Peter F. Stadler

Orcid: 0000-0002-5016-5191

Affiliations:
  • University of Leipzig, Department of Computer Science
  • University of Vienna, Institute for Theoretical Chemistry
  • Max Planck Institute for Biophysical Chemistry


According to our database1, Peter F. Stadler authored at least 349 papers between 1994 and 2024.

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Bibliography

2024
Core Potentials: The Consensus Segmentation Conjecture.
Math. Comput. Sci., December, 2024

RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions.
J. Integr. Bioinform., December, 2024

Reaction rebalancing: a novel approach to curating reaction databases.
J. Cheminformatics, December, 2024

Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions.
Symmetry, September, 2024

Progressive Multiple Alignment of Graphs.
Algorithms, March, 2024

Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction.
J. Comput. Biol., 2024

Limits of experimental evidence in RNA secondary structure prediction.
Frontiers Bioinform., 2024

Transit functions and pyramid-like binary clustering systems.
Discret. Appl. Math., 2024

Democratising Artificial Intelligence for Pandemic Preparedness and Global Governance in Latin American and Caribbean Countries.
CoRR, 2024

Nesting of Touching Polygons.
CoRR, 2024

Directed Transit Functions.
CoRR, 2024

Transit Functions and Clustering Systems.
CoRR, 2024

Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss.
Adv. Appl. Math., 2024

REvolutionH-tl: Reconstruction of Evolutionary Histories tool.
Proceedings of the Comparative Genomics - 21st International Conference, 2024

Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs.
Proceedings of the Algorithms and Discrete Applied Mathematics, 2024

2023
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.
BMC Bioinform., December, 2023

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.
Algorithms Mol. Biol., December, 2023

Relative timing information and orthology in evolutionary scenarios.
Algorithms Mol. Biol., December, 2023

Clustering systems of phylogenetic networks.
Theory Biosci., November, 2023

RNA interaction format: a general data format for RNA interactions.
Bioinform., October, 2023

Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees.
SIAM J. Discret. Math., September, 2023

Local RNA folding revisited.
J. Bioinform. Comput. Biol., August, 2023

Injective Split Systems.
Graphs Comb., August, 2023

Tailored machine learning models for functional RNA detection in genome-wide screens.
Dataset, July, 2023

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs.
Frontiers Bioinform., May, 2023

Planar median graphs and cubesquare-graphs.
Discret. Appl. Math., May, 2023

Quasi-best match graphs.
Discret. Appl. Math., May, 2023

Best Match Graphs With Binary Trees.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Computational History: Challenges and Opportunities of Formal Approaches.
J. Soc. Comput., 2023

Chemically inspired Erdős-Rényi oriented hypergraphs.
CoRR, 2023

The Theory of Gene Family Histories.
CoRR, 2023

Optimisation via encodings: a renormalisation group perspective.
CoRR, 2023

Annotation-Free Identification of Potential Synteny Anchors.
Proceedings of the Bioinformatics and Biomedical Engineering, 2023

Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

On the Realisability of Chemical Pathways.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

Fitch Graph Completion.
Proceedings of the Computing and Combinatorics - 29th International Conference, 2023

2022
Hierarchical and modularly-minimal vertex colorings.
Art Discret. Appl. Math., October, 2022

Generic Context-Aware Group Contributions.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

ExceS-A: an exon-centric split aligner.
J. Integr. Bioinform., 2022

What makes a reaction network "chemical"?
J. Cheminformatics, 2022

Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy.
Entropy, 2022

Compatibility of partitions with trees, hierarchies, and split systems.
Discret. Appl. Math., 2022

From modular decomposition trees to rooted median graphs.
Discret. Appl. Math., 2022

Efficient eigenvalue counts for tree-like networks.
J. Complex Networks, 2022

BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria.
Briefings Bioinform., 2022

Bi-alignments with affine gaps costs.
Algorithms Mol. Biol., 2022

Whitney's connectivity inequalities for directed hypergraphs.
Art Discret. Appl. Math., 2022

Complete edge-colored permutation graphs.
Adv. Appl. Math., 2022

Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2022

2021
Complexity of modification problems for best match graphs.
Theor. Comput. Sci., 2021

Efficient Laplacian spectral density computations for networks with arbitrary degree distributions.
Netw. Sci., 2021

Superbubbles as an empirical characteristic of directed networks.
Netw. Sci., 2021

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.
Nucleic Acids Res., 2021

Compositional Properties of Alignments.
Math. Comput. Sci., 2021

Least resolved trees for two-colored best match graphs.
J. Graph Algorithms Appl., 2021

Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees.
Discret. Math. Theor. Comput. Sci., 2021

The Past as a Stochastic Process.
CoRR, 2021

Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees.
CoRR, 2021

Defining Autocatalysis in Chemical Reaction Networks.
CoRR, 2021

A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set.
CoRR, 2021

Compatibility of Partitions, Hierarchies, and Split Systems.
CoRR, 2021

Weighted Consensus Segmentations.
Comput., 2021

A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations.
BMC Bioinform., 2021

Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more.
Bioinform., 2021

Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.
Briefings Bioinform., 2021

Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis.
Briefings Bioinform., 2021

A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set.
Algorithms Mol. Biol., 2021

Heuristic algorithms for best match graph editing.
Algorithms Mol. Biol., 2021

LazyB: fast and cheap genome assembly.
Algorithms Mol. Biol., 2021

Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs.
Algorithms, 2021

Forman-Ricci Curvature for hypergraphs.
Adv. Complex Syst., 2021

Combining Orthology and Xenology Data in a Common Phylogenetic Tree.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2021

Cut Vertex Transit Functions of Hypergraphs.
Proceedings of the Algorithms and Discrete Applied Mathematics, 2021

Machine Learning Studies of Non-coding RNAs based on Artificially Constructed Training Data.
Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies, 2021

2020
Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards.
Dataset, August, 2020

Are spliced ncRNA host genes distinct classes of lncRNAs?
Theory Biosci., 2020

Average Fitness Differences on NK Landscapes.
Theory Biosci., 2020

Complexity of modification problems for reciprocal best match graphs.
Theor. Comput. Sci., 2020

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.
Nucleic Acids Res., 2020

A probabilistic version of Sankoff's maximum parsimony algorithm.
J. Bioinform. Comput. Biol., 2020

Exact-2-relation graphs.
Discret. Appl. Math., 2020

Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees.
Discret. Appl. Math., 2020

Indirect Identification of Horizontal Gene Transfer.
CoRR, 2020

Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.
CoRR, 2020

Clustering Improves the Goemans-Williamson Approximation for the Max-Cut Problem.
Comput., 2020

From pairs of most similar sequences to phylogenetic best matches.
Algorithms Mol. Biol., 2020

Transit sets of -point crossover operators.
AKCE Int. J. Graphs Comb., 2020

Cograph editing: Merging modules is equivalent to editing P_4s.
Art Discret. Appl. Math., 2020

Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data.
Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

Efficient Algorithms for Co-folding of Multiple RNAs.
Proceedings of the Biomedical Engineering Systems and Technologies, 2020

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding.
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 2020

2019
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

The RNA workbench 2.0: next generation RNA data analysis.
Nucleic Acids Res., 2019

Big Data Competence Center ScaDS Dresden/Leipzig: Overview and selected research activities.
Datenbank-Spektrum, 2019

Generalized Fitch Relations II: Sets of Binary Relations that are explained by Edge-labeled Trees.
CoRR, 2019

Hierarchical Colorings of Cographs.
CoRR, 2019

Best Match Graphs and Reconciliation of Gene Trees with Species Trees.
CoRR, 2019

flowEMMi: an automated model-based clustering tool for microbial cytometric data.
BMC Bioinform., 2019

Ryūtō: network-flow based transcriptome reconstruction.
BMC Bioinform., 2019

SSS-test: a novel test for detecting positive selection on RNA secondary structure.
BMC Bioinform., 2019

Automatic curation of large comparative animal MicroRNA datasets.
Bioinform., 2019

RNApuzzler: efficient outerplanar drawing of RNA-secondary structures.
Bioinform., 2019

Direct Superbubble Detection.
Algorithms, 2019

Axiomatic characterization of transit functions of weak hierarchies.
Art Discret. Appl. Math., 2019

Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2019

A General Framework for Exact Partially Local Alignments.
Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019), 2019

2018
Phylogenetics beyond biology.
Theory Biosci., 2018

Patterning the insect eye: From stochastic to deterministic mechanisms.
PLoS Comput. Biol., 2018

Partially Local Multi-way Alignments.
Math. Comput. Sci., 2018

Finding the K best synthesis plans.
J. Cheminformatics, 2018

Alignments as Compositional Structures.
CoRR, 2018

Accurate mapping of tRNA reads.
Bioinform., 2018

ceRNAs in plants: computational approaches and associated challenges for target mimic research.
Briefings Bioinform., 2018

Axiomatic characterization of transit functions of hierarchies.
Ars Math. Contemp., 2018

Time-consistent reconciliation maps and forbidden time travel.
Algorithms Mol. Biol., 2018

Coordinate systems for supergenomes.
Algorithms Mol. Biol., 2018

Superbubbles revisited.
Algorithms Mol. Biol., 2018

Split-inducing indels in phylogenomic analysis.
Algorithms Mol. Biol., 2018

A short note on undirected Fitch graphs.
Art Discret. Appl. Math., 2018

2017
Design of Artificial Riboswitches as Biosensors.
Sensors, 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Nucleic Acids Res., 2017

Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution.
J. Integr. Bioinform., 2017

Algorithmic Cheminformatics (Dagstuhl Seminar 17452).
Dagstuhl Reports, 2017

Topological Representation of the Transit Sets of k-Point Crossover Operators.
CoRR, 2017

Phylogenomics with Paralogs.
CoRR, 2017

Reconstructing Gene Trees From Fitch's Xenology Relation.
CoRR, 2017

A Survey on Hypergraph Products (Erratum).
CoRR, 2017

Merging Modules is equivalent to Editing P4's.
CoRR, 2017

An Intermediate Level of Abstraction for Computational Systems Chemistry.
CoRR, 2017

Tractable RNA-ligand interaction kinetics.
BMC Bioinform., 2017

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.
Algorithms Mol. Biol., 2017

Algebraic Dynamic Programming on Trees.
Algorithms, 2017

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps.
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Chemical Graph Transformation with Stereo-Information.
Proceedings of the Graph Transformation - 10th International Conference, 2017

2016
Design specifications for cellular regulation.
Theory Biosci., 2016

Algebraic dynamic programming for multiple context-free grammars.
Theor. Comput. Sci., 2016

Associativity and Non-Associativity of Some Hypergraph Products.
Math. Comput. Sci., 2016

Read mapping.
it Inf. Technol., 2016

The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations.
CoRR, 2016

Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary Events.
CoRR, 2016

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.
BMC Bioinform., 2016

SHAPE directed RNA folding.
Bioinform., 2016

Pseudoknots in RNA folding landscapes.
Bioinform., 2016

RNA folding with hard and soft constraints.
Algorithms Mol. Biol., 2016

The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies.
Algorithms Mol. Biol., 2016

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions.
Proceedings of the Graph Transformation - 9th International Conference, 2016

A Software Package for Chemically Inspired Graph Transformation.
Proceedings of the Graph Transformation - 9th International Conference, 2016

2015
Algebraic Dynamic Programming over general data structures.
BMC Bioinform., December, 2015

The relativity of biological function.
Theory Biosci., 2015

Product Grammars for Alignment and Folding.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Connectivity Spaces.
Math. Comput. Sci., 2015

Spiders can be Recognized by Counting Their Legs.
Math. Comput. Sci., 2015

Knowledge-based reasoning to annotate noncoding RNA using multi-agent system.
J. Bioinform. Comput. Biol., 2015

The Grid Property and Product-Like Hypergraphs.
Graphs Comb., 2015

Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s.
CoRR, 2015

Support for Eschenmoser's Glyoxylate Scenario.
CoRR, 2015

Evolution of 3'UTR-associated RNAs.
BMC Bioinform., 2015

A simple data-adaptive probabilistic variant calling model.
Algorithms Mol. Biol., 2015

The relaxed square property.
Australas. J Comb., 2015

2014
Rugged and Elementary Landscapes.
Proceedings of the Theory and Principled Methods for the Design of Metaheuristics, 2014

The genome of the recently domesticated crop plant sugar beet (<i>Beta vulgaris</i>) Open.
Nat., 2014

Generic strategies for chemical space exploration.
Int. J. Comput. Biol. Drug Des., 2014

Unique square property, equitable partitions, and product-like graphs.
Discret. Math., 2014

Algorithmic Cheminformatics (Dagstuhl Seminar 14452).
Dagstuhl Reports, 2014

Simulation of gene family histories.
BMC Bioinform., 2014

TSSAR: TSS annotation regime for dRNA-seq data.
BMC Bioinform., 2014

Lacking alignments? The next-generation sequencing mapper segemehl revisited.
Bioinform., 2014

Challenges in RNA virus bioinformatics.
Bioinform., 2014

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
Bioinform., 2014

snoStrip: a snoRNA annotation pipeline.
Bioinform., 2014

Convex cycle bases.
Ars Math. Contemp., 2014

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.
Algorithms Mol. Biol., 2014

A priori assessment of data quality in molecular phylogenetics.
Algorithms Mol. Biol., 2014

Atom mapping with constraint programming.
Algorithms Mol. Biol., 2014

Dynamic Programming for Set Data Types.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2014

Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2014

A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems.
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Comparative Detection of Processed Small RNAs in Archaea.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction.
Proceedings of the Formal Methods in Macro-Biology - First International Conference, 2014

2013
The correlation of genome size and DNA methylation rate in metazoans.
Theory Biosci., 2013

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.
Nucleic Acids Res., 2013

On the Complexity of Reconstructing Chemical Reaction Networks.
Math. Comput. Sci., 2013

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
Entropy, 2013

Square Property, Equitable Partitions, and Product-like Graphs
CoRR, 2013

Relations between graphs.
Ars Math. Contemp., 2013

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Algorithms Mol. Biol., 2013

How to Multiply Dynamic Programming Algorithms.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

The Trouble with Long-Range Base Pairs in RNA Folding.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Atom Mapping with Constraint Programming.
Proceedings of the Principles and Practice of Constraint Programming, 2013

2012
Hidden treasures in unspliced EST data.
Theory Biosci., 2012

A Survey on Hypergraph Products.
Math. Comput. Sci., 2012

The Cartesian product of hypergraphs.
J. Graph Theory, 2012

Symmetric circular matchings and RNA folding.
Discret. Math., 2012

Diagonalized Cartesian products of s-prime graphs are s-prime.
Discret. Math., 2012

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
CoRR, 2012

From event-labeled gene trees to species trees.
BMC Bioinform., 2012

Addendum: topology and prediction of RNA pseudoknots.
Bioinform., 2012

Fast and sensitive mapping of bisulfite-treated sequencing data.
Bioinform., 2012

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.
Bioinform., 2012

Minimum cycle bases of lexicographic products.
Ars Math. Contemp., 2012

RNA Folding Algorithms with G-Quadruplexes.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2012

A Visual Cross-Database Comparison of Metabolic Networks.
Proceedings of the Advances in Visual Computing - 8th International Symposium, 2012

2011
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.
Nucleic Acids Res., 2011

RNApredator: fast accessibility-based prediction of sRNA targets.
Nucleic Acids Res., 2011

Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
CoRR, 2011

Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis.
BMC Bioinform., 2011

Fast accessibility-based prediction of RNA-RNA interactions.
Bioinform., 2011

A folding algorithm for extended RNA secondary structures.
Bioinform., 2011

Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Bioinform., 2011

Topology and prediction of RNA pseudoknots.
Bioinform., 2011

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.
Bioinform., 2011

PLEXY: efficient target prediction for box C/D snoRNAs.
Bioinform., 2011

Fast local fragment chaining using sum-of-pair gap costs.
Algorithms Mol. Biol., 2011

ViennaRNA Package 2.0.
Algorithms Mol. Biol., 2011

In Silico Evolution of Early Metabolism.
Artif. Life, 2011

MicroRNA or Not MicroRNA?
Proceedings of the Advances in Bioinformatics and Computational Biology, 2011

Phylogenetic Footprinting and Consistent Sets of Local Aligments.
Proceedings of the Combinatorial Pattern Matching - 22nd Annual Symposium, 2011

2010
Visualization of Graph Products.
IEEE Trans. Vis. Comput. Graph., 2010

The primary transcriptome of the major human pathogen <i>Helicobacter pylori</i>.
Nat., 2010

Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History.
J. Bioinform. Comput. Biol., 2010

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.
BMC Bioinform., 2010

<tt>RNAsnoop</tt>: efficient target prediction for H/ACA snoRNAs.
Bioinform., 2010

Target prediction and a statistical sampling algorithm for RNA-RNA interaction.
Bioinform., 2010

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees.
Algorithms Mol. Biol., 2010

Evolution of the Long Non-coding RNAs MALAT1 and MEN<i>beta</i>/<i>epsilon</i>.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2010

Detection of Protein Domains in Eukaryotic Genome Sequences.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2010

Identification and Classification of Small RNAs in Transcriptome Sequence Data.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

RNAz 2.0: Improved Noncoding RNA Detection.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Session Introduction.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

Visual Network Analysis of Dynamic Metabolic Pathways.
Proceedings of the Advances in Visual Computing - 6th International Symposium, 2010

Quantitative Comparison of Genomic-Wide Protein Domain Distributions.
Proceedings of the German Conference on Bioinformatics 2010, 2010

In Silico Evolution of Early Metabolism.
Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, 2010

2009
Defining genes: a computational framework.
Theory Biosci., 2009

<i>Hox</i> cluster duplication in the basal teleost <i>Hiodon alosoides</i> (Osteoglossomorpha).
Theory Biosci., 2009

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures.
PLoS Comput. Biol., 2009

tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Nucleic Acids Res., 2009

Local Algorithms for the Prime Factorization of Strong Product Graphs.
Math. Comput. Sci., 2009

Approximate graph products.
Eur. J. Comb., 2009

Discovering cis-regulatory modules by optimizing barbecues.
Discret. Appl. Math., 2009

A note on fundamental, non-fundamental, and robust cycle bases.
Discret. Appl. Math., 2009

Preface.
Discret. Appl. Math., 2009

Sequence assembly.
Comput. Biol. Chem., 2009

FRANz: reconstruction of wild multi-generation pedigrees.
Bioinform., 2009

Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Bioinform., 2009

Structural profiles of human miRNA families from pairwise clustering.
Bioinform., 2009

Partition function and base pairing probabilities for RNA-RNA interaction prediction.
Bioinform., 2009

A note on quasi-robust cycle bases.
Ars Math. Contemp., 2009

A Topological Approach to Chemical Organizations.
Artif. Life, 2009

Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search.
Proceedings of the German Conference on Bioinformatics 2009, 2009

Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns.
Proceedings of the Bildverarbeitung für die Medizin 2009: Algorithmen - Systeme, 2009

2008
"Genes".
Theory Biosci., 2008

Duplicated RNA genes in teleost Fish genomes.
J. Bioinform. Comput. Biol., 2008

SynBlast: Assisting the analysis of conserved synteny information.
BMC Bioinform., 2008

RNAalifold: improved consensus structure prediction for RNA alignments.
BMC Bioinform., 2008

SnoReport: computational identification of snoRNAs with unknown targets.
Bioinform., 2008

Noisy: Identification of problematic columns in multiple sequence alignments.
Algorithms Mol. Biol., 2008

Process flow for classification and clustering of fruit fly gene expression patterns.
Proceedings of the International Conference on Image Processing, 2008

FRANz: Fast Reconstruction of Wild Pedigrees.
Proceedings of the German Conference on Bioinformatics, 2008

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics.
Proceedings of the Bioinformatics Research and Development, 2008

Visualization of Barrier Tree Sequences Revisited.
Proceedings of the Visualization in Medicine and Life Sciences., 2008

2007
The mitochondrial DNA of <i>Xenoturbella bocki</i>: genomic architecture and phylogenetic analysis.
Theory Biosci., 2007

Evolution of the vertebrate Y RNA cluster.
Theory Biosci., 2007

Towards theoretical formalisms.
Theory Biosci., 2007

Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering.
PLoS Comput. Biol., 2007

U7 snRNAs: A Computational Survey.
Genom. Proteom. Bioinform., 2007

Progressive multiple sequence alignments from triplets.
BMC Bioinform., 2007

CREx: inferring genomic rearrangements based on common intervals.
Bioinform., 2007

RNAstrand: reading direction of structured RNAs in multiple sequence alignments.
Algorithms Mol. Biol., 2007

Homology Search with Fragmented Nucleic Acid Sequence Patterns.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores.
Proceedings of the German Conference on Bioinformatics, 2007

Saddles and Barrier in Landscapes of Generalized Search Operators.
Proceedings of the Foundations of Genetic Algorithms, 9th International Workshop, 2007

2006
Visualization of Barrier Tree Sequences.
IEEE Trans. Vis. Comput. Graph., 2006

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Nucleic Acids Res., 2006

Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences.
Genom. Proteom. Bioinform., 2006

A prime factor theorem for a generalized direct product.
Discuss. Math. Graph Theory, 2006

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BMC Bioinform., 2006

Thermodynamics of RNA-RNA binding.
Bioinform., 2006

Memory efficient folding algorithms for circular RNA secondary structures.
Bioinform., 2006

Local RNA base pairing probabilities in large sequences.
Bioinform., 2006

New journal: Algorithms for Molecular Biology.
Algorithms Mol. Biol., 2006

Multiple sequence alignment with user-defined anchor points.
Algorithms Mol. Biol., 2006

Partition function and base pairing probabilities of RNA heterodimers.
Algorithms Mol. Biol., 2006

Visualization of Lattice-Based Protein Folding Simulations.
Proceedings of the 10th International Conference on Information Visualisation, 2006

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs.
Proceedings of the German Conference on Bioinformatics GCB 2006, 19.09. 2006, 2006

2005
Erratum to "Aggregation of variables and system decomposability: Applications to fitness landscape analysis.
Theory Biosci., 2005

MATH/CHEM/COMP 2004 Contributions.
Theory Biosci., 2005

Evolutionary patterns of non-coding RNAs.
Theory Biosci., 2005

Fast and reliable prediction of noncoding RNAs.
Proc. Natl. Acad. Sci. USA, 2005

Minimum path bases and relevant paths.
Networks, 2005

Multiple sequence alignments of partially coding nucleic acid sequences.
BMC Bioinform., 2005

Multiple sequence alignment with user-defined constraints at GOBICS.
Bioinform., 2005

Neutral Networks of Interacting RNA Secondary Structures.
Adv. Complex Syst., 2005

Non-coding RNAs in <i>Ciona intestinalis</i>.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry.
Proceedings of the Advances in Artificial Life, 8th European Conference, 2005

CelloS: A Multi-level Approach to Evolutionary Dynamics.
Proceedings of the Advances in Artificial Life, 8th European Conference, 2005

2004
Aggregation of variables and system decomposition: Applications to fitness landscape analysis.
Theory Biosci., 2004

Simon-Ando decomposability and fitness landscapes.
Theory Biosci., 2004

The duplication of the <i>Hox</i> gene clusters in teleost fishes.
Theory Biosci., 2004

Editorial.
Theory Biosci., 2004

Prediction of Consensus RNA Secondary Structures Including Pseudoknots.
IEEE ACM Trans. Comput. Biol. Bioinform., 2004

The Footprint Sorting Problem.
J. Chem. Inf. Model., 2004

Counterexamples in Chemical Ring Perception.
J. Chem. Inf. Model., 2004

Conserved RNA secondary structures in viral genomes: a survey.
Bioinform., 2004

Prediction of locally stable RNA secondary structures for genome-wide surveys.
Bioinform., 2004

Alignment of RNA base pairing probability matrices.
Bioinform., 2004

The Partition Function Variant of Sankoff's Algorithm.
Proceedings of the Computational Science, 2004

Conserved RNA Pseudoknots.
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

Multiple sequence alignment with user-defined constraints.
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

2003
Minimum cycle bases of Halin graphs.
J. Graph Theory, 2003

A Graph-Based Toy Model of Chemistry.
J. Chem. Inf. Comput. Sci., 2003

Barrier Trees on Poset-Valued Landscapes.
Genet. Program. Evolvable Mach., 2003

Circuit bases of strongly connected digraphs.
Discuss. Math. Graph Theory, 2003

Molecular Replicator Dynamics.
Adv. Complex Syst., 2003

Design of multi-stable nucleid acid sequences.
Proceedings of the German Conference on Bioinformatics, 2003

Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting.
Proceedings of the Advances in Artificial Life, 7th European Conference, 2003

2002
Combinatorial Landscapes.
SIAM Rev., 2002

Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry.
J. Chem. Inf. Comput. Sci., 2002

Landscapes on spaces of trees.
Appl. Math. Comput., 2002

Minimum cycle bases of product graphs.
Australas. J Comb., 2002

Stochastic pairwise alignments.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001
Neutrality in fitness landscapes.
Appl. Math. Comput., 2001

Glassy States in a shaken Sandbox.
Adv. Complex Syst., 2001

Relevant cycles in Chemical reaction Networks.
Adv. Complex Syst., 2001

2000
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers.
J. Comput. Biol., 2000

Interchangeability of Relevant Cycles in Graphs.
Electron. J. Comb., 2000

RNA Shape Space Topology.
Artif. Life, 2000

1999
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes.
Comput. Chem., 1999

RNA <i>In Silico</i> The Computational Biology of RNA Secondary Structures.
Adv. Complex Syst., 1999

Call for proposals.
Adv. Complex Syst., 1999

An efficient potential for protein sequence design.
Proceedings of the German Conference on Bioinformatics, 1999

Conserved secondary structures in hepatitis B virus DNA.
Proceedings of the German Conference on Bioinformatics, 1999

1998
Combinatorics of RNA Secondary Structures.
Discret. Appl. Math., 1998

Minimal Cycle Bases of Outerplanar Graphs.
Electron. J. Comb., 1998

Amplitude Spectra of Fitness Landscapes.
Adv. Complex Syst., 1998

1997
Algebraic Theory of Recombination Spaces.
Evol. Comput., 1997

Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

1996
Base Pairing Probabilities in a Complete HIV-1 RNA.
J. Comput. Biol., 1996

Canonical approximation of fitness landscapes.
Complex., 1996

Bio-molecular Shapes and Algebraic Structures.
Comput. Chem., 1996

Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers.
Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96), 1996

Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures.
Proceedings of the German Conference on Bioinformatics, 1996

1995
Random walks and orthogonal functions associated with highly symmetric graphs.
Discret. Math., 1995

1994
Landscapes: Complex Optimization Problems and Biopolymer Structures.
Comput. Chem., 1994


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