Peter F. Stadler
Orcid: 0000-0002-5016-5191Affiliations:
- 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 333 papers
between 1994 and 2024.
Collaborative distances:
Collaborative distances:
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Online presence:
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on scopus.com
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on orcid.org
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on id.loc.gov
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on d-nb.info
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On csauthors.net:
Bibliography
2024
RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions.
J. Integr. Bioinform., December, 2024
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
Algorithms Mol. Biol., December, 2023
Algorithms Mol. Biol., December, 2023
Bioinform., October, 2023
Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees.
SIAM J. Discret. Math., September, 2023
Proceedings of the Bioinformatics and Biomedical Engineering, 2023
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023
Proceedings of the Computing and Combinatorics - 29th International Conference, 2023
2022
Art Discret. Appl. Math., October, 2022
IEEE ACM Trans. Comput. Biol. Bioinform., 2022
Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy.
Entropy, 2022
Discret. Appl. Math., 2022
BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria.
Briefings Bioinform., 2022
Art Discret. Appl. Math., 2022
Proceedings of the Advances in Bioinformatics and Computational Biology, 2022
2021
Efficient Laplacian spectral density computations for networks with arbitrary degree distributions.
Netw. Sci., 2021
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.
Nucleic Acids Res., 2021
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
CoRR, 2021
A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set.
CoRR, 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
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs.
Algorithms, 2021
Proceedings of the Advances in Bioinformatics and Computational Biology, 2021
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
Theor. Comput. Sci., 2020
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.
Nucleic Acids Res., 2020
J. Bioinform. Comput. Biol., 2020
Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees.
Discret. Appl. Math., 2020
CoRR, 2020
Comput., 2020
Algorithms Mol. Biol., 2020
Art Discret. Appl. Math., 2020
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
Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020
Proceedings of the Biomedical Engineering Systems and Technologies, 2020
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 2020
2019
IEEE ACM Trans. Comput. Biol. Bioinform., 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
BMC Bioinform., 2019
BMC Bioinform., 2019
Bioinform., 2019
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
Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019), 2019
2018
PLoS Comput. Biol., 2018
ceRNAs in plants: computational approaches and associated challenges for target mimic research.
Briefings Bioinform., 2018
Ars Math. Contemp., 2018
Algorithms Mol. Biol., 2018
2017
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Nucleic Acids Res., 2017
J. Integr. Bioinform., 2017
CoRR, 2017
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.
Algorithms Mol. Biol., 2017
Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017
Proceedings of the Graph Transformation - 10th International Conference, 2017
2016
Theor. Comput. Sci., 2016
Math. Comput. Sci., 2016
The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations.
CoRR, 2016
CoRR, 2016
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.
BMC Bioinform., 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
Proceedings of the Graph Transformation - 9th International Conference, 2016
2015
BMC Bioinform., December, 2015
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
J. Bioinform. Comput. Biol., 2015
Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s.
CoRR, 2015
Algorithms Mol. Biol., 2015
2014
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
Int. J. Comput. Biol. Drug Des., 2014
Discret. Math., 2014
Bioinform., 2014
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
Bioinform., 2014
Algorithms Mol. Biol., 2014
Algorithms Mol. Biol., 2014
Proceedings of the Advances in Bioinformatics and Computational Biology, 2014
Proceedings of the Advances in Bioinformatics and Computational Biology, 2014
Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014
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
Theory Biosci., 2013
IEEE ACM Trans. Comput. Biol. Bioinform., 2013
Nucleic Acids Res., 2013
Math. Comput. Sci., 2013
Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
Entropy, 2013
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.
Algorithms Mol. Biol., 2013
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013
Proceedings of the Advances in Bioinformatics and Computational Biology, 2013
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013
Proceedings of the Principles and Practice of Constraint Programming, 2013
2012
CoRR, 2012
Bioinform., 2012
Proceedings of the Advances in Bioinformatics and Computational Biology, 2012
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
Nucleic Acids Res., 2011
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
CoRR, 2011
BMC Bioinform., 2011
Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Bioinform., 2011
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.
Bioinform., 2011
Algorithms Mol. Biol., 2011
Proceedings of the Advances in Bioinformatics and Computational Biology, 2011
Proceedings of the Combinatorial Pattern Matching - 22nd Annual Symposium, 2011
2010
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
Bioinform., 2010
Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees.
Algorithms Mol. Biol., 2010
Proceedings of the Advances in Bioinformatics and Computational Biology, 2010
Proceedings of the Advances in Bioinformatics and Computational Biology, 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010
Proceedings of the Advances in Visual Computing - 6th International Symposium, 2010
Proceedings of the German Conference on Bioinformatics 2010, 2010
Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, 2010
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
Math. Comput. Sci., 2009
Discret. Appl. Math., 2009
Discret. Appl. Math., 2009
Bioinform., 2009
Bioinform., 2009
Partition function and base pairing probabilities for RNA-RNA interaction prediction.
Bioinform., 2009
Proceedings of the German Conference on Bioinformatics 2009, 2009
Proceedings of the Bildverarbeitung für die Medizin 2009: Algorithmen - Systeme, 2009
2008
BMC Bioinform., 2008
BMC Bioinform., 2008
Bioinform., 2008
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
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
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
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering.
PLoS Comput. Biol., 2007
Algorithms Mol. Biol., 2007
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007
Proceedings of the German Conference on Bioinformatics, 2007
Proceedings of the Foundations of Genetic Algorithms, 9th International Workshop, 2007
2006
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Nucleic Acids Res., 2006
Genom. Proteom. Bioinform., 2006
Discuss. Math. Graph Theory, 2006
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BMC Bioinform., 2006
Bioinform., 2006
Algorithms Mol. Biol., 2006
Algorithms Mol. Biol., 2006
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
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
BMC Bioinform., 2005
Bioinform., 2005
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
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
Theory Biosci., 2004
IEEE ACM Trans. Comput. Biol. Bioinform., 2004
Bioinform., 2004
Proceedings of the Computational Science, 2004
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004
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
J. Chem. Inf. Comput. Sci., 2002
Stochastic pairwise alignments.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002
2001
2000
J. Comput. Biol., 2000
1999
Comput. Chem., 1999
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
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
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
Discret. Math., 1995
1994
Comput. Chem., 1994