. Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the...
Peter F. Stadler, B Arbel Krakhofer, M'exico D. F
submitted to Revista Mexicana de Fisica Local Minima of p-Spin Models Numerical estimates for the number of local optima of p-spin Hamiltonians with p = 3; 4; 5 and 6 are reported. The data can be...
Walter Gr Uner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, ...
c;d, and Peter Schuster a;c;d; a
Peter F. Stadler, Theoretische Biochemie
In many cases fitness landscapes are obtained as particular instances of random fields by assigning a large number of random parameters. Models of this type are often characterized reasonably well by...
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...
Peter F. Stadler, Walter Fontana
The topology of the possible: Formal spaces underlying patterns of evolutionary change B arbel M. R. Stadler
Minimum Cycle Bases of Product Graphs (2007)
Wilfried Imrich, Peter F. Stadler
A construction for a minimal cycle basis for the Cartesian and the strong product of two graphs from the minimal length cycle bases of the factors is presented. Furthermore, we derive asymptotic...
Basic Properties of Filter Convergence Spaces (2007)
This technical report summarized facts from the basic theory of filter convergence spaces and gives detailed proofs for them. Many of the results collected here are well known for various types of...
Glassy States In A Shaken Sandbox (2007)
Peter F. Stadler, Anita Mehta, Jean-marc Luck
Introduction The test of a good lattice model of a complex system is whether it succeeds in capturing the essential physics of a real system in its bid to reduce its technical complexity. Areas as...
Barrier Trees on Poset-Valued Landscapes (2007)
Peter Stadler And, Peter F. Stadler, Christoph Flamm
Fitness landscapes have proved to be a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. Usually, a fitness landscape is considered as a...
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements (2007)
Türker Bıyıkoglu, Wim Hordijk, Josef Leydold, Tomaz Pisanski, Peter F. Stadler
Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the maximal...
Shapes of Tree Representations of Spin-Glass (2007)
Landscapes Wim Hordijk, Wim Hordijk, Jose F. Fontanari, Peter F. Stadler
Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure { a barrier tree { the leaves and internal nodes of which represent,...
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...
Computational RNomics of Drosophilids (2007)
Rose, Dominic, Hackermüller, Jörg, Washietl, Stefan, Reiche, Kristin, Hertel, Jana, Findeiß, Sven, ...
Abstract 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...
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...
Funnels in Energy Landscapes (2007)
Klemm, Konstantin, Flamm, Christoph, Stadler, Peter 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...
Progressive multiple sequence alignments from triplets (2007)
Kruspe, Matthias, Stadler, Peter F
Abstract 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...
Steigele, Stephan, Huber, Wolfgang, Stocsits, Claudia, Stadler, Peter F, Nieselt, Kay
Abstract Background Non-coding RNAs (ncRNAs) are an emerging focus for both computational analysis and experimental research, resulting in a growing number of novel, non-protein coding transcripts...
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...
RNAstrand: reading direction of structured RNAs in multiple sequence alignments (2007)
Reiche, Kristin, Stadler, Peter F
Abstract Motivation Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A...
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...
RNase MRP and the RNA processing cascade in the eukaryotic ancestor (2007)
Woodhams, Michael D, Stadler, Peter F, Penny, David, Collins, Lesley J
Abstract Background Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing...
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...
PCR survey of hox Genes in the goldfish Carassius auratus auratus (2007)
Luo, Jing, Stadler, Peter F., He, Shunping, Meyer, Axel
A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii:...
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
BMC Genomics Research article Computational RNomics of Drosophilids (2007)
Dominic Rose, Jörg Hackermüller, Stefan Washietl, Kristin Reiche, Jana Hertel, Sven Findeiß, ...
© 2007 Rose et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
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
U7 snRNAs: A Computational Survey (2007)
Marz, Manja, Mosig, Axel, Stadler, Bärbel M. R., Stadler, Peter F.
The Mitochondrial DNA of Xenoturbella bocki: Genomic Architecture and Phylogenetic Analysis (2007)
Perseke, Marlen, Hankeln, Thomas, Weich, Bettina, Fritzsch, Guido, Stadler, Peter F., Israelson, Olle, ...
A stochastic model for the evolution of transcription factor binding site abundance (2007)
Wagner, Günter P., Otto, Wolfgang, Lynch, Vincent, Stadler, Peter F.
Evolution of the Vertebrate Y RNA Cluster (2007)
Mosig, Axel, Guofeng, Meng, Stadler, Bärbel M. R., Stadler, Peter F.
Computational RNomics of Drosophilids (2007)
Rose, Dominic, Hackermüller, Jörg, Washietl, Stefan, Findeiß, Sven, Reiche, Kristin, Hertel, Jana, ...
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, ...
RNase MRP and the RNA Processing Cascade in the Eukaryotic Ancestor (2007)
Woodhams, Michael D., Stadler, Peter F., Penny, David, Collins, Lesley J.
CREx: inferring genomic rearrangements based on common intervals (2007)
Bernt, Matthias, Merkle, Daniel, Ramsch, Kai, Fritzsch, Guido, Perseke, Marleen, Bernhard, Detlef, ...
Summary: We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals...
Glassy states in a shaken sandbox (2006)
Stadler, Peter F., Mehta, Anita, Luck, J. M.
Our model of shaken sand, presented in earlier work, has been extended to include a more realistic `glassy' state, i.e., when the sandbox is shaken at very low intensities of vibration. We revisit...
Multiple sequence alignment with user-defined anchor points (2006)
Morgenstern, Burkhard, Prohaska, Sonja J, Pöhler, Dirk, Stadler, Peter F
Abstract Background Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of...
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...
New journal: Algorithms for Molecular Biology (2006)
Morgenstern, Burkhard, Stadler, Peter F
Abstract This editorial announces Algorithms for Molecular Biology , a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic...
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...
Genotype-Phenotype Maps (2006)
The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space equipped at least with...
The genotype-phenotype map (2006)
∗ Address for correspondence Abstract. The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric...
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...
Multiple sequence alignment with user-defined constraints (2006)
Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-menkhoff, Isabelle Schneider, Amarendran R. Subramanian, ...
constraints
Multiple sequence alignment with user-defined constraints (2006)
Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-menkhoff, Isabelle Schneider, Amarendran R. Subramanian, ...
constraints
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...
Algorithms for Molecular Biology Editorial New journal: Algorithms for Molecular Biology (2006)
Burkhard Morgenstern, Peter F Stadler, Burkhard Morgenstern, Peter F Stadler
This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we...
Multiple sequence alignment with user-defined constraints (2006)
Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-menkhoff, Isabelle Schneider, Amarendran R. Subramanian, ...
Abstract: In many situations, automated multi-alignment programs are not able to correctly align families of nucleic acid or protein sequences. Distantly related sequences are generally hard to...
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....
PF: Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data (2006)
doi:10.1093/bioinformatics/btl257
Visualization of Lattice-Based Protein Folding Simulations. (2006)
Pötzsch, Sebastian, Scheuermann, Gerik, Wolfinger, Michael T., Flamm, Christoph, Stadler, Peter F.
Visualization of Barrier Tree Sequences. (2006)
Heine, Christian, Scheuermann, Gerik, Flamm, Christoph, Hofacker, Ivo L., Stadler, Peter F.
Multiple sequence alignment with user-defined anchor points (2006)
Morgenstern, Burkhard, Prohaska, Sonja J., Pohler, Dirk, 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.
The fish specific Hox cluster duplication is coincident with the origin of teleosts (2006)
Crow, Karen D., Stadler, Peter F., Lynch, Vincent J., Amemiya, Chris T., Wagner, Günter P.
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,...
The "Fish-Specific" Hox Cluster Duplication Is Coincident with the Origin of Teleosts (2006)
Crow, Karen D., Stadler, Peter F., Lynch, Vincent J., Amemiya, Chris, Wagner, Günter P.
The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in...
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data (2006)
Hertel, Jana, Stadler, Peter F.
Summary: Recently, genome-wide surveys for non-coding RNAs have provided evidence for tens of thousands of previously undescribed evolutionary conserved RNAs with distinctive secondary structures....
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,...
Statistics of cycles in large networks (2005)
Klemm, Konstantin, Stadler, Peter F.
We present a Markov Chain Monte Carlo method for sampling cycle length in large graphs. Cycles are treated as microstates of a system with many degrees of freedom. Cycle length corresponds to energy...
Comparative promoter region analysis powered by CORG (2005)
Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...
Abstract Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which...
Comparative promoter region analysis powered by CORG (2005)
Dieterich,Christoph, Grossmann,Steffen, Tanzer,Andrea, Röpcke,Stefan, Arndt,Peter F, Stadler,Peter F, ...
Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely...
Nodal Domain Theorems and Bipartite Subgraphs (2005)
Biyikoglu, Türker, Leydold, Josef, Stadler, Peter F.
The Discrete Nodal Domain Theorem states that an eigenfunction of the k-th largest eigenvalue of a generalized graph Laplacian has at most k (weak) nodal domains. We show that the number of strong...
Comparative promoter region analysis powered by CORG (2005)
Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...
Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely...
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...
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry (2005)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Abstract. A Toy Model of an artificial chemistry that treats molecules as graphs was implemented based on a simple Extended Hückel Theory method. Here we describe an extension of the model that...
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
Peter F. Stadler, Mario Mörl Leipzig, Robert Giegerich Bielefeld, Prof Dr, Peter F. Stadler, Prof Dr, ...
This workshop will bring together the RNA Research Community from Germany and neighboring countries. It strives to provide a program that emphasizes the common interests of experimentalists and...
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, ...
CelloS: A Multi-level Approach to Evolutionary Dynamics (2005)
Attolini, Camille Stephan-Otto, Stadler, Peter F., Flamm, Christoph
Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences (2005)
Stocsits, Roman R., Hofacker, Ivo L., Fried, Claudia, Stadler, Peter F.
Comparative promoter region analysis powered by CORG (2005)
Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Ropcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...
Wagner, Günter P., Takahashi, Kazuhiko, Lynch, Vincent, Prohaska, Sonja J., Fried, Claudia, Stadler, Peter F., ...
Evolution of MicroRNAs Located Within Hox Gene Clusters (2005)
Tanzer, Andrea, Amemiya, Chris T., Kim, Chang-Bae, Stadler, Peter F.
Multiple sequence alignment with user-defined constraints at GOBICS (2005)
Morgenstern, Burkhard, Prohaska, Sonja J., Werner, Nadine, Weyer-Menkhoff, Jan, Schneider, Isabelle, Subramanian, Amarendran R., ...
The "Fish Specific" Hox Cluster Duplication is Coincident with the Origin of Teleosts (2005)
Crow, Karen D, Stadler, Peter F., Lynch, Vincent J., Amemiya, Chris, Wagner, Günter P.
The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in...
Non-coding RNAs in Ciona intestinalis (2005)
Missal, Kristin, Rose, Dominic, Stadler, Peter F.
Motivation: The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes are...
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...
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry (2005)
Christoph Flamm, Peter F. Stadler
Abstract. A Toy Model of an artificial chemistry that treats molecules as graphs was implemented based on a simple Extended H"uckel Theory method. Here we describe an extension of the model that...
The "Fish Specific" Hox Cluster Duplication is Coincident with the Origin of Teleosts (2005)
Crow, Karen D, Stadler, Peter F., Lynch, Vincent J., Amemiya, Chris, Wagner, Günter P.
The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in...
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...
The topology of evolutionary biology (2004)
Summary. Central notions in evolutionary biology are intrinsically topological. This claim is maybe most obvious for the discontinuities associated with punctuated equilibria. Recently, a...
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...
Molecular evolution of a microRNA cluster (2004)
Andrea Tanzer, Peter F. Stadler, Interdisziplinäres Zentrum Für
MicroRNAs (miRNAs) form a class of noncoding RNA genes whose products are small single-stranded RNAs with a length of about 22 nt. These are involved in the regulation of translation
Transitions from Nonliving to Living Matter (2004)
Rasmussen, Steen, Chen, Liaohai, Deamer, David, Krakauer, David C., Packard, Norman H., Stadler, Peter F., ...
Simon Ando Decomposability and Fitness Landscapes (2004)
Shpak, Max, Stadler, Peter F., Wagner, Günter P., Altenberg, Lee
Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests (2004)
Wagner, Günter P., Fried, Claudia, Prohaska, Sonja J., Stadler, Peter F.
Graph Grammars as Models for the Evolution of Developmental Pathways (2004)
Beck, Martin, Benkö, Gil, Eble, Gunther J., Müller, Stefan, Stadler, Peter F., Flamm, Christoph
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
Stadler, Peter F., Fried, Claudia, Prohaska, Sonja J., Bailey, Wendy J., Misof, Bernhard Y., Ruddle, Frank H., ...
Copeland, Claudia S., Heyers, Oliver, Kalinna, Bernd H., Bachmair, Andreas, Stadler, Peter F., Hofacker, Ivo L., ...
The Footprint Sorting Problem (2004)
Fried, Claudia, Hordijk, Wim, Prohaska, Sonja J., Stadler, Claus R., Stadler, Peter F.
Conserved RNA Secondary Structures in Flaviviridae Genomes (2004)
Thurner, Caroline, Witwer, Christina, Hofacker, Ivo L., Stadler, Peter F.
Counterexamples in Chemical Ring Perception (2004)
Berger, Franziska, Flamm, Christoph, Gleiss, Petra M., Leydold, Josef, Stadler, Peter F.
The Shark HoxN cluster is homologous to the Human HoxD cluster (2004)
Prohaska, Sonja J., Fried, Claudia, Amemiya, Chris T., Ruddle, Frank H., Wagner, Günter P., Stadler, Peter F.
Aggregation of Variables and System Decomposition: Applications to Fitness Landscape Analysis (2004)
Shpak, Max, Stadler, Peter F., Wagner, Günter P., Hermisson, Joachim
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution (2004)
Chiu, C-H., Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism (2004)
Rasmussen, Steen, Chen, Liaohai, Stadler, Bärbel M.R., Stadler, Peter F.
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements (2004)
Biyikoglu, Türker, Hordijk, Wim, Leydold, Josef, Pisanski, Tomaz, Stadler, Peter F.
Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests (2004)
Wagner, Günter P., Fried, Claudia, Prohaska, Sonja J., Stadler, Peter F.
In many eukaryotic genomes only a small fraction of the DNA codes for proteins but the non-protein coding DNA harbors important genetic elements directing the development and the physiology of the...
Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests (2004)
Wagner, Günter P., Fried, Claudia, Prohaska, Sonja J., Stadler, Peter F.
In many eukaryotic genomes only a small fraction of the DNA codes for proteins, but the non-protein coding DNA harbors important genetic elements directing the development and the physiology of the...
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...
Multiple sequence alignment with user-defined constraints @ GOBICS (2004)
Morgenstern, Burkhard, Werner, Nadine, Prohaska, Sonja J., Steinkamp, Rasmus, Schneider, Isabelle, Subramanian, Amarendran R., ...
Summary: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution (2004)
Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish...
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...
P.: Graph grammars as models for the evolution of developmental pathways (2004)
Martin Beck, Gil Benkö, Gunther J. Eble, Christoph Flamm, Stefan Müller, Peter F. Stadler, ...
The large quantity and ready availability of developmental-genetic data, coupled with increased rigor and detail in the characterization of morphological phenotypes, has made the genotype-phenotype...
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...
Multi-Phase Artificial Chemistry, in H (2004)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Artificial chemistries can be used to explore the generic properties of chemical reaction networks. In order to simulate for instance scenarios of prebiotic evolution the model must be close enough...
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...
Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests (2004)
Wagner, Günter P., Fried, Claudia, Prohaska, Sonja J., Stadler, Peter F.
In many eukaryotic genomes only a small fraction of the DNA codes for proteins but the non-protein coding DNA harbors important genetic elements directing the development and the physiology of the...
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...
Multiple sequence alignment with user-defined constraints @ GOBICS (2004)
Morgenstern, Burkhard, Werner, Nadine, Prohaska, Sonja J., Steinkamp, Rasmus, Schneider, Isabelle, Subramanian, Amarendran R., ...
Summary: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful...
Phase transition and landscape statistics of the number partitioning problem (2003)
Stadler, Peter F., Hordijk, Wim, Fontanari, Jos{é} F.
The phase transition in the number partitioning problem (NPP), i.e., the transition from a region in the space of control parameters in which almost all instances have many solutions to a region in...
Shapes of tree representations of spin-glass landscapes (2003)
Hordijk, Wim, Fontanari, Jose F., Stadler, Peter F.
Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure -- a barrier tree -- the leaves and internal nodes of which represent,...
litsift: Automated text categorization in bibliographic search (2003)
Lukas C. Faulstich, Peter F. Stadler
In bioinformatics there exist research topics that cannot be uniquely characterized by a set of key words because relevant key words are (i) also heavily used in other contexts and (ii) often omitted...
Networks in Molecular Evolution - A Common Theme at All Levels (2003)
Peter Schuster, Peter F. Stadler
INTRODUCTION N etworks of different kinds and sizes appear at different levels of molecular evolution. Networks have a natural representation as graphs or hypergraphs of various kinds. It is not...
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...
Centers of complex networks (2003)
Stefan Wuchty, Peter F. Stadler
Abstract. The central vertices in complex networks are of particular interest because they might play the role of organizational hubs. Here, we consider three different geometric centrality measures,...
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...
Centers of Complex Networks (2003)
Stefan Wuchty, Peter F. Stadler
The central vertices in complex networks are of particular interest because they might play the role of organizational hubs. Here, we consider three di#erent geometric centrality measures,...
Circuit Bases of Strongly Connected Digraphs (2003)
Petra Gleiss, Josef Leydold, Peter F. Stadler
The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected...
Circuit bases of strongly connected digraphs (2003)
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected...
Landscapes and effective fitness (2003)
Peter F. Stadler, Christopher R. Stephens
∗ Address for correspondence Abstract. The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged...
A graph-based toy model of chemistry (2003)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks...
Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting (2003)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Abstract. We use a Toy Model of chemistry that represents molecules in terms of usual structural formulae to generate large chemical reaction networks. An extremely simplified quantum mechanical...
Phylogenetic footprint patterns in large gene clusters (2003)
Sonja J. Prohaska, Claudia Fried, Christoph Flamm, Peter F. Stadler
Introduction. Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. Since these elements are subject to stabilizing...
Surveys of Phylogenetic Footprints in Large Gene Clusters (2003)
Claudia Fried Sonja, Sonja J. Prohaska, Christoph Flamm, Günter P. Wagner, Peter F. Stadler
Introduction Gene regulatory regions in noncoding genomic sequences are subject to stabilizing selection and therefore evolve much slower than adjacent non-functional DNA. The resulting phylogenetic...
Aggregation of variables and system decomposition: applications to fitness landscape analysis (2003)
Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson
Copy of DecompPaper.nb 1 In this paper we present general results on aggregation of variables, specifically as it applies to decomposable (partitionable) dynamical systems. We show that a particular...
A graph-based toy model of chemistry (2003)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks...
litsift: Automated Text Categorization in Bibliographic Search (2003)
Faulstich, Lukas C., Stadler, Peter F., Thurner, Caroline, Witwer, Christina
Biological Realistic Landscapes (2003)
Peter F. Stadler, El Malpais Nm, Bandelier Nm, White Sands
More abstractly: A landscape is a triple (V, X, f) where V is a set of configurations. E.g.: gene sequences, tours of travelling salesman, spin configurations; f is a cost or fitness function f: V...
Graph Laplacians, Nodal Domains, and Hyperplane Arrangements (2002)
Biyikoglu, Türker, Hordijk, Wim, Leydold, Josef, Pisanski, Tomaz, Stadler, Peter F.
Eigenvectors of the Laplacian of a graph G have received increasing attention in the recent past. Here we investigate their so-called nodal domains, i.e., the connected components of the maximal...
Networks in molecular evolution (2002)
Peter Schuster, Peter F. Stadler
Networks are a common theme at all levels of molecular evolution: Networks of metastable states and their connecting saddle points determine structure and folding kinetics of biopolymers. Neutral...
Recombination spaces, metrics, and pretopologies (2002)
The topological features of genotype spaces given a genetic operator have a substantial impact on the course of evolution. We explore the structure of the recombination spaces arising from four...
Basic Properties of Closure Spaces (2002)
This technical report summarized facts from the basic theory of generalized closure spaces and gives detailed proofs for them. Many of the results collected here are well known for various types of...
Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism (2002)
Steen Rasmussen, Liaohai Chen, Peter F. Stadler
A synthetic proto-organism could be self-assembled by integrating a lipid protocontainer with a proto-metabolic subsystem and a proto-genetic subsystem. This three-component system can use energy and...
Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism (2002)
Steen Rasmussen, Liaohai Chen, Peter F. Stadler
A synthetic proto-organism could be self-assembled by integrating a lipid protocontainer with a proto-metabolic subsystem and a proto-genetic subsystem. This three-component system can use energy and...
Molecular Replicator Dynamics (2002)
B Arbel, Peter F. Stadler, Peter F. Stadler
this article, fortunately, the precise chemical instantiation of the earliest replicons is largely irrelevant, because their basic kinetic properties depend more on the logics of the replication...
Networks in molecular evolution (2002)
Peter Schuster, Peter F. Stadler
Networks are a common theme at all levels of molecular evolution: Networks of metastable states and their connecting saddle points determine structure and folding kinetics of biopolymers. Neutral...
Secondary structure prediction for aligned RNA sequences (2002)
Ivo L. Hofacker, Martin Fekete, Peter F. Stadler
RNA secondary structure prediction, conserved substructures, compensatory mutations.
Barrier Trees on Poset-Valued Landscapes (2002)
Peter F. Stadler, Christoph Flamm
Fitness landscapes have proved to be a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. Usually, a fitness landscape is considered as a...
Networks in molecular evolution (2002)
Peter Schuster, Peter F. Stadler, Chemie Molekulare
etworks of different kinds and sizes appear at different levels of molecular evolution. Networks have a natural representation as graphs or hypergraphs of various kinds. It is not surprising,...
Glassy states in a shaken sandbox (2001)
Stadler, Peter F., Mehta, Anita, Luck, J. M.
Our model of shaken sand, presented in earlier work, has been extended to include a more realistic `glassy' state, i.e., when the sandbox is shaken at very low intensities of vibration. We revisit...
Stadler, Peter F., Mehta, Anita, Luck, Jean-Marc
We present a simple model of a vibrated box of sand, and discuss its dynamics in terms of two parameters reflecting static and dynamic disorder respectively. The fluidised, intermediate and frozen...
Circuit Bases of Strongly Connected Digraphs (2001)
Gleiss, Petra M., Leydold, Josef, Stadler, Peter F.
The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected...
Minimum Path Bases and Relevant Paths (2001)
Gleiss, Petra M., Leydold, Josef, Stadler, Peter F.
Given an undirected graph G(V,E) and a vertex subset U\subseteq V the U-space is the vector space over GF(2) spanned by the paths with end-points in U and the cycles in G(V,E). We extend Vismara's...
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 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...
Fast Fourier Transform for Fitness Landscapes (2001)
Dan Rockmore, Peter Kostelec, Wim Hordijk, Peter F. Stadler, Peter F
We cast some classes of fitness landscapes as problems in spectral analysis on various Cayley graphs. In particular, landscapes derived from RNA folding are realized on Hamming graphs and analyzed in...
Discrete Nodal Domain Theorems (2001)
Brian Davies Josef, E. Brian Davies, Peter F. Stadler
We give a detailed proof for two discrete analogues of Courant's Nodal Domain Theorem. 1 Introduction Courant's famous Nodal Domain Theorem for elliptic operators on Riemannian manifolds...
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...
Higher separation axioms in generalized closure spaces (2001)
∗ corresponding author The hierarchy of separation axioms that is familiar from topological spaces generalizes to spaces with an isotone and expansive closure function. Neither additivity nor...
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...
Circuit Bases of Strongly Connected Digraphs (2001)
Petra Gleiss, Josef Leydold, Peter F. Stadler
The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected...
The topology of the possible: Formal spaces underlying patterns of evolutionary change (2001)
Peter F. Stadler, Gug Nter, P. Wagner, Walter Fontana-a
The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space equipped with a notion...
Evolution in Systems of Ligation-Based Replicators (2001)
Peter F. Stadler, Peter R. Wills
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...
Higher Separation Axioms in Generalized Closure Spaces (2001)
The hierarchy of separation axioms that is familiar from topological spaces generalizes to spaces with an isotone and expansive closure function. Neither additivity nor idempotence of the closure...
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...
Discrete Nodal Domain Theorems (2000)
Davies, E. Brian, Leydold, Josef, Stadler, Peter F.
We give a detailed proof for two discrete analogues of Courant's Nodal Domain Theorem.
Small Cycles in Small Worlds (2000)
Gleiss, Petra M., Stadler, Peter F., Wagner, Andreas, Fell, David A.
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...
Landscape statistics of the low autocorrelated binary string problem (2000)
Ferreira, Fernando F., Fontanari, Jose Fernando, Stadler, Peter F.
The statistical properties of the energy landscape of the low autocorrelated binary string problem (LABSP) are studied numerically and compared with those of several classic disordered models. Using...
Discrete Nodal Domain Theorems (2000)
Davies, Brian E., Leydold, Josef, Stadler, Peter F.
We give a detailed proof for two discrete analogues of Courant's Nodal Domain Theorem. (author's abstract)
Discrete Nodal Domain Theorems (2000)
Davies, Brian E., Gladwell, Graham M. L., Leydold, Josef, Stadler, Peter F.
We give a detailed proof for two discrete analogues of Courant's Nodal Domain Theorem. (author's abstract)
Some properties of Robinson graphs (2000)
Gottfried Tinborer, Oliver Bastert, Oliver Bastert, Dan Rockmore, Dan Rockmore, ...
basterr, gott inmathemat ik. tu-muenchen. de
Peter F. Stadler, Gunter P. Wagner
According to the Darwinian theory of evolution, adaptation results from spontaneously generated genetic variation and natural selection. Mathematical models of this process can be seen as describing...
Discrete Models of Biopolymers (2000)
Peter Schuster, Peter F. Stadler
Discretized models of biopolymer structures can be used not only as approximations of the actual spatial structures but also as a computationally feasible approach to the generic features of the...
Interchangeability of Relevant Cycles in Graphs (2000)
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
The set R of relevant cycles of a graph G is the union of its minimum cycle bases. We introduce a partition of R such that each cycle in a class W can be expressed as a sum of other cycles in W and...
Minimum Cycle Bases of Halin Graphs (2000)
Halin graphs are planar 3-connected graphs that consist of a tree and a cycle connecting the end vertices of the tree. It is shown that all Halin graphs that are not "necklaces" have a...
Small Cycles in Small Worlds (2000)
Petra M. Gleiss, Peter F. Stadler, Andreas Wagner, David A. Fell
this paper we will represent a network as a simple (unweighted, undirected) graph G(V, E) with vertex set V and edge set E. A cycle in G is a closed path which meets each of its vertices and edges...
Discrete Nodal Domain Theorems (2000)
E. Brian Davies, Josef Leydold, Peter F. Stadler
We give a detailed proof for two discrete analogues of Courant's Nodal Domain Theorem. 1 Introduction Courant's famous Nodal Domain Theorem for elliptic operators on Riemannian manifolds...
Interchangeability of Relevant Cycles in Graphs (2000)
Petra M. Gleiss, Josef Leydold, Peter F. Stadler, Address For Correspondence
The set R of relevant cycles of a graph G is the union of its minimum cycle bases. We introduce a partition of R such that each cycle in a class W can be expressed as a sum of other cycles in W and...
Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions (2000)
Peter F. Stadler, Peter Schuster
this paper that the concentrations [A] and [B] of the building blocks are bu#ered, i.e., constant. The crucial step of the replication mechanism is the formation of an intermediate species ABCC which...
Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions (2000)
Peter F. Stadler, Peter Schuster
this paper that the concentrations [A] and [B] of the building blocks are buered, i.e., constant. The crucial step of the replication mechanism is the formation of an intermediate species ABCC which...
Landscape Statistics of the Low Autocorrelated Binary String Problem (2000)
Fernando F. Ferreira, Jose F. Fontanari, Peter F. Stadler, Peter F
. The statistical properties of the energy landscape of the low autocorrelated binary string problem (LABSP) are studied numerically and compared with those of several classic disordered models....
Some Properties of Robinson Graphs (2000)
Oliver Bastert, Dan Rockmore, Peter F. Stadler, Gottfried Tinhofer, Àáâ Ãäåæç
Robinson graphs are configuration graphs over sets of phylogenetic trees. Their neighbor relation is given by all possible crossovers along inner edges of these trees. We show that Robinson graphs...
Discrete Nodal Domain Theorems (2000)
Brian Davies Graham, E. Brian Davies, Peter F. Stadler
We prove two discrete analogues of Courant's Nodal Domain Theorem.
Metastable States in High Order Short-Range Spin Glasses (1999)
De Oliveira, Viviane M., Fontanari, J. F., Stadler, Peter F.
The mean number of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination...
Interchangeability of Relevant Cycles in Graphs (1999)
Gleiss, Petra M., Leydold, Josef, Stadler, Peter F.
The set R of relevant cycles of a graph G is the union of its minimum cycle bases. We introduce a partition of R such that each cycle in a class W can be expressed as a sum of other cycles in W and...
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...
Metastable States in High Order Short-Range Spin Glasses (1999)
J. F. Fontanari, Peter F. Stadler, Peter F
. The mean number hN i of metastable states in higher order shortrange spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination...
Relevant Cycles in Biopolymers and Random Graphs (1999)
Petra M. Gleiss, Peter F. Stadler
Short cycles are an important characteristic of molecular graphs in organic chemistry as well as in structural biology. Minimum cycle bases are of particular interest, despite the fact that they are...
RNA Shape Space Topology (1999)
Jan Cupal, Stephan Kopp, Peter F. Stadler
The distinction between continuous and discontinuous transitions is a longstanding problem in the theory of evolution. Continuity being a topological property, we present a formalism that treats the...
Discrete Models of Biopolymers (1999)
Peter Schuster, Peter F. Stadler
Discretized models of biopolymer structures can be used not only as approximations of the actual spatial structures but also as a computationally feasible approach to the generic features of the...
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...
Topology In Phenotype Space (1999)
Jan Cupal, Peter Schuster, Peter F. Stadler
Introduction The course of biological evolution cannot be understood without the dichotomy of genotype and phenotype. While variation is introduced by mutation or recombination at the genotypic...
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...
Peter F. Stadler, Rudi Seitz, Günter P. Wagner
this paper is the following, rather surprising
Viral RNA and Evolved Mutational Robustness (1999)
Andreas Wagner, Peter F. Stadler
Many properties of organisms show great robustness against mutations. Whether this robustness is an evolved property or intrinsic to genetic systems is by and large unknown. An evolutionary origin of...
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...
Spectral Landscape Theory (1999)
INTRODUCTION Evolutionary change is caused by the spontaneously generated genetic variation and its subsequent fixation by drift and/or selection. Consequently, the main focus of evolutionary theory...
Peter F. Stadler, Rudi Seitz, Günter P. Wagner
this paper is the following, rather surprising
Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reaction (1999)
Peter F. Stadler, Peter Schuster
A class of autocatalytic reaction networks based on template depending litigation and higher order...
Minimal Cycle Bases of Outerplanar Graphs (1998)
Leydold, Josef, Stadler, Peter F.
2-connected outerplanar graphs have a unique minimal cycle basis with length 2|E|-|V|. They are the only Hamiltonian graphs with a cycle basis of this length. (author's abstract)
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...
Minimal Cycle Bases of Outerplanar Graphs (1998)
Josef Leydold, Peter F. Stadler
2-connected outerplanar graphs have a unique minimal cycle basis with length 2jEj \Gamma jV j. They are the only Hamiltonian graphs with a cycle basis of this length. Keywords: Minimal Cycle Basis,...
The Evolution of Diversity in Replicator Networks (1998)
Robert Happel, Peter 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...
Nature and Evolution of Early Replicons (1998)
Peter Schuster, Peter F. Stadler, Stadler Early
RNA and protein molecules were found to be both templates for replication and specific catalysts for biochemical reactions. RNA molecules, although very difficult to obtain via plausible synthetic...
Minimal Cycle Bases of Outerplanar Graphs (1998)
Josef Leydold, Peter F. Stadler
2-connected outerplanar graphs have a unique minimal cycle basis with length 2|E|-|V|. They are the only Hamiltonian graphs with a cycle basis of this length. Keywords: Minimal Cycle Basis,...
Neutrality In Fitness Landscapes (1998)
Christian M. Reidys, Peter F. Stadler
The interplay of ruggedness and neutrality in fitness landscapes plays an important role in explaining the dynamics of evolutionary adaptation. While various measures of ruggedness (correlation...
Minimal Cycle Bases of Outerplanar Graphs (1998)
Josef Leydold, Peter F. Stadler
2-connected outerplanar graphs have a unique minimal cycle basis with length 2jEj \Gamma jV j. They are the only Hamiltonian graphs with a cycle basis of this length. Keywords: Minimal Cycle Basis,...
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...
Minimal Cycle Bases of Outerplanar Graphs (1998)
Josef Leydold, Peter F. Stadler
2-connected outerplanar graphs have a unique minimal cycle basis with length 2jEj \Gamma jV j. They are the only Hamiltonian graphs with a cycle basis of this length. Keywords: Minimal Cycle Basis,...
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...
Nature and Evolution of Early Replicons (1998)
Peter Schuster, Peter F. Stadler, Stadler Early
RNA and protein molecules were found to be both templates for replication and specific catalysts for biochemical reactions. RNA molecules, although very difficult to obtain via plausible synthetic...
Amplitude Spectra of Fitness Landscapes (1998)
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 obtained...
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...
Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers (1997)
Fitness landscapes are an important concept in molecular evolution since evolutionary adaptation as well as in vitro selection of biomolecules can be viewed as a hill-climbing-like process. Global...
Sequence Redundancy in Biopolymers A Study on RNA and Protein Structures (1997)
Peter Schuster And, Peter Schuster, Peter F. Stadler
Mapping sequences onto biopolymer structures is characterized by redundancy since the numbers of sequences exceed the numbers of structures. The degree of Redundancy depends on the notion of...
Autocatalytic Networks with Intermediates I: Irreversible Reactions (1997)
Robert Hecht, Robert Happel, Peter Schuster, Peter F. Stadler
A class of autocatalytic reaction networks based on template dependent replication and specific catalysis is considered. Trimolecular "elementrary steps" of simple replicator dynamics are...
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...
RNA Structures with Pseudo-Knots - Graph-Theoretical and Combinatorial Properties (1997)
Peter F. Stadler, Christian Haslinger
Secondary structures of nucleic acids are a particularly interesting class of contact structures. Many important RNA molecules contain pseudoknots, which are excluded explicitly by the definition of...
Correlation Length, Isotropy, and Meta-stable States (1997)
Ricardo Garcia-Pelayo, Peter F. Stadler, M'exico D. F
A landscape is rugged if it has many local optima, if it gives rise to short adaptive walks, and if it exhibits a rapidly decreasing pair-correlation function (and hence if it has a short correlation...
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...
Sequence Redundancy in Biopolymers - A Study on RNA and Protein Structures (1997)
Peter Schuster, Peter F. Stadler
Mapping sequences onto biopolymer structures is characterized by redundancy since the numbers of sequences exceed the numbers of structures. The degree of Redundancy depends on the notion of...
Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation (1997)
Peter R. Wills, Stuart A. Kauffman, Peter F. Stadler
The theory of autocatalytic binary ligation is reviewed within the context of a consistently applied MichaelisMenten quasi-steady-state approximation to obtain explicit analytical results describing...
Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler
Detailed knowledge of the energy landscape of a biopolymer molecule is a prerequisite for understanding its folding kinetics and its final spatial structure. In the case of RNA we consider the energy...
Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers (1997)
Fitness landscapes are an important concept in molecular evolution since evolutionary adaptation as well as in vitro selection of biomolecules can be viewed as a hill-climbing-like process. Global...
Autocatalytic Networks with Translation (1996)
Robert Happel, Robert Hecht, Peter F. Stadler
We consider the kinetics of an autocatalytic reaction network in which replication and catalytic action is separatedby a translation step. We find that the behavior of such a system is closely...
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...
Isotropy and Metastable States - The Landscape of the XY Hamiltonian Revisited (1996)
Ricardo Garcia-Pelayo, Peter F. Stadler, M'exico D. F
The number of local optima is an important characteristic of a landscape. It appears to depend on the pair-correlation of the landscape as well as on its deviations from statistical isotropy. We use...
Random Field Models For Fitness Landscapes (1996)
Peter Stadler And, Peter F. Stadler, Theoretische Biochemie
In many cases fitness landscapes are obtained as particular instances of random fields by assigning a large number of random parameters. Models of this type are often characterized reasonably well by...
Canonical Approximation of Fitness Landscapes (1996)
Robert Happel, Peter F. Stadler, Theoretische Biochemie
We present a method for approximating a fitness landscape as a superposition of "elementary" landscapes. Given a correlation function of the landscape in question we show that the relative...
Bio-Molecular Shapes and Algebraic Structures (1996)
Christian Reidys, Peter F. Stadler
Shapes of biological macromolecules --- RNA, DNA, and proteins --- can be represented by abstract algebraic structures provided as suitably coarse resolution is chosen. These abstract structures, for...
Local Minima in the Graph Bipartitioning Problem (1996)
Arbel Krakhofer, Peter F. Stadler
We report numerical simulations on the number of local minima in the landscape of the Graph Bipartitioning Problem and provide an explanation in terms of the correlation length of its landscape. PACS...
Approximate Scaling Properties of RNA Free Energy Landscapes (1996)
Subbiah Baskaran, Peter F. Stadler, Peter Schuster
RNA free energy landscapes are analyzed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size...
Smoothness Within Ruggedness: The Role of Neutrality in Adaptation (1996)
Martijn Huynen, Peter F. Stadler, Walter Fontana
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 which...
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...
Local Minima in the Graph Bipartitioning Problem (1996)
Bärbel Krakhofer, B Arbel Krakhofer, Peter F. Stadler
We report numerical simulations on the number of local minima in the landscape of the Graph Bipartitioning Problem and provide an explanation in terms of the correlation length of its landscape. PACS...
Base Pairing Probabilities in a Complete HIV-1 RNA (1996)
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By...
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...
Canonical Approximation of Landscapes (1996)
Peter F. Stadler, Robert Happel
Correlation functions are important characteristics of (fitness) landscapes. We use the Fourier decomposition of landscapes in order to characterize the set of all the possible autocorrelation...
Base Pairing Probabilities in a Complete HIV-1 RNA (1996)
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base-pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill [33]. By analyzing...
Local Minima of p-Spin Models (1996)
Peter F. Stadler, Bärbel Krakhofer
Numerical estimates for the number of local optima of p-spin Hamiltonians with p=3;4;5 and 6 are reported. The data can be explained by means of a simple estimate in terms of the "correlation...
Landscapes and Their Correlation Functions (1996)
Peter F. Stadler, Theoretische Biochemie
Fitness landscapes are an important concept in molecular evolution. Many important examples of landscapes in physics and combinatorial optimization, which are widely used as model landscapes in...
Bio-Molecular Shapes and Algebraic Structures (1996)
Christian Reidys, Peter F. Stadler
Shapes of biological macromolecules --- RNA, DNA, and proteins --- can be represented by abstract algebraic structures provided as suitably coarse resolution is chosen. These abstract structures, for...
Base Pairing Probabilities in a Complete HIV-1 RNA (1996)
Martijn A. Huynen, Alan Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By...
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...
Autocatalytic Replication in a CSTR and Constant Organization (1995)
Robert Happel And, Peter F. Stadler, Theoretische Biochemie, Replicator Equation
The dynamics of a network of autocatalytically replicating species in a continuously stirred tank reactor can be described by a replicator equation in the limit of small flux rates. Introduction. A...
Dynamics of Small Autocatalytic Reaction Networks II : Replication, Mutation and Catalysis (1995)
Peter F. Stadler, Wolfgang Schnabl, Christian Forst, Peter Schuster
. Mutation is introduced into autocatalytic reaction networks. The differential equations obtained are neither of replicator type nor can they be transformed straightway into a linear equation....
Autocatalytic Replication in a CSTR and Constant Organization (1995)
Robert Happel, Peter F. Stadler, Theoretische Biochemie, Replicator Equation
The dynamics of a network of autocatalytically replicating species in a continuously stirred tank reactor can be described by a replicator equation in the limit of small flux rates. Introduction. A...
Generic Properties of Combinatory Maps - Neutral Networks of RNA Secondary Structures (1995)
Christian Reidys, Peter F. Stadler, Peter Schuster
Random graph theory is used to model relationships between sequences and secondary structures of RNA molecules. Sequences folding into identical structures form neutral networks which percolate...
Dynamics of Small Autocatalytic Reaction Network II: Replication, Mutation and Catalysis (1994)
Stadler, Peter F., Schnabl, Wolfgang, Forst, Christian V., Schuster, Peter
Mutation is introduced into autocatalytic reaction networks. Examples of low dimensional dynamical systems --- n = 2, 3 and 4 --- are discussed and complete qualitative analysis is presented. Error...
Permanence of Sparse Autocatalytic Networks (1994)
Peter F. Stadler, Peter Schuster, Schuster Permanence
Some global dynamical properties of catalytic networks, in particular permanence, are closely related with a directed graph representing the differential equation. It can be shown that for every...
The Influence of Mutation on Autocatalytic Reaction Networks (1994)
Peter F. Stadler, Juan Carlos Nuno
A particular class of ordinary differential equations (ODE) describing catalyzed, template-induced, and erroneous replication is investigated. The ODEs can be split into a replicator part accounting...
Random Walks and Orthogonal Functions Associated with Highly Symmetric Graphs (1994)
The relationship of orthogonal functions associated with vertex transitive graphs and random walks on such graphs is investigated. We use this relations to characterize the exponentially decaying...
Linear Operators on Correlated Landscapes (1994)
In this contribution we consider the effect of a class of "averaging operators " on isotropic fitness landscapes. Explicit expressions for the correlation function of the averaged...
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...
Immune Networks Modeled by Replicator Equations (1994)
Peter F. Stadler, Peter Schuster, Alan S. Perelson
In order to evaluate the role of idiotypic networks in the operation of the immune system a number of mathematical models have been formulated. Here we examine a class of B-cell models in which cell...
The Dynamics of Adaptive Parties under Spatial Voting (1994)
John H. Miller, Peter F. Stadler
We explore the dynamics of a model of two-party competition under spatial voting. The parties are allowed to incrementally adapt their platforms by following the voting gradient imposed by the...
Neutrality in fitness landscapes (1993)
Abstract. Fitness landscapes are a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. A fitness landscape is a mapping from a configuration...
Random Catalytic Reaction Networks (1993)
Peter F. Stadler, Walter Fontana, John H. Miller
We study networks that are a generalization of replicator (or Lotka-Volterra) equations. They model the dynamics of a population of object types whose binary interactions determine the specific type...
Statistics of RNA Melting Kinetics (1993)
Manfred Tacker, Walter Fontana, Peter F. Stadler, Peter Schuster
We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that assigns structure...
Why Some Fitness Landscapes are Fractal (1993)
Edward D. Weinberger, Peter F. Stadler
Many biological and biochemical measurements, e.g. the "fitness" of a particular genome, or the binding affinity to a particular substrate, can be treated as a "fitness...
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...
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...
Landscapes - Complex Optimization Problems and Biopolymer Structures (1993)
Peter Schuster, Peter F. Stadler
The evolution of RNA molecules in replication assays, viroids and RNA viruses can be viewed as an adaptation process on a 'fitness' landscape. The dynamics of evolution is hence tightly...
Neutrality in fitness landscapes (1993)
Abstract. Fitness landscapes are a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. A fitness landscape is a mapping from a configuration...
Error Thresholds on Correlated Fitness Landscapes (1992)
Sebastian Bonhoeffer, Peter F. Stadler
The evolution of molecular quasispecies on two different complex fitness landscapes, the Sherrington Kirkpatrick spin glass and the Graph Bipartitioning landscape, is investigated in dependence on...
The Landscape of the Traveling Salesman Problem (1992)
Max Planck, Karl Friedrich Bonhoeffer, Wolfgang Schnabel, Peter F. Stadler, Peter F. Stadler
The landscapes of Traveling Salesman Problems are investigated by random walk techniques. The autocorrelation functions for different metrics on the space of tours are calculated. The landscape turns...
The Probability of Permanence (1992)
Peter F. Stadler, Robert Happel, Correspondence Peter, F. Stadler
Numerical experiments suggest that cooperation is a very rare phenomenon in autocatalytic networks with more than some 5 interacting species. There is strong evidence that the probability for a...
Correlation Structure of the Landscape of the Graph-Bipartitioning-Problem (1992)
Max Planck, Robert Happel, Peter F. Stadler, Peter F. Stadler
The relaxation of random walks and the autocorrelation function on the landscape of the graphbipartitioning problem (GBP) are calculated. 1. Introduction The investigation of the correlation...
Complementary Replication (1991)
Differential equations for the kinetics of complementary replicating macromolecules in a flow reactor are derived. It is shown that such a model has many features in common with the differential...
Dynamics of Autocatalytic Reaction Networks IV: Inhomogeneous Replicator Networks (1991)
The inhomogeneous replicator equation is derived as the continuous time model for parallel first and second order autocatalytic replication of macromolecules in a flow reactor based on mass action...
Wolfgang Schnabl, Peter F. Stadler, Christian Forst, Peter Schuster, W. Schnabl Chaotic
Two chaotic attractors observed in Lotka-Volterra equations of dimension n = 3 are shown to represent two di#erent cross-sections of one and the same chaotic regime. The strange attractor is studied...
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...
Mandl, Christian W., Holzmann, Heidemarie, Meixner, Tamara, Rauscher, Susanne, Stadler, Peter F., Allison, Steven L., ...
The flavivirus genome is a positive-strand RNA molecule containing a single long open reading frame flanked by noncoding regions (NCR) that mediate crucial processes of the viral life cycle. The 3′...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish...
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...
Comparative promoter region analysis powered by CORG
Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...
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, ...
New journal: Algorithms for Molecular Biology
Morgenstern, Burkhard, Stadler, Peter F
This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we...
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
Multiple sequence alignment with user-defined anchor points
Morgenstern, Burkhard, Prohaska, Sonja J, Pöhler, Dirk, 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...
Mandl, Christian W., Holzmann, Heidemarie, Meixner, Tamara, Rauscher, Susanne, Stadler, Peter F., Allison, Steven L., ...
The flavivirus genome is a positive-strand RNA molecule containing a single long open reading frame flanked by noncoding regions (NCR) that mediate crucial processes of the viral life cycle. The 3′...
Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
Chiu, Chi-hua, Dewar, Ken, Wagner, Günter P., Takahashi, Kazuhiko, Ruddle, Frank, Ledje, Christina, ...
The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish...
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...
Comparative promoter region analysis powered by CORG
Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...
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, ...
New journal: Algorithms for Molecular Biology
Morgenstern, Burkhard, Stadler, Peter F
This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we...
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
Multiple sequence alignment with user-defined anchor points
Morgenstern, Burkhard, Prohaska, Sonja J, Pöhler, Dirk, Stadler, Peter F
RNase MRP and the RNA processing cascade in the eukaryotic ancestor
Woodhams, Michael D, Stadler, Peter F, Penny, David, Collins, Lesley J
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...
Circuit Bases of Strongly Connected Digraphs
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
The cycle space of a strongly connected graph has a basis consisting of directed circuits. The concept of relevant circuits is introduced as a generalization of the relevant cycles in undirected...
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...
Evolution in Systems of Ligation-Based Replicators
Peter F. Stadler, Peter R. Wills
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...
Minimum Cycle Bases of Product Graphs
Wilfried Imrich, Peter F. Stadler
A construction for a minimal cycle basis for the Cartesian and the strong product of two graphs from the minimal length cycle bases of the factors is presented. Furthermore, we derive asymptotic...
Christian M. Reidys, Peter F. Stadler
Fitness landscapes have proven to be a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. A fitness landscape is a mapping from a...
Peter F. Stadler, Anita Mehta, Jean-Marc Luck
We present a simple model of a vibrated box of sand, and discuss its dynamics in terms of two parameters reflecting static and dynamic disorder respectively. The fluidised, intermediate and frozen...
Recombination Spaces, Metrics, and Pretopologies
Peter F. Stadler, Max Shpak, GŸnter P. Wagner
The topological features of genotype spaces given a genetic operator have a substantial impact on the course of evolution. We explore the structure of the recombination spaces arising from four...
Oliver Bastert, Dan Rockmore, Peter F. Stadler, Gottfried Tinhofer
Combinatorial optimization problems defined on sets of phylogenetic trees are an important issue in computational biology, for instance the problem of reconstruction a phylogeny using maximum...
The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change
Peter F. Stadler, GŸnter P. Wagner, Walter Fontana
The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space equipped with a notion...
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 networks...
Landscape Statistics of the Low Autocorrelated Binary String Problem
Fernando F. Feirreira, José F. Fontanari, Peter F. Stadler
The statistical properties of the energy landscape of the low autocorrelated binary string problem (LABSP) are studied numerically and compared with those of several classic disordered models. Using...
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...
Fast Fourier Transform for Fitness Landscapes
Dan Rockmore, Peter Kostelec, Wim Hordijk, Peter F. Stadler
We cast some classes of fitness landscapes as problems in spectral analysis on various Cayley graphs. In particular, landscapes derived from RNA folding are realized on Hamming graphs and analyzed in...
Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions
Peter F. Stadler, Peter Schuster
A class of autocatalytic reaction networks based on template dependent ligation and higher order catalysis is analyzed. Apart from an irreversible ligation reaction we consider only reversible...
Metastable States in High Order Short-Range Spin Glasses
J. F. Fontanari, Peter F. Stadler
The mean number (N) of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination...
Interchangeability of Relevant Cycles in Graphs
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
The set R of relevant cycles of a graph G is the union of its minimum cycle bases. We introduce a partition of R such that each cycle in a class W can be expressed as a sum of other cycles and W and...
Relevant Cycles in Biopolymers and Random Graphs
Petra M. Gleiss, Peter F. Stadler
Short cycles are an important characteristic of molecular graphs in organic chemistry as well as in structural biology. Minimum cycle bases are of particular interest, despite the fact that they are...
Jan Cupal, Stephan Kopp, Peter F. Stadler
The distinction between continuous and discontinuous transitions is a long-standing problem in the theory of evolution. Continuity being a topological property, we present a formalism that treats the...
Viral RNA and Evolved Mutational Robustness
Andreas Wagner, Peter F. Stadler
Many properties of organisms show great robustness against mutations. Whether this robustness is an evolved property or intrinsic to genetic systems is by and large unknown. An evolutionary origin of...
Evolvability of Complex Characters
Peter F. Stadler, Rudi Seitz, Günter P. Wagner
The effect of recombination on genotypes can be represented in the form of P-structures, i.e. a map from the set of pairs of genotypes to the power set of genotypes. The interpretation is that the...
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...
Nature and Evolution of Early Replicons
Peter Schuster, Peter F. Stadler
RNA and protein molecules were found to be both templates for replication and specific catalysts for biochemical reactions. RNA molecules, although very difficult to obtain via plausible synthetic...
Neutrality in Fitness Landscapes
Christian M. Reidys, Peter F. Stadler
The interplay of ruggedness and neutrality in fitness landscapes plays an important role in explaining the dynamics of evolutionary adaptation. While various measures of ruggedness (correlation...
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...
Amplitude Spectra of Fitness Landscapes
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 obtained...
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...
Minimal Cycle Bases of Outerplanar Graphs
Josef Leydold, Peter F. Stadler
Two-connected outerplanar graphs have a unique minimal cycle basis with length $2|E|-|V|$. They are the only Hamiltonian graphs with a cycle basis of this length.
Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers
Fitness landscapes are an important concept in molecular evolution since evolutionary adaptation as well as {\it in vitro} selection of biomolecules can be viewed as a hill-climbing-like process....
Sequence Redundancy in Biopolymers: A Study on RNA and Protein Structures
Peter Schuster, Peter F. Stadler
Mapping sequences onto biopolymer structures is characterized by redundancy since the numbers of sequences exceed the numbers of structures. The degree of Redundancy depends on the notion of...
Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation
Peter R. Wills, Stuart A. Kauffman, Peter F. Stadler
The theory of autocatalytic binary ligation is reviewed within the context of a rigorously applied Michaelis-Menten quasi-steady-state approximation to obtain explicit analytical results describing...
The Evolution of Diversity in Replicator Networks
Robert Happel, Peter 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...
RNA Structures wth Pseudo-Knots
Peter F. Stadler, Christian Haslinger
Secondary structures of nucleic acids are a particularly interessting class of contact structures. Many important RNA molecules contain pseudoknots, which are excluded explicitly by the definition of...
Complex Adaptations and the Structure of Recombination Spaces
Gunter P. Wagner, Peter F. Stadler
According to the Darwinian theory of evolution, adaptation results from spontaneously generated genetic variation and natural selection. Mathematical models of this process can be seen as describing...
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...
Secondary Structure of the 3'-Non-Coding Region of Flavivirus Genomes
Susanne Rauscher, Christoph Flamm, Christian W. Mandl, Franz X. Heinz, Peter F. Stadler
The prediction of the complete matrix of base pairing probabilities was applied to the 3' non-coding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary...
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...
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...
Computational RNomics of Drosophilids
Rose, Dominic, Hackermüller, Jörg, Washietl, Stefan, Reiche, Kristin, Hertel, Jana, Findeiß, Sven, ...
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...
Noisy: Identification of problematic columns in multiple sequence alignments
Dress, Andreas WM, Flamm, Christoph, Fritzsch, Guido, Grünewald, Stefan, Kruspe, Matthias, Prohaska, Sonja J, ...
NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES
RNA molecules interact by forming inter-molecular base pairs that compete with the intra-molecular base pairs of their secondary structures. We investigate the patterns of neutral mutations in RNAs...
RELEVANT CYCLES IN CHEMICAL REACTION NETWORKS
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...
GLASSY STATES IN A SHAKEN SANDBOX
PETER F. STADLER, ANITA MEHTA, JEAN-MARC LUCK
Our model of shaken sand, presented in earlier work, has been extended to include a more realistic 'glassy' state, i.e. when the sandbox is shaken at very low intensities of vibration. We revisit...
Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with...
The Algebraic Theory of Recombination Spaces
Peter F. Stadler, Gunjter P. Wagner
A new mathematical representaion 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 the power...
Isotropy and Metastable States: The Landscape of the XY Hamiltonian Revisited
Ricardo Garcia-Pelayo, Peter F. Stadler
The number of local optima is an important characteristic of a landscape. It appears to depend on the pair-correlation of the landscape as well as on its deviations from statistical isotropy. We use...
Autocatalytic Networks with Intermediates I: Irreversible Reactions
Robert Hecht, Robert Happel, Peter Schuster, Peter F. Stadler
A class of autocatalytic reaction networks based on template dependent replication and specific catalysis is considered. Trimolecular "elementary strps" of simple replicator dynamics are resolved...
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...
Local Minima in the Graph Bipartitioning Problem
Barbel Krakhofer, Peter F. Stadler
We report numerical simulations on the number of local minima in the landscape of the Graph Bipartitioning Problem and provide an
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...
Bio-Molecular Shapes and Algebraic Structures
Christian Reidys, Peter F. Stadler
Shapes of biological macromolecules---RNA, DNA, and proteins---can be represented by abstract algebraic structures provided as suitably coarse resolution is chosen. These abstract structures, for...
Andreas Schwienhorst, Andreas Schober, Rolf Guenther, Peter F. Stadler
> Synthesis of random libraries of polynucleotide sequences has become a standard procedure of biotechnology; in combination with amplification methods such as the polymerase chain reaction (PCR) [1]...
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...
Approximate Scaling Properties of RNA Free Energy Landscapes
Subbiah Baskaran, Peter F. Stadler, Peter Schuster
RNA free energy landscapes are analyzed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and...
Peter F. Stadler, Barbel Krakhofer
Numerical estimates for the number of local optima of p-spin Hamiltonians with p=3,4,5, and 6 are reported. The data can be explained by means of a simple estimate in terms of the "correlation...
Random Field Models for Fitness Landscapes
Peter F. Stadler, Robert Happel
In many cases fitness landscapes are obtained as particular instances of random fields by assigning a large number of random parameters. Models of this type are often characterized reasonably well by...
Canonical Approximation of Fitness Landscapes
Robert Happel, Peter F. Stadler
We present a method for approximating a fitness landscapes as a superposition of "elementary" landscapes. Given a correlation function of the landscape in question we show that the relative...
Landscapes and Their Correlation Functions
Fitness landscapes are an important concept in molecular evolution. Many important examples of landscapes in physics and combinatorial optimization, which are widely used as model landscapes in...
Autocatalytic Networks with Translation
Robert Happel, Robert Hecht, Peter F. Stadler
We consider the kinetics of an autocatalytic reaction network in which replication and catalytic action is separated by a translation step. We find that the behavior of such a system is closely...
Autocatalytic Replication in a CSTR and Constant Organization
Robert Happel, Peter F. Stadler
The dynamics of a network of autocatalytically replicating species in a continuously stirred tank reactor can be described by a replicator equation in the limit of small flux rates.
Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures
Christian Reidys, Peter F. Stadler, Peter Schuster
Random graph theory is used to model relationships between sequences and secondary structure of RNA molecules. Sequences folding into identical structures form neutral networks which percolate...
Base Pairing Probabilities in a Complete HIV-1 RNA
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by MasCaskill (1990). By analyzing...
Canonical Approximation of Landscapes
Peter F. Stadler, Robert Happel
Correlation functions are important characteristics of (fitness) landscapes. We use the fourier expansion of landscapes in order to characterize the set of all the possible autocorrelation functions...
The Dynamics of Adaptive Parties under Spatial Voting
John H. Miller, Peter F. Stadler
We explore the dynamics of a model of two-party competition under spatial voting. the parties are allowed to {\it incrementally} adapt their platforms by following the voting gradient imposed by the...
Permanence of Sparse Autocatalytic Networks
Peter F. Stadler, Peter Schuster
Some global dynamical properties of catalytic networks, in particular permanence, are closely related with a directed graph representing the differential equation. It can be shown that for every...
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...
Dynamics of Small Autocatalytic Reaction Networks II: Replication, Mutation and Catalysis
Peter F. Stadler, Wolfgang Schnabl, Christian V. Forst, Peter Schuster
Mutation is introduced into autocatalytic reaction networks. The differential equations obtained are neither of replicator type nor can they be transformed straightway into a linear equation....
The Influence of Mutation on Autocatalytic Reaction Networks
Peter F. Stadler, Juan Carlos Nu\~no
A particular class of ordinary differential equations (ODE) describing catalyzed, template-induced, and erroneous replication is investigated. The ODEs can be split into a replicator part accounting...
Landscapes Complex Optimization Problems and Biopolymer Structures
Peter Schuster, Peter F. Stadler
The evolution of RNA molecules in replication assays, viroids and RNA viruses can be viewed as an adaptation process on a ``fitness'' landscape. The dynamics of evolution is hence tightly linked to...
Immune Networks Modeled by Replicator Equations
Peter F. Stadler, Peter Schuster, Alan S. Perelson
In order to evaluate the role of idiotypic networks in the operation of the immune system a number of mathematical models have been formulated. Here we examine a class of B-cell models in which cell...
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...
Statistics of RNA Melting Kinectics
Manfred Tacker, Walter Fontana, Peter F. Stadler, Peter Schuster
We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that assigns structure...
Linear Operators on Correlated Landscapes
In this contribution we consider the effect of a class of ``averaging operators'' on isotropic fitness landscapes. Explicit expressions for the correlation function of the averaged landscapes are...
Random Walks and Orthogonal Functions Associated with Highly Symmetric Graphs
The relationship of orthogonal functions associated with vertex transitive graphs and random walks on such graphs is investigated. We use this relations to characterize the exponentially decaying...
RNAalifold: improved consensus structure prediction for RNA alignments
Bernhart, Stephan H, Hofacker, Ivo L, Will, Sebastian, Gruber, Andreas R, Stadler, Peter F
Non-coding RNA annotation of the genome of Trichoplax adhaerens
Hertel, Jana, De Jong, Danielle, Marz, Manja, Rose, Dominic, Tafer, Hakim, Tanzer, Andrea, ...
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...
Hoffmann, Steve, Cepok, Sabine, Grummel, Verena, Lehmann-Horn, Klaus, Hackermueller, Jörg, Stadler, Peter F., ...
The formation of antibodies to interferon-beta (IFN-β), a protein-based disease-modifying agent for multiple sclerosis (MS), is a problem in clinical practice. These antibodies may neutralize the...
Hoffmann, Steve, Cepok, Sabine, Grummel, Verena, Lehmann-Horn, Klaus, Hackermüller, Jörg, Stadler, Peter F., ...
Prohaska, Sonja J., Stadler, Peter F.
In order to describe a cell at molecular level, a notion of a “gene” is neither necessary nor helpful. It is sufficient to consider the molecules (i.e., chromosomes, transcripts, proteins) and...
Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)
Chambers, Karen E., McDaniell, Ryan, Raincrow, Jeremy D., Deshmukh, Maya, Stadler, Peter F., Chiu, Chi-hua
Large-scale—even genome-wide—duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the most species-rich vertebrate clade, underwent a “fish-specific...
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
Jühling, Frank, Mörl, Mario, Hartmann, Roland K., Sprinzl, Mathias, Stadler, Peter F., Pütz, Joern
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...
FRANz: reconstruction of wild multi-generation pedigrees
Riester, Markus, Stadler, Peter F., Klemm, Konstantin
Summary: 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...
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
Hoffmann, Steve, Otto, Christian, Kurtz, Stefan, Sharma, Cynthia M., Khaitovich, Philipp, Vogel, Jörg, ...
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...
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...
Accurate and efficient reconstruction of deep phylogenies from structured RNAs
Stocsits, Roman R., Letsch, Harald, Hertel, Jana, Misof, Bernhard, Stadler, Peter F.
Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly...
Defining genes: a computational framework
Stadler, Peter F., Prohaska, Sonja J., Forst, Christian V., Krakauer, David C.
The precise elucidation of the gene concept has become the subject of intense discussion in light of results from several, large high-throughput surveys of transcriptomes and proteomes. In previous...