Peter F. Stadler

ORCID

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 170

Top Venues

CoRR

Algorithms Mol. Biol.

Bioinform.

BMC Bioinform.

Publications

Sarah von Löhneysen, Mario Mörl, Peter F. Stadler
Limits of experimental evidence in RNA secondary structure prediction. Frontiers Bioinform. 4 (2024)
Marcos E. González Laffitte, Peter F. Stadler
Progressive Multiple Alignment of Graphs. Algorithms 17 (3) (2024)
Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler
Transit functions and pyramid-like binary clustering systems. Discret. Appl. Math. 357 (2024)
Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler
Reaction rebalancing: a novel approach to curating reaction databases. J. Cheminformatics 16 (1) (2024)
John Anders, Peter F. Stadler
RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions. J. Integr. Bioinform. 20 (3) (2024)
José Antonio Ramírez-Rafael, Annachiara Korchmaros, Katia Aviña-Padilla, Alitzel López Sánchez, Andrea Arlette España-Tinajero, Marc Hellmuth, Peter F. Stadler, Maribel Hernández-Rosales
REvolutionH-tl: Reconstruction of Evolutionary Histories tool. RECOMB-CG (2024)
Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler
Transit Functions and Clustering Systems. CoRR (2024)
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. J. Comput. Biol. 31 (6) (2024)
Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, Peter F. Stadler
Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. CALDAM (2024)
Arun Anil, Manoj Changat, Lekshmi Kamal K. Sheela, Ameera Vaheeda Shanavas, John J. Chavara, Prasanth G. Narasimha-Shenoi, Bruno J. Schmidt, Peter F. Stadler
Directed Transit Functions. CoRR (2024)
David Schaller, Tom Hartmann, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Relative timing information and orthology in evolutionary scenarios. Algorithms Mol. Biol. 18 (1) (2023)
Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu
Fitch Graph Completion. CoRR (2023)
Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. BMC Bioinform. 24 (1) (2023)
Angel Garcia-Chung, Marisol Bermúdez-Montaña, Peter F. Stadler, Jürgen Jost, Guillermo Restrepo
Chemically inspired Erdős-Rényi oriented hypergraphs. CoRR (2023)
David Schaller, Marc Hellmuth, Peter F. Stadler
Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees. SIAM J. Discret. Math. 37 (3) (2023)
Annachiara Korchmaros, David Schaller, Marc Hellmuth, Peter F. Stadler
Quasi-best match graphs. Discret. Appl. Math. 331 (2023)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. ISBRA (2023)
Marc Hellmuth, Katharina T. Huber, Vincent Moulton, Guillaume E. Scholz, Peter F. Stadler
Injective Split Systems. Graphs Comb. 39 (4) (2023)
Jürgen Jost, Roberto Lalli, Manfred D. Laubichler, Eckehard Olbrich, Jürgen Renn, Guillermo Restrepo, Peter F. Stadler, Dirk Wintergrün
Computational History: Challenges and Opportunities of Formal Approaches. J. Soc. Comput. 4 (3) (2023)
Paul Klemm, Peter F. Stadler, Marcus Lechner
Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. Frontiers Bioinform. 3 (2023)
Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu
Fitch Graph Completion. COCOON (2) (2023)
Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, Peter F. Stadler
Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. CoRR (2023)
Richard A. Schäfer, Dominik Rabsch, Guillaume E. Scholz, Peter F. Stadler, Wolfgang R. Hess, Rolf Backofen, Jörg Fallmann, Björn Voß
RNA interaction format: a general data format for RNA interactions. Bioinform. 39 (10) (2023)
Marc Hellmuth, Peter F. Stadler
The Theory of Gene Family Histories. CoRR (2023)
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms Mol. Biol. 18 (1) (2023)
Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. ISBRA (2023)
Marc Hellmuth, David Schaller, Peter F. Stadler
Clustering systems of phylogenetic networks. Theory Biosci. 142 (4) (2023)
Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth
Planar median graphs and cubesquare-graphs. Discret. Appl. Math. 331 (2023)
Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K. Beckmann, Ivo L. Hofacker, Sarah von Löhneysen, Peter F. Stadler
Local RNA folding revisited. J. Bioinform. Comput. Biol. 21 (4) (2023)
Konstantin Klemm, Anita Mehta, Peter F. Stadler
Optimisation via encodings: a renormalisation group perspective. CoRR (2023)
Karl Käther, Steffen Lemke, Peter F. Stadler
Annotation-Free Identification of Potential Synteny Anchors. IWBBIO (1) (2023)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Best Match Graphs With Binary Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (3) (2023)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. CoRR (2023)
Franziska Reinhardt, Peter F. Stadler
ExceS-A: an exon-centric split aligner. J. Integr. Bioinform. 19 (1) (2022)
Dustyn Eggers, Christian Höner zu Siederdissen, Peter F. Stadler
Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar. BSB (2022)
Tom Hartmann, Max Bannach, Martin Middendorf, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Complete edge-colored permutation graphs. Adv. Appl. Math. 139 (2022)
Grover E. C. Guzman, Peter F. Stadler, André Fujita
Efficient eigenvalue counts for tree-like networks. J. Complex Networks 10 (5) (2022)
Carmen Bruckmann, Peter F. Stadler, Marc Hellmuth
From modular decomposition trees to rooted median graphs. Discret. Appl. Math. 310 (2022)
Peter F. Stadler, Sebastian Will
Bi-alignments with affine gaps costs. Algorithms Mol. Biol. 17 (1) (2022)
Marc Hellmuth, David Schaller, Peter F. Stadler
Clustering Systems of Phylogenetic Networks. CoRR (2022)
Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler
Generic Context-Aware Group Contributions. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Robson Bonidia, Anderson P. Avila-Santos, Breno Lívio Silva de Almeida, Peter F. Stadler, Ulisses Nunes da Rocha, Danilo Sipoli Sanches, André C. P. L. F. de Carvalho
BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria. Briefings Bioinform. 23 (4) (2022)
David Schaller, Tom Hartmann, Manuel Lafond, Nicolas Wieseke, Marc Hellmuth, Peter F. Stadler
Relative Timing Information and Orthology in Evolutionary Scenarios. CoRR (2022)
Anahy Santiago Arguello, Peter F. Stadler
Whitney's connectivity inequalities for directed hypergraphs. Art Discret. Appl. Math. 5 (1) (2022)
Marc Hellmuth, David Schaller, Peter F. Stadler
Compatibility of partitions with trees, hierarchies, and split systems. Discret. Appl. Math. 314 (2022)
Robson Parmezan Bonidia, Anderson P. Avila-Santos, Breno Lívio Silva de Almeida, Peter F. Stadler, Ulisses Nunes da Rocha, Danilo Sipoli Sanches, André C. P. L. F. de Carvalho
Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy. Entropy 24 (10) (2022)
Stefan Müller, Christoph Flamm, Peter F. Stadler
What makes a reaction network "chemical"? J. Cheminformatics 14 (1) (2022)
Dulce I. Valdivia, Maribel Hernández-Rosales, Manuela Geiß, Peter F. Stadler, Marc Hellmuth
Hierarchical and modularly-minimal vertex colorings. Art Discret. Appl. Math. 6 (2) (2022)
Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard, David Schaller, Peter F. Stadler
Combining Orthology and Xenology Data in a Common Phylogenetic Tree. BSB (2021)
Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. Briefings Bioinform. 22 (5) (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Least resolved trees for two-colored best match graphs. CoRR (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Least resolved trees for two-colored best match graphs. J. Graph Algorithms Appl. 25 (1) (2021)
David Schaller, Marc Hellmuth, Peter F. Stadler
A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set. CoRR (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. CoRR (2021)
Carmen Bruckmann, Peter F. Stadler, Marc Hellmuth
From Modular Decomposition Trees to Rooted Median Graphs. CoRR (2021)
Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth
Planar Median Graphs and Cubesquare-Graphs. CoRR (2021)
David Schaller, Marc Hellmuth, Peter F. Stadler
Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees. CoRR (2021)
John Anders, Hannes Petruschke, Nico Jehmlich, Sven-Bastiaan Haange, Martin von Bergen, Peter F. Stadler
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. BMC Bioinform. 22 (1) (2021)
Halima Saker, Rainer Machné, Jörg Fallmann, Douglas B. Murray, Ahmad M. Shahin, Peter F. Stadler
Weighted Consensus Segmentations. Comput. 9 (2) (2021)
Wilmer Leal, Guillermo Restrepo, Peter F. Stadler, Jürgen Jost
Forman-Ricci Curvature for hypergraphs. Adv. Complex Syst. 24 (1) (2021)
David Schaller, Peter F. Stadler, Marc Hellmuth
Complexity of modification problems for best match graphs. Theor. Comput. Sci. 865 (2021)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Defining Autocatalysis in Chemical Reaction Networks. CoRR (2021)
Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler
Compositional Properties of Alignments. Math. Comput. Sci. 15 (4) (2021)
Mirele C. S. F. Costa, João Victor de Araújo Oliveira, Waldeyr M. C. Silva, Rituparno Sen, Jörg Fallmann, Peter F. Stadler, Maria Emília M. T. Walter
Machine Learning Studies of Non-coding RNAs based on Artificially Constructed Training Data. BIOINFORMATICS (2021)
Jonas Coelho Kasmanas, Alexander Bartholomäus, Felipe Borim Corrêa, Tamara L. Tal, Nico Jehmlich, Gunda Herberth, Martin von Bergen, Peter F. Stadler, André Carlos Ponce de Leon Ferreira de Carvalho, Ulisses Nunes da Rocha
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. Nucleic Acids Res. 49 (Database-Issue) (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Best Match Graphs with Binary Trees. AlCoB (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. Algorithms 14 (4) (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Heuristic algorithms for best match graph editing. Algorithms Mol. Biol. 16 (1) (2021)
Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. Briefings Bioinform. 22 (5) (2021)
David Schaller, Marc Hellmuth, Peter F. Stadler
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set. Algorithms Mol. Biol. 16 (1) (2021)
Thomas Gatter, Peter F. Stadler
Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more. Bioinform. 37 (23) (2021)
Marc Hellmuth, David Schaller, Peter F. Stadler
Compatibility of Partitions, Hierarchies, and Split Systems. CoRR (2021)
David H. Wolpert, Michael H. Price, Stefani A. Crabtree, Timothy A. Kohler, Jürgen Jost, James Evans, Peter F. Stadler, Hajime Shimao, Manfred D. Laubichler
The Past as a Stochastic Process. CoRR (2021)
Fabian Gärtner, Felix Kühnl, Carsten R. Seemann, Christian Höner zu Siederdissen, Peter F. Stadler
Superbubbles as an empirical characteristic of directed networks. Netw. Sci. 9 (1) (2021)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Heuristic Algorithms for Best Match Graph Editing. CoRR (2021)
Grover E. C. Guzman, Peter F. Stadler, André Fujita
Efficient Laplacian spectral density computations for networks with arbitrary degree distributions. Netw. Sci. 9 (3) (2021)
Thomas Gatter, Sarah von Löhneysen, Jörg Fallmann, Polina Drozdova, Tom Hartmann, Peter F. Stadler
LazyB: fast and cheap genome assembly. Algorithms Mol. Biol. 16 (1) (2021)
Manoj Changat, Ferdoos Hossein Nezhad, Peter F. Stadler
Cut Vertex Transit Functions of Hypergraphs. CALDAM (2021)
Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard, David Schaller, Peter F. Stadler
Combining Orthology and Xenology Data in a Common Phylogenetic Tree. CoRR (2021)
Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler
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. 23 (1) (2021)
Adrian Fritz, Marc Hellmuth, Peter F. Stadler, Nicolas Wieseke
Cograph editing: Merging modules is equivalent to editing P_4s. Art Discret. Appl. Math. 3 (2) (2020)
Yangjing Long, Peter F. Stadler
Exact-2-relation graphs. Discret. Appl. Math. 285 (2020)
Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler
Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees. Discret. Appl. Math. 283 (2020)
Manoj Changat, Prasanth G. Narasimha-Shenoi, Ferdoos Hossein Nezhad, Matjaz Kovse, Shilpa Mohandas, Abisha Ramachandran, Peter F. Stadler
Transit sets of -point crossover operators. AKCE Int. J. Graphs Comb. 17 (1) (2020)
Dulce I. Valdivia, Manuela Geiß, Maribel Hernández-Rosales, Peter F. Stadler, Marc Hellmuth
Hierarchical and Modularly-Minimal Vertex Colorings. CoRR (2020)
Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. BSB (2020)
David Schaller, Peter F. Stadler, Marc Hellmuth
Complexity of Modification Problems for Best Match Graphs. CoRR (2020)
David Schaller, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Indirect Identification of Horizontal Gene Transfer. CoRR (2020)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) (2020)
Wim Hordijk, Stuart A. Kauffman, Peter F. Stadler
Average Fitness Differences on NK Landscapes. Theory Biosci. 139 (1) (2020)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS (2020)
David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
Best Match Graphs with Binary Trees. CoRR (2020)
Manuela M. do Almo, Isabel G. Sousa, Waldeyr Mendes Cordeiro da Silva, Thomas Gatter, Peter F. Stadler, Steve Hoffmann, Andrea Queiroz Maranhão, Marcelo M. Brigido
Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile. BSB (2020)
Angel E. Rodriguez-Fernandez, Bernardo A. Gonzalez-Torres, Ricardo Menchaca-Mendez, Peter F. Stadler
Clustering Improves the Goemans-Williamson Approximation for the Max-Cut Problem. Comput. 8 (3) (2020)
Marc Hellmuth, Manuela Geiß, Peter F. Stadler
Complexity of modification problems for reciprocal best match graphs. Theor. Comput. Sci. 809 (2020)
Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López, Marcos González Laffitte, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernandez-Rosales
From pairs of most similar sequences to phylogenetic best matches. Algorithms Mol. Biol. 15 (1) (2020)
Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, Peter F. Stadler
Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. WABI (2020)
Tom Hartmann, Max Bannach, Martin Middendorf, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Complete Edge-Colored Permutation Graphs. CoRR (2020)
Rituparno Sen, Jörg Fallmann, Maria Emília M. T. Walter, Peter F. Stadler
Are spliced ncRNA host genes distinct classes of lncRNAs? Theory Biosci. 139 (4) (2020)
Gábor Balogh, Stephan H. Bernhart, Peter F. Stadler, Jana Schor
A probabilistic version of Sankoff's maximum parsimony algorithm. J. Bioinform. Comput. Biol. 18 (1) (2020)

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Publication Activity (10 Years)

Top Topics

Top Venues

Peter F. Stadler