Stadler, Peter F. - Institut für Informatik, Universität Leipzig

• Alignment of RNA Base Pairing Probability Ivo L. Hofacker, Stephan H.F. Bernhart and Peter F. Stadler
• Spectral Landscape Theory Peter F. Stadler
• The Topology of Evolutionary Biology Barbel M. R. Stadler1
• Identification and Classification of Small RNAs in Transcriptome Sequence Data D. Langenberger1, C.I. Bermudez-Santana1,2 , P.F. Stadler1,3, S. Hoffmann1
• Evolution of Mitochondrial Gene Orders in Echinoderms
• Phase transition and landscape statistics of the number partitioning problem Peter F. Stadler,1, 2, 3
• Alignments of Mitochondrial Genome Arrangements
• Towards a Theory of Landscapes Peter F. Stadler a;b;\Lambda
• Smoothness within ruggedness: the role of neutrality in adaptation
• Multiple sequence alignment with user-defined constraints @ GOBICS
• Preprint manuscript No. (will be inserted by the editor)
• Minimum Path Bases and Relevant Paths Petra M. Gleissa
• Design of multistable RNA molecules CHRISTOPH FLAMM,1
• Evolution of the Vertebrate Y RNA Cluster Axel Mosig a,b
• Autocatalytic Networks with Translation Robert Happel a , Robert Hecht a , and Peter F. Stadler a;b;\Lambda
• Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation
• The Topology of Evolutionary Biology Barbel M. R. Stadler 1 and Peter F. Stadler 2,3,4
• Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting
• Computational Chemistry with RNA Secondary Structures
• Fractal geometry of spin-glass models J. F. Fontanari
• R. Giegerich et al. (eds.) Computer Science and Biology. GCB'99 Hannover, Germany. Univ. Bielefeld 1999, pp. 7379
• COMBINATORIAL LANDSCAPES # CHRISTIAN M. REIDYS + AND PETER F. STADLER #
• Dynamics of Autocatalytic Reaction Networks IV: Inhomogeneous Replicator Networks
• Automated Text Categorization in Bibliographic Search Lukas C. Faulstich
• Complementary Replication Peter F. Stadler
• Canonical Approximation of Landscapes Peter F. Stadler a;b;\Lambda and Robert Happel a
• Evidence for Independent Hox gene duplications in the hagfish lineage
• The topology of the possible: Formal spaces underlying patterns of
• Prediction of Structured NonCoding RNAs in the Genomes of the Nematodes
• The Evolution of Diversity in Replicator Networks
• The Influence of Mutation on Autocatalytic Reaction Networks
• Centers of Complex Networks Stefan Wuchty,
• CelloS: a Multi-level Approach to Evolutionary Camille Stephan-Otto Attolini1
• Molecular Evolution of a MicroRNA Cluster Andrea Tanzer a,b
• EVOLUTIONARY GENOMICS OF microRNAs AND THEIR RELATIVES
• Evolution of Vault RNAs Peter F. Stadler a,b,c,d
• Landscapes and Their Correlation Functions Peter F. Stadler a;b;\Lambda
• CelloS: a Multilevel Approach to Evolutionary Camille StephanOtto Attolini 1 , Peter F. Stadler 12 , and Christoph Flamm 1
• Statistics of RNA Melting Kinetics Manfred Tacker a , Walter Fontana b ,
• Autocatalytic Networks with Intermediates I: Irreversible Reactions
• Secondary Structure Prediction for Aligned RNA Sequences
• Thermodynamics of RNARNA Binding Ulrike Muckstein 1 , Hakim Tafer 1 , Jorg Hackermuller 2 , Stephan Bernhard 1 ,
• Conserved RNA Pseudoknots Caroline Thurner 1 , Ivo L. Hofacker 1 , Peter F. Stadler 1,2
• Research Article for BMC Evolutionary Biology 11 March 2006
• Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
• Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs
• Carnival of SL RNAs: Structural variants and the possibility of a common origin
• Multiple sequence alignment with userdefined constraints
• QuasiIndependence, Homology and the Unity of Type: A Topological Theory of Characters
• Shapes of tree representations of spinglass Wim Hordijk a , Jose F. Fontanari a
• GENERIC PROPERTIES OF THE SEQUENCESTRUCTURE RELATIONS OF BIOPOLYMERS
• Neutral Networks in Protein Space A Computational Study Based on
• Multiple sequence alignment with user-defined constraints
• Graph Laplacians, Nodal Domains, and Hyperplane Arrangements
• Fitness Landscapes Peter F. Stadler
• Landscapes on Spaces of Trees Oliver Bastert a , Dan Rockmore b , Peter F. Stadler c,d , and
• The ToyChem Package: A Computational Toolkit Implementing a
• Fast and reliable prediction of noncoding RNAs Stefan Washietl 1 , Ivo L. Hofacker 1 & Peter F. Stadler 1,2,#
• Counterexamples in Chemical Ring Perception
• J. Complex Systems (1998) 1, 39{66 Amplitude Spectra of Fitness
• ECCB 2005 Pages 12 Evolution of the Vertebrate ParaHox Clusters
• arXiv:cond-mat/0506493v120Jun2005 Statistics of cycles in large networks
• APPLICATIONS NOTE Local Base Pairing Probabilities in Large RNAs
• Local algorithms for the prime factorization of strong product graphs
• Quasi-Independence, Homology and the Unity of Type: A Topological Theory of Characters
• Conserved RNA Secondary Structures in Picornaviridae Genomes
• Full Characterization of a Strange Attractor Chaotic Dynamics in Lowdimensional Replicator Systems
• Canonical Approximation of Fitness Landscapes Robert Happel a and Peter F. Stadler a;b;\Lambda
• The E#ect of RNA Secondary Structures on RNALigand Binding and the Modifier RNA
• Evolvability of Complex Characters: Population Dependent Fourier Decomposition of Fitness
• Discrete Nodal Domain Theorems E. Brian Davies a , Graham M.L. Gladwell b , Josef Leydold c ,
• Local Minima of pSpin Models Estados metaestables para los Hamiltonianos de p espines
• The Tedious Task of Finding Homologous Non-coding RNA Genes
• Landscapes and Effective Fitness Peter F. Stadler,,,
• SIZE VARIATION AND STRUCTURAL CONSERVATION OF VERTEBRATE TELOMERASE , Axel Mosig||
• A Prime Factor Theorem for a Generalized Direct Product
• Conserved RNA Secondary Structures in Viral Genomes: Ivo L. Hofacker 1 , Peter F. Stadler 1,2 , Roman Stocsits 1
• R. Giegerich et al. (eds.) Computer Science and Biology. GCB'99 Hannover, Germany. Univ. Bielefeld 1999, pp. 107112
• RNA Structures with PseudoKnots GraphTheoretical and Combinatorial Properties
• Metastable States in High Order ShortRange Spin Viviane M. de Oliveira a , J. F. Fontanari a , and Peter F.
• Nature and Evolution of Early Replicons Peter Schuster a;b;\Lambda and Peter F. Stadler a;b
• Automatic Detection of Conserved Base Pairing Patterns
• Complex Optimization Problems and Biopolymer Structures Peter Schuster a;b;c;\Lambda and Peter F. Stadler a;b
• Correlation Length, Isotropy, and Metastable States Ricardo Garc' iaPelayo a and Peter F. Stadler b;c;\Lambda
• Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions
• A Note on Fundamental, Non-fundamental, and Robust Cycle Bases
• The Footprint Sorting Problem Claudia Fried +,# , Wim
• Minimum Path Bases and Relevant Paths Petra M. Gleiss a , Josef Leydold b , Peter F. Stadler a,c
• A Note On Minimum Path Bases Petra M. Gleiss a , Josef Leydold b , Peter F. Stadler a,c
• Adv. Complex Systems (2001) 1, 1--000 Relevant Cycles in Chemical Reaction
• Barrier Trees of Degenerate Landscapes 1 Christoph Flamm a,# , Ivo L. Hofacker a , Peter F. Stadler a,b ,
• Shaking a Box of Sand Peter F. Stadler
• Permanence of Sparse Autocatalytic Networks Peter F. Stadler 1;2;\Lambda and Peter Schuster 1;2;3
• Peter F. Stadler: List of Publications [1] Peter F Stadler and Peter Schuster. Dynamics of small autocatalytic reaction networks I
• Divergence of Conserved NonCoding Sequences: Rate Estimates and Relative
• Approximate Scaling Properties of RNA Free Energy Landscapes
• Secondary Structure of the 3'NonCoding Region of Flavivirus Genomes
• arXiv:condmat/0506493 Statistics of cycles in large networks
• Exploring Protein Sequence Space Using Knowledge Based Aderonke Babajide a , Robert Farber c;d Ivo L. Hofacker a ,
• Surveying Phylogenetic Footprints in Large Gene Clusters
• Fitness Landscapes Arising from the SequenceStructure Maps of Biopolymers
• Defining Genes A Computational Framework
• FRANz: Fast reconstruction of wild pedigrees Markus Riester1
• The fish specific Hox cluster duplication is coincident with the origin of teleosts Research Article
• Centers of Complex Networks Stefan Wuchty +,# and Peter F. Stadler #,,
• Molecular Evolution of a MicroRNA Cluster Andrea Tanzer a,b and Peter F. Stadler a,b
• The Dynamics of Adaptive Parties under Spatial Voting John H. Miller a;b;\Lambda and Peter F. Stadler b;c
• R. Hofstaedt and T. Lengauer and M. Loeffler and D. Schomburg (eds.) Computer Science and Biology 96, Univ. Leipzip 1996, pp. 184186
• Algorithm Independent Properties of RNA Secondary Structure Predictions
• Interchangeability of Relevant Cycles in Graphs Petra M. Gleiss a , Josef Leydold b,# and Peter F. Stadler a,c
• Fitness Landscapes Peter F. Stadler
• Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism
• Evidence for Independent Hox gene duplications in the hagfish lineage
• The Partition Function Variant of Sankoff's Ivo L. Hofacker1
• Saddles and Barrier in Landscapes of Generalized Search Operators
• Design of MultiStable RNA Molecules Christoph Flamm a , Ivo L. Hofacker a,# , Sebastian MaurerStroh a ,
• ProtoOrganism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism
• The Partition Function Variant of Sanko#'s Ivo L. Hofacker 1 and Peter F. Stadler 1,2
• The Shark HoxN cluster is homologous to the Human HoxD cluster
• Generic Properties of Combinatory Maps Neutral Networks of RNA Secondary Structures
• Fractal geometry of spinglass models J. F. Fontanari
• HammingChromatography Andreas Schwienhorst 1,2 , Andreas Schober 1,2 , Rolf Gnther 2,5 and Peter F. Stadler 3,4
• MUTATION IN BRIEF HUMAN MUTATION Mutation in Brief #341 (2000) Online
• Recombination Spaces, Metrics, and Pretopologies Barbel M. R. Stadler#
• NODAL DOMAIN THEOREMS AND BIPARTITE SUBGRAPHS TURKER BiYiKO GLU, JOSEF LEYDOLD, AND PETER F. STADLER
• The Footprint Sorting Problem Claudia Fried,
• NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
• RNA MultiStructure Landscapes A Study Based on Temperature Dependent Partition Functions
• Interchangeability of Relevant Cycles in Graphs: Petra M. Gleiss a , Josef Leydold b,# and Peter F. Stadler a,c
• CIRCUIT BASES OF STRONGLY CONNECTED Petra M. Gleiss
• Small Cycles in Small Worlds Petra M. Gleiss, 1 Peter F. Stadler 1, , 2 Andreas Wagner 2, , 3 and David A. Fell 4
• Discrete Models of Biopolymers Peter Schuster a,b,# and Peter F. Stadler a,b
• Sequence Redundancy in Biopolymers A Study on RNA and Protein Structures
• Random Walks and Orthogonal Functions Associated with Highly Symmetric Graphs
• Complex Adaptations and the Structure of Recombination Spaces
• Dynamics of Small Autocatalytic Reaction Networks II : Replication, Mutation and Catalysis
• Statistics of Landscapes Based on Free Energies, Replication and Degradation Rate Constants of
• Stochastic Pairwise Alignments Ulrike Muckstein a , Ivo L. Hofacker a,# , and Peter F. Stadler a,b
• Monatshefte fur Chemie (Chemical Monthly) 125: 167188 (1994) Fast Folding and Comparison of RNA
• Memory E#cient Folding Algorithms for Circular RNA Secondary Structures
• Recombination Spaces, Metrics, and Pretopologies B arbel M. R. Stadler # , Peter F. Stadler #,# , Max Shpak + ,
• Regulatory Signals in Genomic Sequences Sonja J. Prohaska, Axel Mosig, and Peter F. Stadler
• Memory Efficient Folding Algorithms for Circular RNA Secondary Structures
• Independent HoxCluster Duplications in Claudia Fried #,+ , Sonja J. Prohaska #,+ ,
• Partition Function and Base Pairing Probabilities of RNA Heterodimers
• RNA In Silico The Computational Biology of RNA
• Fast Fourier Transform for Fitness Landscapes Dan Rockmore a , Peter Kostelec a , Wim Hordijk b , Peter F.
• From Sequences to Shapes and back: A Case Study in RNA Secondary Structures
• Prediction of Locally Stable RNA Secondary Structures for GenomeWide Surveys
• Design of MultiStable Nucleic Acid Sequences Ingrid G. Abfalter 1 , Christoph Flamm 1 , Peter F. Stadler 1,2
• Minimum Cycle Bases of Halin Graphs
• Landscape statistics of the low autocorrelated binary string problem
• Exact Folding Dynamics of RNA Secondary Michael T. Wolfingera
• U7 snRNAs: A Computational Survey Manja Lindemeyer a
• Networks in Molecular Evolution PETER SCHUSTER & PETER F. STADLER
• SynBlast: Assisting the Analysis of Conserved Synteny Information
• EPJ manuscript No. (will be inserted by the editor)
• RNA Family Section. RNA Biology 0 (0): 0 A novel family of plasmid-transferred anti-sense ncRNAs
• Graph Laplacians, Nodal Domains, and Hyperplane Arrangements
• BIOINFORMATICS Vol. 00 no. 00 2011
• The Landscape of the Traveling Salesman Problem Peter F. Stadler y
• Basic Properties of Filter Convergence B arbel M. R. Stadler + , Peter F. Stadler +,#,#
• NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY CAMILLE STEPHANOTTO ATTOLINI
• Mutation in Autocatalytic Reaction Networks An Analysis based on Perturbation Theory
• GLASSY STATES IN A SHAKEN SANDBOX PETER F. STADLER
• Computational Chemistry with RNA Secondary Structures
• BIOINFORMATICS Vol. 00 no. 00
• Adv. Complex Systems (2001) 1, 1000 Relevant Cycles in Chemical Reaction
• Local Minima in the Graph Bipartitioning Problem B arbel Krakhofer a and Peter F. Stadler a;b;\Lambda
• Random Catalytic Reaction Networks Peter F.Stadler a;b , Walter Fontana a;c , John H.Miller a;d
• Autocatalytic Replication in a CSTR and Constant Organization
• Prediction of Consensus RNA Secondary Structures Including Pseudoknots
• Genomewide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional
• Barrier Trees on PosetValued Landscapes Peter F. Stadler a,b,c and Christoph Flamm a
• MODELING RNA FOLDING Ivo L. Hofacker
• Exclusion of Repetitive DNA Elements from Gnathostome Hox Clusters
• Landscapes and E#ective Fitness Peter F. Stadler ,+,#,# and Christopher R. Stephens
• Progressive Multiple Sequence Alignments from Triplets Matthias Kruspe1
• Shaking a Box of Sand Peter F. Stadler
• miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes
• HOX clusters of Latimeria: Complete characterization provides further evidence for
• Immune Networks Modeled by Replicator Equations Peter F. Stadler ab\Lambda , Peter Schuster abc , and Alan S. Perelson d
• Anisotropy in Fitness Landscapes Peter F. Stadler a;b;\Lambda and Walter Gr uner a;c
• RNA Shape Space Topology Jan Cupal a , Stephan Kopp a,b , Peter F. Stadler a,c,#
• The Algebraic Theory of Recombination Spaces Peter F. Stadler a;b and G unter P. Wagner c;\Lambda
• PREDICTION OF RNA BASE PAIRING PROBABILITIES USING MASSIVELY PARALLEL COMPUTERS
• The Probability of Permanence Peter F. Stadler a;b;\Lambda and Robert Happel a
• MOLECULAR REPLICATOR DYNAMICS ARBEL M. R. STADLER
• Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
• Correlation Structure of the Landscape of the GraphBipartitioningProblem
• A GraphBased Toy Model of Chemistry Gil Benko + , Christoph Flamm +,# , and Peter F. Stadler + ,,#
• Alignments of Mitochondrial Genome Arrangements
• Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
• MultiPhase Artificial Chemistry Gil Benko 1 , Christoph Flamm 2 , Peter F. Stadler 1,2
• Barrier Trees of Degenerate Landscapes1 Christoph Flamma,
• Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters
• Surveying Phylogenetic Footprints in Large Gene Clusters
• COMBINATORIAL LANDSCAPES CHRISTIAN M. REIDYS AND PETER F. STADLER
• In silico Evolution of Early Metabolism Alexander Ullrich1
• RNAz 2.0: improved noncoding RNA detection Andreas R. GRUBER1,2, Sven FINDEISS1, Stefan WASHIETL2,3,
• Peter F. Stadler: List of Publications [1] Peter F Stadler and Peter Schuster. Dynamics of small autocatalytic reaction networks I
• Noname manuscript No. (will be inserted by the editor)
• Reconstruction of pedigrees in clonal plant populations Markus Riester,a
• Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees
• Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem
• BarMap: RNA Folding on Dynamic Energy Ivo L. Hofacker, a
• Nematode sbRNAs: homologs of vertebrate Y RNAs Ilenia Boria,a,b, Andreas R. Gruber,b,+, Andrea Tanzer,b,c, Stephan Bernhartb, Ronny Lorenzb,
• NON-CODING RNAs Alexander Donatha, Sven Findeia, Jana Hertela, Manja Marza, Wolfgang Ottoa, Christine
• Innovation in Gene Regulation The Case of Chromatin Computation
• Conservation laws for voter-like models on random directed networks
• BIOINFORMATICS Vol. 00 no. 00 2009
• Comparative Analysis of Eukaryotic U3 snoRNA Manja Marza
• Also available on http://amc.imfm.si PREPRINT (2009) 17
• BIOINFORMATICS Vol. 00 no. 00 2009
• Accurate and efficient reconstruction of deep phylogenies from structured RNAs
• Evolution of 7SK RNA and its Protein Partners in Metazoa Manja Marza,, Alexander Donatha,, Nina Verstraeteb, Van Trung Nguyenb, Peter F. Stadlera,c-f ,
• Strategies for Homology-Based ncRNA Gene Annotation Axel Mosiga,b
• Mutate Now, Die Later Evolutionary Dynamics with Delayed Selection
• Conserved Introns Reveal Novel Transcripts in Drosophila melanogaster
• Detecting Phylogenetic Footprint Clusters by Optimizing Barbeques Axel Mosig1
• Approximate Graph Products Marc Hellmutha
• Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens
• BIOINFORMATICS Vol. 00 no. 00 2008
• A Topological Approach to Chemical Organizations
• June 17, 2008 20:31 WSPC/INSTRUCTION FILE fugu DUPLICATED RNA GENES IN TELEOST FISH GENOMES
• Arthropod 7SK RNA Andreas R. Gruber a
• Preprint manuscript No. (will be inserted by the editor)
• October 10, 2007 3:56 Proceedings Trim Size: 9in x 6in biomat A STORY OF GROWING CONFUSION
• Noisy: Identification of Problematic Columns in Multiple Sequence Alignments
• Folding Kinetics of Large RNAs Michael Geis a
• A PCR Survey of Xenoturbella bocki Hox Guido Fritzsch a,b
• Preprint manuscript No. (will be inserted by the editor)
• SnoReport: Computational identification of snoRNAs with unknown targets
• SnoReport: Computational identification of snoRNAs with unknown targets
• Computational RNomics of Drosophilids Dominic Rose1
• Vol. 00 no. 00 2005 CREx: Inferring Genomic Rearrangements Based on
• Hairpins in a Haystack: Recognizing microRNA Precursors in Comparative Genomics Data
• Prediction of Structured Non-Coding RNAs in the Genomes of the Nematodes
• Partition Function and Base Pairing Probabilities of RNA Heterodimers
• A Prime Factor Theorem for a Generalized Direct Product
• Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic
• The Expansion of the Metazoan MicroRNA Repertoire Jana Hertel1
• NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY CAMILLE STEPHAN-OTTO ATTOLINI
• Explicit Collision Simulation of Chemical Reactions in a Graph Based Artifical Chemistry
• Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
• Fast and reliable prediction of noncoding RNAs Stefan Washietl1
• Evolution of MicroRNAs Located Within Hox Gene Clusters
• Discrete Models of Biopolymers Peter Schuster a,b, and Peter F. Stadlera,b
• Conserved RNA Pseudoknots Caroline Thurner 1
• Alignment of RNA Base Pairing Probability Ivo L. Hofacker, Stephan H.F. Bernhart and Peter F. Stadler
• Gene Phylogenies and Protein-Protein Interactions: Possible Artifacts Resulting
• Aggregation of Variables and System Decomposition: Applications
• Multi-Phase Artificial Chemistry Gil Benko1, Christoph Flamm2, Peter F. Stadler1,2
• Graph Grammars as Models for the Evolution of Developmental Martin Beck1, Gil Benko2,3, Gunther J. Eble 3,4 Christoph Flamm5, Stefan Muller5, Peter F. Stadler1,3,5
• Surveying Phylogenetic Footprints in Large Gene Clusters
• Exclusion of Repetitive DNA Elements from Gnathostome Hox Clusters
• Counterexamples in Chemical Ring Perception
• The Shark HoxN cluster is homologous to the Human HoxD cluster
• Prediction of Locally Stable RNA Secondary Structures for Genome-Wide Surveys
• Higher Separation Axioms in Generalized Closure Spaces
• Automated Text Categorization in Bibliographic Search Lukas C. Faulstich
• Conserved RNA Secondary Structures in Viral Genomes: Ivo L. Hofacker1
• On the Evolution of Primitive Genetic Codes Gnter Weberndorfer, Ivo L. Hofacker and Peter F. Stadler
• A Graph-Based Toy Model of Chemistry , Christoph Flamm,
• CIRCUIT BASES OF STRONGLY CONNECTED Petra M. Gleiss
• MOLECULAR REPLICATOR DYNAMICS BARBEL M. R. STADLER
• Shapes of tree representations of spin-glass Wim Hordijka
• Stochastic Pairwise Alignments Ulrike Mucksteina
• Minimum Cycle Bases of Product Graphs Wilfried Imricha,1
• Landscapes on Spaces of Trees Oliver Bastert a
• Secondary Structure Prediction for Aligned RNA Sequences
• Basic Properties of Closure Spaces Barbel M. R. Stadler
• Evolution in Systems of Ligation-Based Replicators
• GLASSY STATES IN A SHAKEN SANDBOX PETER F. STADLER
• Discrete Nodal Domain Theorems E. Brian Davies a
• The ToyChem Package: A Computational Toolkit Implementing a
• The topology of the possible: Formal spaces underlying patterns of
• Landscape statistics of the low autocorrelated binary string problem
• Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting
• Statistics of RNA Secondary Structures y Walter Fontana b;c , Danielle A. M.Konings d , Peter F. Stadler a
• On the Evolution of Primitive Genetic Codes Gnter Weberndorfer, Ivo L. Hofacker and Peter F. Stadler
• Networks in Molecular Evolution PETER SCHUSTER & PETER F. STADLER
• Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
• last changes: August 5, 1992 Error Thresholds on Correlated Fitness Landscapes
• Homology Search with Fragmented Nucleic Acid Sequence Patterns
• Design of Multi-Stable Nucleic Acid Sequences Ingrid G. Abfalter1
• Fast Fourier Transform for Fitness Landscapes Dan Rockmorea, Peter Kosteleca, Wim Hordijkb, Peter F.
• Manuscript manuscript No. (will be inserted by the editor)
• Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution
• Conserved RNA Secondary Structures in Picornaviridae Genomes
• Exact Folding Dynamics of RNA Secondary Michael T. Wolfinger a , W. Andreas SvrcekSeiler a , Christoph
• Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution
• NEUTRALITY IN FITNESS LANDSCAPES CHRISTIAN M. REIDYS AND PETER F. STADLER
• Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic
• Evolution of MicroRNAs Located Within Hox Gene Clusters
• Phase transition and landscape statistics of the number partitioning problem Peter F. Stadler, 1, 2, 3 Wim Hordijk, 4 and Jose F. Fontanari 4
• Error propagation in the hypercycle P. R. A. Campos and J. F. Fontanari
• Linear Operators on Correlated Landscapes Peter F. Stadler
• Viral RNA and Evolved Mutational Robustness Andreas Wagner a;c;\Lambda and Peter F. Stadler b;c
• RNA Folding and Combinatory Landscapes Walter Fontana c;d , Peter F. Stadler a;b;c , Erich G. Bornberg--Bauer a ,
• BioMolecular Shapes and Algebraic Structures Christian Reidys a;\Lambda and Peter F. Stadler b;c
• Base Pairing Probabilities in a Complete HIV1 RNA Martijn A. Huynen a;b;\Lambda , Alan S. Perelson a ,
• Higher Separation Axioms in Generalized Closure Spaces
• Gene Phylogenies and ProteinProtein Interactions: Possible Artifacts Resulting
• APPLICATIONS NOTE fragrep: Efficient Search for Fragmented Patterns
• Evolution in Systems of LigationBased Replicators
• Explicit Collision Simulation of Chemical Reactions in a Graph Based Artifical Chemistry
• Graph Grammars as Models for the Evolution of Developmental Martin Beck 1 , Gil Benko 2,3 , Gunther J. Eble 3,4 Christoph Flamm 5 , Stefan Muller 5 , Peter F. Stadler 1,3,5
• Automatic Detection of Conserved RNA Structure Elements
• Why Some Fitness Landscapes are Fractal Edward D. Weinberger a;y and Peter F. Stadler a;b;c;\Lambda
• Minimal Cycle Bases of Outerplanar Graphs Josef Leydold a and Peter F. Stadler b;c;\Lambda
• NODAL DOMAIN THEOREMS AND BIPARTITE SUBGRAPHS # URKER BYKO
• Density of States, Metastable States, and Saddle Points Exploring the Energy Landscape of an RNA Molecule
• Thermodynamics of RNA-RNA Binding Ulrike Muckstein1
• Comparative promoter region analysis powered by CORG. Christoph Dieterich1
• Prediction of Consensus RNA Secondary Structures Including Pseudoknots
• Confidential Preprint manuscript No. (will be inserted by the editor)
• Independent Hox-Cluster Duplications in Claudia Fried,
• Fakult at f ur Mathematik Some Properties of Robinson Graphs
• R. Giegerich et al. (eds.) Computer Science and Biology. GCB'99 Hannover, Germany. Univ. Bielefeld 1999, pp. 915
• Equitable Partitions, Coherent Algebras and Random Walks: Applications to the Correlation
• The Expansion of the Metazoan MicroRNA Repertoire Jana Hertel 1 , Manuela Lindemeyer 1 , Kristin Missal 1 , Claudia Fried 1 , Andrea Tanzer 1,2 , Christoph
• APPLICATIONS NOTE 2005 Local Base Pairing Probabilities in Large RNAs
• Random Field Models For Fitness Landscapes Peter F. Stadler a;b;\Lambda and Robert Happel a
• E. Simoudis, J. Han, and U. Fayyad (eds.) Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining,
• Minimum Cycle Bases of Product Graphs Wilfried Imrich a,1 and Peter F. Stadler b,c
• Basic Properties of Closure Spaces B arbel M. R. Stadler + , Peter F. Stadler +,#,#
• The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA
• Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative
• The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and
• A Note On Minimum Path Bases Petra M. Gleissa
• Translational Control by RNA-RNA Interaction Improved Computation of RNA-RNA Binding
• Basic Properties of Filter Convergence Barbel M. R. Stadler
• Genome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional
• MODELING RNA FOLDING Ivo L. Hofacker
• ECCB 2005 Pages 1--2 Evolution of the Vertebrate ParaHox Clusters
• Europhysics Letters PREPRINT Exploring the lower part of discrete polymer model energy
• COMBINATORICS OF RNA SECONDARY STRUCTURES * IVO L. HOFACKER y , PETER SCHUSTER z AND PETER F. STADLER \Lambda