Peter F. Stadler

404 papers A* 1A 4B 5C 9Misc 4Journal 321Unranked 55

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Boredom as homeostasis of cognitive resource utilization using spiking neural networks. Neurocomputing Patrick Schöfer, James Danckert, Peter F. Stadler, Martin Bogdan
2026	J	`jnl`	Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data. Algorithms Mol. Biol. Nora Beier, Thomas Gatter, Jakob L. Andersen, Peter F. Stadler
2026	—	`conf`	Directed Weakly Modular Graphs and Their Directed Interval Functions. CALDAM Lekshmi Kamal K. Sheela, Manoj Changat, M. R. Chithra, Peter F. Stadler
2026	J	`jnl`	SynRXN: An Open Benchmark and Curated Dataset for Computational Reaction Modeling. CoRR Tieu-Long Phan, Nhu-Ngoc Nguyen Song, Peter F. Stadler
2025	—	`conf`	A Sankoff-Rousseau-Like Algorithm for Minimizing Lateral Gene Transfers and Losses on Single Origin Characters. RECOMB-CG Alitzel López Sánchez, Guillaume E. Scholz, Peter F. Stadler, Manuel Lafond
2025	J	`jnl`	Assembly in Directed Hypergraphs. CoRR Christoph Flamm, Daniel Merkle, Peter F. Stadler
2025	J	`jnl`	Characterizations of undirected 2-quasi best match graphs. CoRR Annachiara Korchmaros, Guillaume E. Scholz, Peter F. Stadler
2025	J	`jnl`	Crossover operators for molecular graphs with an application to virtual drug screening. J. Cheminformatics Nico Domschke, Bruno J. Schmidt, Thomas Gatter, Richard Golnik, Paul Eisenhuth, Fabian Liessmann, Jens Meiler, Peter F. Stadler
2025	C	`conf`	Extension of Partial Atom-To-Atom Maps: Uniqueness and Algorithms. WABI Marcos E. González Laffitte, Tieu-Long Phan, Peter F. Stadler
2025	—	`conf`	Integrating High-Throughput RNA-RNA Interaction Data Into RNA Secondary Structure Prediction. ISBRA (2) Denis Skibinski, Thomas Spicher, Leonhard Sidl, Paulína Holotová, Yingjie Pan, Maximilian Faissner, Cristian A. Velandia-Huerto, Ronny Lorenz, Maria Waldl, Hua-Ting Yao, Peter F. Stadler
2025	J	`jnl`	On the Cut-Vertex and the Interval Transit Functions of Hypergraphs. Graphs Comb. Ameera Vaheeda Shanavas, Manoj Changat, Peter F. Stadler
2025	J	`jnl`	Pathway Realizability in Chemical Networks. J. Comput. Biol. Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2025	J	`jnl`	Prime Implicant Explanations for Reaction Feasibility Prediction. CoRR Klaus Weinbauer, Tieu-Long Phan, Peter F. Stadler, Thomas Gärtner, Sagar Malhotra
2025	J	`jnl`	Primitive, edge-short, isometric, and pantochordal cycles. Art Discret. Appl. Math. Gover E. C. Guzman, Marcos E. González Laffitte, André Fujita, Peter F. Stadler
2025	J	`jnl`	TRAMbio: a flexible python package for graph rigidity analysis of macromolecules. BMC Bioinform. Nicolas Handke, Thomas Gatter, Franziska Reinhardt, Peter F. Stadler
2025	J	`jnl`	Transit functions and clustering systems. Art Discret. Appl. Math. Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler
2025	J	`jnl`	Unbiased anchors for reliable genome-wide synteny detection. Algorithms Mol. Biol. Karl Käther, Andreas Remmel, Steffen Lemke, Peter F. Stadler
2024	J	`jnl`	Core Potentials: The Consensus Segmentation Conjecture. Math. Comput. Sci. Anahy Santiago Arguello, Guillaume E. Scholz, Peter F. Stadler
2024	J	`jnl`	Democratising Artificial Intelligence for Pandemic Preparedness and Global Governance in Latin American and Caribbean Countries. CoRR André C. P. L. F. de Carvalho, Robson Bonidia, Jude Dzevela Kong, Mariana Dauhajre, Cláudio José Struchiner, Guilherme Tegoni Goedert, Peter F. Stadler, Maria Emília M. T. Walter, Danilo Sipoli Sanches, Troy Day, Marcia Castro, John Edmunds, Manuel Colomé-Hidalgo, Demian Arturo Herrera Morban, Edian F. Franco, Cesar Ugarte-Gil, Patricia Espinoza-Lopez, Gabriel Carrasco-Escobar, Ulisses Nunes da Rocha
2024	J	`jnl`	Directed Transit Functions. CoRR Arun Anil, Manoj Changat, Lekshmi Kamal K. Sheela, Ameera Vaheeda Shanavas, John J. Chavara, Prasanth G. Narasimha-Shenoi, Bruno J. Schmidt, Peter F. Stadler
2024	J	`jnl`	Limits of experimental evidence in RNA secondary structure prediction. Frontiers Bioinform. Sarah von Löhneysen, Mario Mörl, Peter F. Stadler
2024	J	`jnl`	Nesting of Touching Polygons. CoRR Carsten R. Seemann, Peter F. Stadler, Marc Hellmuth
2024	J	`jnl`	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 Marcos E. González Laffitte, Klaus Weinbauer, Tieu-Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, Peter F. Stadler
2024	J	`jnl`	Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. J. Comput. Biol. Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2024	J	`jnl`	Progressive Multiple Alignment of Graphs. Algorithms Marcos E. González Laffitte, Peter F. Stadler
2024	—	`conf`	REvolutionH-tl: Reconstruction of Evolutionary Histories tool. RECOMB-CG José Antonio Ramírez-Rafael, Annachiara Korchmaros, Katia Aviña-Padilla, Alitzel López Sánchez, Andrea Arlette España-Tinajero, Marc Hellmuth, Peter F. Stadler, Maribel Hernández-Rosales
2024	J	`jnl`	RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions. J. Integr. Bioinform. John Anders, Peter F. Stadler
2024	J	`jnl`	Reaction rebalancing: a novel approach to curating reaction databases. J. Cheminformatics Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler
2024	J	`jnl`	Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss. Adv. Appl. Math. Bruno J. Schmidt, Tom Hartmann, Peter F. Stadler
2024	—	`conf`	Squares in Cycles: Prediction of G-Quadruplexes in Circular RNA Secondary Stuctures. BSB Ronny Lorenz, Peter F. Stadler
2024	J	`jnl`	TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success. J. Integr. Bioinform. Gábor Balogh, Natasha Jorge, Célia Dupain, Maud Kamal, Nicolas Servant, Christophe Le Tourneau, Peter F. Stadler, Stephan H. Bernhart
2024	J	`jnl`	Transit Functions and Clustering Systems. CoRR Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler
2024	J	`jnl`	Transit functions and pyramid-like binary clustering systems. Discret. Appl. Math. Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler
2024	—	`conf`	Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. CALDAM Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, Peter F. Stadler
2023	—	`conf`	Annotation-Free Identification of Potential Synteny Anchors. IWBBIO (1) Karl Käther, Steffen Lemke, Peter F. Stadler
2023	J	`jnl`	Best Match Graphs With Binary Trees. IEEE ACM Trans. Comput. Biol. Bioinform. David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2023	J	`jnl`	Chemically inspired Erdős-Rényi oriented hypergraphs. CoRR Angel Garcia-Chung, Marisol Bermúdez-Montaña, Peter F. Stadler, Jürgen Jost, Guillermo Restrepo
2023	J	`jnl`	Clustering systems of phylogenetic networks. Theory Biosci. Marc Hellmuth, David Schaller, Peter F. Stadler
2023	J	`jnl`	Computational History: Challenges and Opportunities of Formal Approaches. J. Soc. Comput. Jürgen Jost, Roberto Lalli, Manfred D. Laubichler, Eckehard Olbrich, Jürgen Renn, Guillermo Restrepo, Peter F. Stadler, Dirk Wintergrün
2023	J	`jnl`	Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. BMC Bioinform. Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler
2023	—	`conf`	Fitch Graph Completion. COCOON (2) Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu
2023	J	`jnl`	Fitch Graph Completion. CoRR Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu
2023	J	`jnl`	Injective Split Systems. Graphs Comb. Marc Hellmuth, Katharina T. Huber, Vincent Moulton, Guillaume E. Scholz, Peter F. Stadler
2023	J	`jnl`	Local RNA folding revisited. J. Bioinform. Comput. Biol. Maria Waldl, Thomas Spicher, Ronny Lorenz, Irene K. Beckmann, Ivo L. Hofacker, Sarah von Löhneysen, Peter F. Stadler
2023	J	`jnl`	Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms Mol. Biol. Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2023	—	`conf`	On the Realisability of Chemical Pathways. ISBRA Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2023	J	`jnl`	On the Realisability of Chemical Pathways. CoRR Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2023	J	`jnl`	Optimisation via encodings: a renormalisation group perspective. CoRR Konstantin Klemm, Anita Mehta, Peter F. Stadler
2023	J	`jnl`	Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal Gene Transfer in Gene Trees. SIAM J. Discret. Math. David Schaller, Marc Hellmuth, Peter F. Stadler
2023	—	`conf`	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. ISBRA Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2023	J	`jnl`	Planar median graphs and cubesquare-graphs. Discret. Appl. Math. Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth
2023	J	`jnl`	Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. Frontiers Bioinform. Paul Klemm, Peter F. Stadler, Marcus Lechner
2023	J	`jnl`	Quasi-best match graphs. Discret. Appl. Math. Annachiara Korchmaros, David Schaller, Marc Hellmuth, Peter F. Stadler
2023	J	`jnl`	RNA interaction format: a general data format for RNA interactions. Bioinform. Richard A. Schäfer, Dominik Rabsch, Guillaume E. Scholz, Peter F. Stadler, Wolfgang R. Hess, Rolf Backofen, Jörg Fallmann, Björn Voß
2023	J	`jnl`	Relative timing information and orthology in evolutionary scenarios. Algorithms Mol. Biol. David Schaller, Tom Hartmann, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2023	J	`jnl`	The Theory of Gene Family Histories. CoRR Marc Hellmuth, Peter F. Stadler
2023	J	`jnl`	Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. CoRR Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, Peter F. Stadler
2022	—	`conf`	Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar. BSB Dustyn Eggers, Christian Höner zu Siederdissen, Peter F. Stadler
2022	J	`jnl`	AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories. Softw. David Schaller, Marc Hellmuth, Peter F. Stadler
2022	J	`jnl`	Bi-alignments with affine gaps costs. Algorithms Mol. Biol. Peter F. Stadler, Sebastian Will
2022	J	`jnl`	BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria. Briefings Bioinform. 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
2022	J	`jnl`	Clustering Systems of Phylogenetic Networks. CoRR Marc Hellmuth, David Schaller, Peter F. Stadler
2022	J	`jnl`	Compatibility of partitions with trees, hierarchies, and split systems. Discret. Appl. Math. Marc Hellmuth, David Schaller, Peter F. Stadler
2022	J	`jnl`	Complete edge-colored permutation graphs. Adv. Appl. Math. Tom Hartmann, Max Bannach, Martin Middendorf, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2022	J	`jnl`	Efficient eigenvalue counts for tree-like networks. J. Complex Networks Grover E. C. Guzman, Peter F. Stadler, André Fujita
2022	J	`jnl`	ExceS-A: an exon-centric split aligner. J. Integr. Bioinform. Franziska Reinhardt, Peter F. Stadler
2022	J	`jnl`	From modular decomposition trees to rooted median graphs. Discret. Appl. Math. Carmen Bruckmann, Peter F. Stadler, Marc Hellmuth
2022	J	`jnl`	Generic Context-Aware Group Contributions. IEEE ACM Trans. Comput. Biol. Bioinform. Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler
2022	J	`jnl`	Hierarchical and modularly-minimal vertex colorings. Art Discret. Appl. Math. Dulce I. Valdivia, Maribel Hernández-Rosales, Manuela Geiß, Peter F. Stadler, Marc Hellmuth
2022	J	`jnl`	Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy. Entropy 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
2022	J	`jnl`	Relative Timing Information and Orthology in Evolutionary Scenarios. CoRR David Schaller, Tom Hartmann, Manuel Lafond, Nicolas Wieseke, Marc Hellmuth, Peter F. Stadler
2022	J	`jnl`	What makes a reaction network "chemical"? J. Cheminformatics Stefan Müller, Christoph Flamm, Peter F. Stadler
2022	J	`jnl`	Whitney's connectivity inequalities for directed hypergraphs. Art Discret. Appl. Math. Anahy Santiago Arguello, Peter F. Stadler
2021	J	`jnl`	A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic Trees on a Common Leaf Set. CoRR David Schaller, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set. Algorithms Mol. Biol. David Schaller, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. BMC Bioinform. John Anders, Hannes Petruschke, Nico Jehmlich, Sven-Bastiaan Haange, Martin von Bergen, Peter F. Stadler
2021	—	`ed.`	Advances in Bioinformatics and Computational Biology - 14th Brazilian Symposium on Bioinformatics, BSB 2021, Virtual Event, November 22-26, 2021, Proceedings BSB Peter F. Stadler, Maria Emília M. T. Walter, Maribel Hernandez-Rosales, Marcelo M. Brigido
2021	J	`jnl`	Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. Algorithms David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. CoRR David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	—	`conf`	Best Match Graphs with Binary Trees. AlCoB David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	—	`conf`	Combining Orthology and Xenology Data in a Common Phylogenetic Tree. BSB Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard, David Schaller, Peter F. Stadler
2021	J	`jnl`	Combining Orthology and Xenology Data in a Common Phylogenetic Tree. CoRR Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard, David Schaller, Peter F. Stadler
2021	J	`jnl`	Compatibility of Partitions, Hierarchies, and Split Systems. CoRR Marc Hellmuth, David Schaller, Peter F. Stadler
2021	J	`jnl`	Complexity of modification problems for best match graphs. Theor. Comput. Sci. David Schaller, Peter F. Stadler, Marc Hellmuth
2021	J	`jnl`	Compositional Properties of Alignments. Math. Comput. Sci. Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler
2021	J	`jnl`	Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. Briefings Bioinform. Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
2021	—	`conf`	Cut Vertex Transit Functions of Hypergraphs. CALDAM Manoj Changat, Ferdoos Hossein Nezhad, Peter F. Stadler
2021	J	`jnl`	Defining Autocatalysis in Chemical Reaction Networks. CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2021	J	`jnl`	Efficient Laplacian spectral density computations for networks with arbitrary degree distributions. Netw. Sci. Grover E. C. Guzman, Peter F. Stadler, André Fujita
2021	J	`jnl`	Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. Briefings Bioinform. Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger
2021	J	`jnl`	Forman-Ricci Curvature for hypergraphs. Adv. Complex Syst. Wilmer Leal, Guillermo Restrepo, Peter F. Stadler, Jürgen Jost
2021	J	`jnl`	From Modular Decomposition Trees to Rooted Median Graphs. CoRR Carmen Bruckmann, Peter F. Stadler, Marc Hellmuth
2021	J	`jnl`	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. Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler
2021	J	`jnl`	Heuristic Algorithms for Best Match Graph Editing. CoRR David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	Heuristic algorithms for best match graph editing. Algorithms Mol. Biol. David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. Nucleic Acids Res. 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
2021	J	`jnl`	LazyB: fast and cheap genome assembly. Algorithms Mol. Biol. Thomas Gatter, Sarah von Löhneysen, Jörg Fallmann, Polina Drozdova, Tom Hartmann, Peter F. Stadler
2021	J	`jnl`	Least resolved trees for two-colored best match graphs. CoRR David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	Least resolved trees for two-colored best match graphs. J. Graph Algorithms Appl. David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2021	—	`conf`	Machine Learning Studies of Non-coding RNAs based on Artificially Constructed Training Data. BIOINFORMATICS 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
2021	J	`jnl`	Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees. CoRR David Schaller, Marc Hellmuth, Peter F. Stadler
2021	J	`jnl`	Planar Median Graphs and Cubesquare-Graphs. CoRR Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth
2021	J	`jnl`	Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more. Bioinform. Thomas Gatter, Peter F. Stadler
2021	J	`jnl`	Superbubbles as an empirical characteristic of directed networks. Netw. Sci. Fabian Gärtner, Felix Kühnl, Carsten R. Seemann, Christian Höner zu Siederdissen, Peter F. Stadler
2021	J	`jnl`	The Past as a Stochastic Process. CoRR David H. Wolpert, Michael H. Price, Stefani A. Crabtree, Timothy A. Kohler, Jürgen Jost, James Evans, Peter F. Stadler, Hajime Shimao, Manfred D. Laubichler
2021	J	`jnl`	Weighted Consensus Segmentations. Comput. Halima Saker, Rainer Machné, Jörg Fallmann, Douglas B. Murray, Ahmad M. Shahin, Peter F. Stadler
2020	J	`jnl`	A probabilistic version of Sankoff's maximum parsimony algorithm. J. Bioinform. Comput. Biol. Gábor Balogh, Stephan H. Bernhart, Peter F. Stadler, Jana Schor
2020	—	`conf`	Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile. BSB 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
2020	J	`jnl`	Are spliced ncRNA host genes distinct classes of lncRNAs? Theory Biosci. Rituparno Sen, Jörg Fallmann, Maria Emília M. T. Walter, Peter F. Stadler
2020	J	`jnl`	Average Fitness Differences on NK Landscapes. Theory Biosci. Wim Hordijk, Stuart A. Kauffman, Peter F. Stadler
2020	J	`jnl`	Best Match Graphs with Binary Trees. CoRR David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler
2020	J	`jnl`	Clustering Improves the Goemans-Williamson Approximation for the Max-Cut Problem. Comput. Angel E. Rodriguez-Fernandez, Bernardo A. Gonzalez-Torres, Ricardo Menchaca-Méndez, Peter F. Stadler
2020	J	`jnl`	Cograph editing: Merging modules is equivalent to editing P_4s. Art Discret. Appl. Math. Adrian Fritz, Marc Hellmuth, Peter F. Stadler, Nicolas Wieseke
2020	J	`jnl`	Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. CoRR David Schaller, Manuela Geiß, Peter F. Stadler, Marc Hellmuth
2020	J	`jnl`	Complete Edge-Colored Permutation Graphs. CoRR Tom Hartmann, Max Bannach, Martin Middendorf, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2020	J	`jnl`	Complexity of Modification Problems for Best Match Graphs. CoRR David Schaller, Peter F. Stadler, Marc Hellmuth
2020	J	`jnl`	Complexity of modification problems for reciprocal best match graphs. Theor. Comput. Sci. Marc Hellmuth, Manuela Geiß, Peter F. Stadler
2020	—	`conf`	Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. BSB Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm
2020	C	`conf`	Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. WABI Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, Peter F. Stadler
2020	—	`conf`	Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2020	—	`conf`	Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2020	J	`jnl`	Exact-2-relation graphs. Discret. Appl. Math. Yangjing Long, Peter F. Stadler
2020	J	`jnl`	From pairs of most similar sequences to phylogenetic best matches. Algorithms Mol. Biol. Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos E. González Laffitte, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernandez-Rosales
2020	J	`jnl`	Generalized Fitch Graphs III: Symmetrized Fitch maps and Sets of Symmetric Binary Relations that are explained by Unrooted Edge-labeled Trees. CoRR Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler
2020	J	`jnl`	Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees. Discret. Appl. Math. Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler
2020	J	`jnl`	Hierarchical and Modularly-Minimal Vertex Colorings. CoRR Dulce I. Valdivia, Manuela Geiß, Maribel Hernández-Rosales, Peter F. Stadler, Marc Hellmuth
2020	J	`jnl`	Indirect Identification of Horizontal Gene Transfer. CoRR David Schaller, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2020	J	`jnl`	Superbubbles as an Empirical Characteristic of Directed Networks. CoRR Fabian Gärtner, Felix Kühnl, Carsten R. Seemann, Christian Höner zu Siederdissen, Peter F. Stadler
2020	J	`jnl`	TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. Nucleic Acids Res. Felipe Borim Corrêa, João Pedro Saraiva, Peter F. Stadler, Ulisses Nunes da Rocha
2020	J	`jnl`	Transit sets of -point crossover operators. AKCE Int. J. Graphs Comb. Manoj Changat, Prasanth G. Narasimha-Shenoi, Ferdoos Hossein Nezhad, Matjaz Kovse, Shilpa Mohandas, Abisha Ramachandran, Peter F. Stadler
2019	—	`conf`	A General Framework for Exact Partially Local Alignments. BIOINFORMATICS Falco Kirchner, Nancy Retzlaff, Peter F. Stadler
2019	J	`jnl`	Automatic curation of large comparative animal MicroRNA datasets. Bioinform. Ali M. Yazbeck, Peter F. Stadler, Kifah Tout, Jörg Fallmann
2019	J	`jnl`	Axiomatic characterization of transit functions of weak hierarchies. Art Discret. Appl. Math. Manoj Changat, Prasanth G. Narasimha-Shenoi, Peter F. Stadler
2019	J	`jnl`	Best Match Graphs and Reconciliation of Gene Trees with Species Trees. CoRR Manuela Geiß, Marcos González, Alitzel López Sánchez, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández-Rosales, Peter F. Stadler
2019	—	`conf`	Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. CIBB Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler
2019	J	`jnl`	Big Data Competence Center ScaDS Dresden/Leipzig: Overview and selected research activities. Datenbank-Spektrum Erhard Rahm, Wolfgang E. Nagel, Eric Peukert, René Jäkel, Fabian Gärtner, Peter F. Stadler, Daniel Wiegreffe, Dirk Zeckzer, Wolfgang Lehner
2019	J	`jnl`	Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. IEEE ACM Trans. Comput. Biol. Bioinform. Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2019	J	`jnl`	Complexity of Modification Problems for Reciprocal Best Match Graphs. CoRR Marc Hellmuth, Manuela Geiß, Peter F. Stadler
2019	J	`jnl`	Direct Superbubble Detection. Algorithms Fabian Gärtner, Peter F. Stadler
2019	J	`jnl`	Generalized Fitch Relations II: Sets of Binary Relations that are explained by Edge-labeled Trees. CoRR Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler
2019	J	`jnl`	Hierarchical Colorings of Cographs. CoRR Dulce I. Valdivia, Manuela Geiß, Marc Hellmuth, Maribel Hernández-Rosales, Peter F. Stadler
2019	J	`jnl`	RNApuzzler: efficient outerplanar drawing of RNA-secondary structures. Bioinform. Daniel Wiegreffe, Daniel Alexander, Peter F. Stadler, Dirk Zeckzer
2019	J	`jnl`	Ryūtō: network-flow based transcriptome reconstruction. BMC Bioinform. Thomas Gatter, Peter F. Stadler
2019	J	`jnl`	SSS-test: a novel test for detecting positive selection on RNA secondary structure. BMC Bioinform. Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjic, Peter F. Stadler, Katja Nowick
2019	J	`jnl`	The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Res. Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning
2019	J	`jnl`	flowEMMi: an automated model-based clustering tool for microbial cytometric data. BMC Bioinform. Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller
2018	J	`jnl`	A short note on undirected Fitch graphs. Art Discret. Appl. Math. Marc Hellmuth, Yangjing Long, Manuela Geiß, Peter F. Stadler
2018	J	`jnl`	Accurate mapping of tRNA reads. Bioinform. Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl, Peter F. Stadler, Fabian Amman
2018	J	`jnl`	Accurate mapping of tRNA reads. Bioinform. Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl, Peter F. Stadler, Fabian Amman
2018	J	`jnl`	Alignments as Compositional Structures. CoRR Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler
2018	J	`jnl`	Axiomatic characterization of transit functions of hierarchies. Ars Math. Contemp. Manoj Changat, Ferdoos Hossein Nezhad, Peter F. Stadler
2018	J	`jnl`	Coordinate systems for supergenomes. Algorithms Mol. Biol. Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller, Peter F. Stadler
2018	J	`jnl`	Finding the K best synthesis plans. J. Cheminformatics Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler
2018	J	`jnl`	Forman-Ricci Curvature for Hypergraphs. CoRR Wilmer Leal, Guillermo Restrepo, Peter F. Stadler, Jürgen Jost
2018	J	`jnl`	Partially Local Multi-way Alignments. Math. Comput. Sci. Nancy Retzlaff, Peter F. Stadler
2018	J	`jnl`	Patterning the insect eye: From stochastic to deterministic mechanisms. PLoS Comput. Biol. Haleh Ebadi, Michael Perry, Keith Short, Konstantin Klemm, Claude Desplan, Peter F. Stadler, Anita Mehta
2018	J	`jnl`	Phylogenetics beyond biology. Theory Biosci. Nancy Retzlaff, Peter F. Stadler
2018	J	`jnl`	Split-inducing indels in phylogenomic analysis. Algorithms Mol. Biol. Alexander Donath, Peter F. Stadler
2018	J	`jnl`	Superbubbles revisited. Algorithms Mol. Biol. Fabian Gärtner, Lydia Müller, Peter F. Stadler
2018	J	`jnl`	Time-consistent reconciliation maps and forbidden time travel. Algorithms Mol. Biol. Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2018	J	`jnl`	ceRNAs in plants: computational approaches and associated challenges for target mimic research. Briefings Bioinform. Alexandre Rossi Paschoal, Irma Lozada-Chávez, Douglas Silva Domingues, Peter F. Stadler
2017	J	`jnl`	A Short Note on Undirected Fitch Graphs. CoRR Manuela Geiß, Marc Hellmuth, Yangjing Long, Peter F. Stadler
2017	J	`jnl`	A Survey on Hypergraph Products (Erratum). CoRR Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
2017	J	`jnl`	Algebraic Dynamic Programming on Trees. Algorithms Sarah Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler
2017	J	`jnl`	Algorithmic Cheminformatics (Dagstuhl Seminar 17452). Dagstuhl Reports Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017	J	`jnl`	An Intermediate Level of Abstraction for Computational Systems Chemistry. CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017	B	`conf`	Chemical Graph Transformation with Stereo-Information. ICGT Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017	J	`jnl`	Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017	J	`jnl`	Design of Artificial Riboswitches as Biosensors. Sensors Sven Findeiß, Maja Etzel, Sebastian Will, Mario Mörl, Peter F. Stadler
2017	C	`conf`	Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. WABI Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2017	J	`jnl`	Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. CoRR Nikolai Nøjgaard, Manuela Geiß, Peter F. Stadler, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth
2017	J	`jnl`	From event labeled gene trees to species trees. CoRR Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler
2017	J	`jnl`	Local algorithms for the prime factorization of strong product graphs. CoRR Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler
2017	J	`jnl`	Merging Modules is equivalent to Editing P4's. CoRR Marc Hellmuth, Adrian Fritz, Nicolas Wieseke, Peter F. Stadler
2017	J	`jnl`	Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. Algorithms Mol. Biol. Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler
2017	J	`jnl`	Phylogenomics with Paralogs. CoRR Marc Hellmuth, Nicolas Wieseke, Marcus Lechner, Hans-Peter Lenhof, Martin Middendorf, Peter F. Stadler
2017	J	`jnl`	Reconstructing Gene Trees From Fitch's Xenology Relation. CoRR Manuela Geiß, John Anders, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
2017	J	`jnl`	The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen
2017	J	`jnl`	Topological Representation of the Transit Sets of k-Point Crossover Operators. CoRR Manoj Changat, Prasanth G. Narasimha-Shenoi, Ferdoos Hossein Nezhad, Matjaz Kovse, Shilpa Mohandas, Abisha Ramachandran, Peter F. Stadler
2017	J	`jnl`	Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution. J. Integr. Bioinform. Ali M. Yazbeck, Kifah R. Tout, Peter F. Stadler, Jana Hertel
2017	J	`jnl`	Tractable RNA-ligand interaction kinetics. BMC Bioinform. Felix Kühnl, Peter F. Stadler, Sebastian Will
2016	B	`conf`	A Software Package for Chemically Inspired Graph Transformation. ICGT Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2016	J	`jnl`	A Software Package for Chemically Inspired Graph Transformation. CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2016	J	`jnl`	Algebraic dynamic programming for multiple context-free grammars. Theor. Comput. Sci. Maik Riechert, Christian Höner zu Siederdissen, Peter F. Stadler
2016	J	`jnl`	Associativity and Non-Associativity of Some Hypergraph Products. Math. Comput. Sci. Richard H. Hammack, Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
2016	B	`conf`	Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. ICGT Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
2016	J	`jnl`	Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. CoRR Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
2016	J	`jnl`	Design specifications for cellular regulation. Theory Biosci. David C. Krakauer, Lydia Müller, Sonja J. Prohaska, Peter F. Stadler
2016	J	`jnl`	Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary Events. CoRR Marc Hellmuth, Maribel Hernandez-Rosales, Yangjing Long, Peter F. Stadler
2016	J	`jnl`	Pseudoknots in RNA folding landscapes. Bioinform. Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
2016	J	`jnl`	RNA folding with hard and soft constraints. Algorithms Mol. Biol. Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
2016	J	`jnl`	Read mapping. it Inf. Technol. Steve Hoffmann, Peter F. Stadler
2016	J	`jnl`	SHAPE directed RNA folding. Bioinform. Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
2016	J	`jnl`	SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. BMC Bioinform. João Victor de Araújo Oliveira, Fabrizio Costa, Rolf Backofen, Peter F. Stadler, Maria Emília Telles Walter, Jana Hertel
2016	J	`jnl`	The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations. CoRR Marc Hellmuth, Peter F. Stadler, Nicolas Wieseke
2016	J	`jnl`	The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. Algorithms Mol. Biol. Henrike Indrischek, Nicolas Wieseke, Peter F. Stadler, Sonja J. Prohaska
2015	J	`jnl`	A simple data-adaptive probabilistic variant calling model. Algorithms Mol. Biol. Steve Hoffmann, Peter F. Stadler, Korbinian Strimmer
2015	J	`jnl`	Algebraic Dynamic Programming over general data structures. BMC Bioinform. Christian Höner zu Siederdissen, Sonja J. Prohaska, Peter F. Stadler
2015	J	`jnl`	Connectivity Spaces. Math. Comput. Sci. Bärbel M. R. Stadler, Peter F. Stadler
2015	J	`jnl`	Evolution of 3'UTR-associated RNAs. BMC Bioinform. Jan Engelhardt, Peter F. Stadler
2015	J	`jnl`	Knowledge-based reasoning to annotate noncoding RNA using multi-agent system. J. Bioinform. Comput. Biol. Wosley Arruda, Daniel S. Souza, Célia Ghedini Ralha, Maria Emília M. T. Walter, Tainá Raiol, Marcelo M. Brigido, Peter F. Stadler
2015	J	`jnl`	Product Grammars for Alignment and Folding. IEEE ACM Trans. Comput. Biol. Bioinform. Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
2015	J	`jnl`	Spiders can be Recognized by Counting Their Legs. Math. Comput. Sci. Sarah Berkemer, Ricardo Régis Cavalcante Chaves, Adrian Fritz, Marc Hellmuth, Maribel Hernandez-Rosales, Peter F. Stadler
2015	J	`jnl`	Support for Eschenmoser's Glyoxylate Scenario. CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2015	J	`jnl`	Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s. CoRR Marc Hellmuth, Adrian Fritz, Nicolas Wieseke, Peter F. Stadler
2015	J	`jnl`	The Grid Property and Product-Like Hypergraphs. Graphs Comb. Lydia Ostermeier, Peter F. Stadler
2015	J	`jnl`	The relativity of biological function. Theory Biosci. Manfred D. Laubichler, Peter F. Stadler, Sonja J. Prohaska, Katja Nowick
2015	J	`jnl`	The relaxed square property. Australas. J Comb. Marc Hellmuth, Tilen Marc, Lydia Ostermeier, Peter F. Stadler
2014	—	`conf`	50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. FMMB Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014	C	`conf`	A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. WABI Sebastian Will, Peter F. Stadler
2014	J	`jnl`	A priori assessment of data quality in molecular phylogenetics. Algorithms Mol. Biol. Bernhard Misof, Karen Meusemann, Björn Marcus von Reumont, Patrick Kück, Sonja J. Prohaska, Peter F. Stadler
2014	J	`jnl`	Algorithmic Cheminformatics (Dagstuhl Seminar 14452). Dagstuhl Reports Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014	J	`jnl`	Atom mapping with constraint programming. Algorithms Mol. Biol. Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm
2014	J	`jnl`	Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. Bioinform. Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin
2014	J	`jnl`	Challenges in RNA virus bioinformatics. Bioinform. Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer
2014	—	`conf`	Comparative Detection of Processed Small RNAs in Archaea. IWBBIO Christian Höner zu Siederdissen, Sarah Berkemer, Fabian Amman, Axel Wintsche, Sebastian Will, Sonja J. Prohaska, Peter F. Stadler
2014	J	`jnl`	Convex cycle bases. Ars Math. Contemp. Marc Hellmuth, Josef Leydold, Peter F. Stadler
2014	—	`conf`	Dynamic Programming for Set Data Types. BSB Christian Höner zu Siederdissen, Sonja J. Prohaska, Peter F. Stadler
2014	J	`jnl`	Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des. Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014	—	`conf`	Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115. BSB Hugo W. Schneider, Sebastian Bartschat, Gero Doose, Lucas Maciel, Erick Pizani, Marcelo Bassani, Fernando Araripe Torres, Sebastian Will, Tainá Raiol, Marcelo M. Brigido, Maria Emília Telles Walter, Peter F. Stadler
2014	J	`jnl`	Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. Algorithms Mol. Biol. Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler, Rolf Backofen
2014	J	`jnl`	Lacking alignments? The next-generation sequencing mapper segemehl revisited. Bioinform. Christian Otto, Peter F. Stadler, Steve Hoffmann
2014	—	`ch.`	Rugged and Elementary Landscapes. Theory and Principled Methods for the Design of Metaheuristics Konstantin Klemm, Peter F. Stadler
2014	J	`jnl`	Simulation of gene family histories. BMC Bioinform. Maribel Hernandez-Rosales, Nicolas Wieseke, Marc Hellmuth, Peter F. Stadler
2014	J	`jnl`	Spiders can be recognized by counting their legs. CoRR Sarah Berkemer, Ricardo Régis Cavalcante Chaves, Adrian Fritz, Marc Hellmuth, Maribel Hernandez-Rosales, Peter F. Stadler
2014	J	`jnl`	TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinform. Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß
2014	J	`jnl`	The Relaxed Square Property. CoRR Marc Hellmuth, Tilen Marc, Lydia Ostermeier, Peter F. Stadler
2014	J	`jnl`	The genome of the recently domesticated crop plant sugar beet ( Nat. Juliane C. Dohm, André E. Minoche, Daniela Holtgräwe, Salvador Capella-Gutiérrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Thomas Rosleff Sörensen, Ralf Stracke, Richard Reinhardt, Alexander Goesmann, Thomas Kraft, Britta Schulz, Peter F. Stadler, Thomas Schmidt, Toni Gabaldón, Hans Lehrach, Bernd Weisshaar, Heinz Himmelbauer
2014	J	`jnl`	Unique square property, equitable partitions, and product-like graphs. Discret. Math. Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
2014	J	`jnl`	snoStrip: a snoRNA annotation pipeline. Bioinform. Sebastian Bartschat, Stephanie Kehr, Hakim Tafer, Peter F. Stadler, Jana Hertel
2013	J	`jnl`	2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
2013	A	`conf`	Atom Mapping with Constraint Programming. CP Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm
2013	C	`conf`	Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. WABI Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler
2013	J	`jnl`	Generic Strategies for Chemical Space Exploration CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2013	—	`conf`	How to Multiply Dynamic Programming Algorithms. BSB Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
2013	J	`jnl`	LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol. Biol. Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen
2013	J	`jnl`	Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, Peter F. Stadler
2013	J	`jnl`	On the Complexity of Reconstructing Chemical Reaction Networks. CoRR Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
2013	J	`jnl`	On the Complexity of Reconstructing Chemical Reaction Networks. Math. Comput. Sci. Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
2013	J	`jnl`	Relations between graphs. Ars Math. Contemp. Jan Hubicka, Jürgen Jost, Yangjing Long, Peter F. Stadler, Ling Yang
2013	J	`jnl`	Square Property, Equitable Partitions, and Product-like Graphs CoRR Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
2013	J	`jnl`	The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res. Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
2013	—	`conf`	The Trouble with Long-Range Base Pairs in RNA Folding. BSB Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, Sebastian Will
2013	J	`jnl`	The correlation of genome size and DNA methylation rate in metazoans. Theory Biosci. Marcus Lechner, Manja Marz, Christian Ihling, Andrea Sinz, Peter F. Stadler, Veiko Krauss
2013	—	`conf`	ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation. BSB Wosley Arruda, Célia Ghedini Ralha, Tainá Raiol, Marcelo M. Brigido, Maria Emília M. T. Walter, Peter F. Stadler
2012	J	`jnl`	A Survey on Hypergraph Products. Math. Comput. Sci. Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
2012	—	`conf`	A Visual Cross-Database Comparison of Metabolic Networks. ISVC (2) Markus Rohrschneider, Peter F. Stadler, Gerik Scheuermann
2012	J	`jnl`	Addendum: topology and prediction of RNA pseudoknots. Bioinform. Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel
2012	J	`jnl`	Diagonalized Cartesian products of s-prime graphs are s-prime. Discret. Math. Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
2012	J	`jnl`	Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinform. Christian Otto, Peter F. Stadler, Steve Hoffmann
2012	J	`jnl`	From event-labeled gene trees to species trees. BMC Bioinform. Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler
2012	J	`jnl`	Hidden treasures in unspliced EST data. Theory Biosci. Jan Engelhardt, Peter F. Stadler
2012	J	`jnl`	Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2012	J	`jnl`	Minimum cycle bases of lexicographic products. Ars Math. Contemp. Marc Hellmuth, Philipp-Jens Ostermeier, Peter F. Stadler
2012	—	`conf`	RNA Folding Algorithms with G-Quadruplexes. BSB Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler
2012	J	`jnl`	Symmetric circular matchings and RNA folding. Discret. Math. Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler
2012	J	`jnl`	The Cartesian product of hypergraphs. J. Graph Theory Lydia Ostermeier, Marc Hellmuth, Peter F. Stadler
2012	J	`jnl`	deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinform. David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin
2011	J	`jnl`	A folding algorithm for extended RNA secondary structures. Bioinform. Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
2011	J	`jnl`	Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinform. Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler
2011	J	`jnl`	DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, Steve Hoffmann
2011	J	`jnl`	Fast accessibility-based prediction of RNA-RNA interactions. Bioinform. Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker
2011	J	`jnl`	Fast local fragment chaining using sum-of-pair gap costs. Algorithms Mol. Biol. Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler
2011	J	`jnl`	In Silico Evolution of Early Metabolism. Artif. Life Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, Christoph Flamm
2011	J	`jnl`	Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete CoRR Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2011	—	`conf`	MicroRNA or Not MicroRNA? BSB David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, Peter F. Stadler
2011	J	`jnl`	PLEXY: efficient target prediction for box C/D snoRNAs. Bioinform. Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, Hakim Tafer
2011	B	`conf`	Phylogenetic Footprinting and Consistent Sets of Local Aligments. CPM Wolfgang Otto, Peter F. Stadler, Sonja J. Prohaska
2011	J	`jnl`	Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinform. Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F. Stadler, Sonja J. Prohaska
2011	J	`jnl`	RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res. Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker
2011	J	`jnl`	Topology and prediction of RNA pseudoknots. Bioinform. Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel
2011	J	`jnl`	ViennaRNA Package 2.0. Algorithms Mol. Biol. Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
2011	J	`jnl`	maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinform. Peter Menzel, Peter F. Stadler, Jan Gorodkin
2010	—	`ed.`	Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings BSB Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler
2010	—	`conf`	Detection of Protein Domains in Eukaryotic Genome Sequences. BSB Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
2010	—	`conf`	Evolution of the Long Non-coding RNAs MALAT1 and MEN BSB Peter F. Stadler
2010	J	`jnl`	G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinform. Mario Fasold, Peter F. Stadler, Hans Binder
2010	Misc	`conf`	Identification and Classification of Small RNAs in Transcriptome Sequence Data. Pacific Symposium on Biocomputing David Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann
2010	C	`conf`	In Silico Evolution of Early Metabolism. ALIFE Alexander Ullrich, Christoph Flamm, Markus Rohrschneider, Peter F. Stadler
2010	J	`jnl`	Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Algorithms Mol. Biol. Christian Arnold, Peter F. Stadler
2010	—	`conf`	Quantitative Comparison of Genomic-Wide Protein Domain Distributions. GCB Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
2010	Misc	`conf`	RNAz 2.0: Improved Noncoding RNA Detection. Pacific Symposium on Biocomputing Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
2010	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler
2010	J	`jnl`	Target prediction and a statistical sampling algorithm for RNA-RNA interaction. Bioinform. Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler
2010	J	`jnl`	Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History. J. Bioinform. Comput. Biol. Manja Marz, Nathalie Vanzo, Peter F. Stadler
2010	J	`jnl`	The primary transcriptome of the major human pathogen Nat. Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jérémy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler, Jörg Vogel
2010	—	`conf`	Visual Network Analysis of Dynamic Metabolic Pathways. ISVC (1) Markus Rohrschneider, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, Gerik Scheuermann
2010	J	`jnl`	Visualization of Graph Products. IEEE Trans. Vis. Comput. Graph. Stefan Jänicke, Christian Heine, Marc Hellmuth, Peter F. Stadler, Gerik Scheuermann
2009	J	`jnl`	A Topological Approach to Chemical Organizations. Artif. Life Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler
2009	J	`jnl`	A note on fundamental, non-fundamental, and robust cycle bases. Discret. Appl. Math. Konstantin Klemm, Peter F. Stadler
2009	J	`jnl`	A note on quasi-robust cycle bases. Ars Math. Contemp. Philipp-Jens Ostermeier, Marc Hellmuth, Josef Leydold, Konstantin Klemm, Peter F. Stadler
2009	J	`jnl`	Approximate graph products. Eur. J. Comb. Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler
2009	—	`conf`	Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns. Bildverarbeitung für die Medizin Andreas Heffel, Sonja J. Prohaska, Peter F. Stadler, Gerhard Kauer, Jens-Peer Kuska
2009	J	`jnl`	Defining genes: a computational framework. Theory Biosci. Peter F. Stadler, Sonja J. Prohaska, Christian V. Forst, David C. Krakauer
2009	J	`jnl`	Discovering cis-regulatory modules by optimizing barbecues. Discret. Appl. Math. Axel Mosig, Türker Bíyíkoglu, Sonja J. Prohaska, Peter F. Stadler
2009	J	`jnl`	Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinform. David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovich, Peter F. Stadler
2009	J	`jnl`	FRANz: reconstruction of wild multi-generation pedigrees. Bioinform. Markus Riester, Peter F. Stadler, Konstantin Klemm
2009	J	`jnl`	Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Comput. Biol. Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller
2009	—	`ed.`	German Conference on Bioinformatics 2009, 28th to 30th September 2009, Martin Luther University Halle-Wittenberg, Germany GCB Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, Peter F. Stadler
2009	J	`jnl`	Local Algorithms for the Prime Factorization of Strong Product Graphs. Math. Comput. Sci. Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler
2009	—	`conf`	Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. GCB Peter Menzel, Jan Gorodkin, Peter F. Stadler
2009	J	`jnl`	Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinform. Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler
2009	J	`jnl`	Preface. Discret. Appl. Math. Andreas W. M. Dress, Bülent Karasözen, Peter F. Stadler, Gerhard-Wilhelm Weber
2009	J	`jnl`	Sequence assembly. Comput. Biol. Chem. K. Scheibye-Alsing, Steve Hoffmann, A. Frankel, Peter Jensen, Peter F. Stadler, Y. Mang, Niels Tommerup, M. J. Gilchrist, A.-B. Nygård, Susanna Cirera, Claus B. Jørgensen, Merete Fredholm, Jan Gorodkin
2009	J	`jnl`	Structural profiles of human miRNA families from pairwise clustering. Bioinform. Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin
2009	J	`jnl`	tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz
2008	J	`jnl`	"Genes". Theory Biosci. Sonja J. Prohaska, Peter F. Stadler
2008	J	`jnl`	Duplicated RNA genes in teleost Fish genomes. J. Bioinform. Comput. Biol. Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler
2008	—	`conf`	FRANz: Fast Reconstruction of Wild Pedigrees. German Conference on Bioinformatics Markus Riester, Peter F. Stadler, Konstantin Klemm
2008	J	`jnl`	Noisy: Identification of problematic columns in multiple sequence alignments. Algorithms Mol. Biol. Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
2008	B	`conf`	Process flow for classification and clustering of fruit fly gene expression patterns. ICIP Andreas Heffel, Peter F. Stadler, Sonja J. Prohaska, Gerhard Kauer, Jens-Peer Kuska
2008	J	`jnl`	RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinform. Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler
2008	J	`jnl`	SnoReport: computational identification of snoRNAs with unknown targets. Bioinform. Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
2008	J	`jnl`	SynBlast: Assisting the analysis of conserved synteny information. BMC Bioinform. Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska
2008	—	`conf`	Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. BIRD Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker
2008	—	`ch.`	Visualization of Barrier Tree Sequences Revisited. Visualization in Medicine and Life Sciences Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2007	J	`jnl`	CREx: inferring genomic rearrangements based on common intervals. Bioinform. Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf
2007	J	`jnl`	Evolution of the vertebrate Y RNA cluster. Theory Biosci. Axel Mosig, Guofeng Meng, Bärbel M. R. Stadler, Peter F. Stadler
2007	A	`ed.`	Foundations of Genetic Algorithms, 9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers FOGA Christopher R. Stephens, Marc Toussaint, L. Darrell Whitley, Peter F. Stadler
2007	C	`conf`	Homology Search with Fragmented Nucleic Acid Sequence Patterns. WABI Axel Mosig, Julian J.-L. Chen, Peter F. Stadler
2007	J	`jnl`	Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
2007	J	`jnl`	Progressive multiple sequence alignments from triplets. BMC Bioinform. Matthias Kruspe, Peter F. Stadler
2007	J	`jnl`	RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol. Biol. Kristin Reiche, Peter F. Stadler
2007	A	`conf`	Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler
2007	—	`conf`	Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. German Conference on Bioinformatics Axel Mosig, Peter Menzel, Peter F. Stadler
2007	J	`jnl`	The mitochondrial DNA of Theory Biosci. Marleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelsson, Detlef Bernhard, Martin Schlegel
2007	J	`jnl`	Towards theoretical formalisms. Theory Biosci. Olaf Breidbach, Jürgen Jost, Peter F. Stadler
2007	J	`jnl`	U7 snRNAs: A Computational Survey. Genom. Proteom. Bioinform. Manja Marz, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler
2006	J	`jnl`	A prime factor theorem for a generalized direct product. Discuss. Math. Graph Theory Wilfried Imrich, Peter F. Stadler
2006	J	`jnl`	Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinform. Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2006	—	`conf`	Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. German Conference on Bioinformatics Axel Mosig, Ivo L. Hofacker, Peter F. Stadler
2006	J	`jnl`	Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences. Genom. Proteom. Bioinform. Axel Mosig, Katrin Sameith, Peter F. Stadler
2006	—	`conf`	Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. ISMB (Supplement of Bioinformatics) Jana Hertel, Peter F. Stadler
2006	J	`jnl`	Local RNA base pairing probabilities in large sequences. Bioinform. Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler
2006	J	`jnl`	Memory efficient folding algorithms for circular RNA secondary structures. Bioinform. Ivo L. Hofacker, Peter F. Stadler
2006	J	`jnl`	Multiple sequence alignment with user-defined anchor points. Algorithms Mol. Biol. Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler
2006	J	`jnl`	New journal: Algorithms for Molecular Biology. Algorithms Mol. Biol. Burkhard Morgenstern, Peter F. Stadler
2006	J	`jnl`	Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol. Stephan H. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
2006	J	`jnl`	Thermodynamics of RNA-RNA binding. Bioinform. Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
2006	J	`jnl`	Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2006	C	`conf`	Visualization of Lattice-Based Protein Folding Simulations. IV Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm
2006	J	`jnl`	miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res. Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker
2005	—	`conf`	CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
2005	J	`jnl`	Erratum to "Aggregation of variables and system decomposability: Applications to fitness landscape analysis. Theory Biosci. Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson
2005	J	`jnl`	Evolutionary patterns of non-coding RNAs. Theory Biosci. Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer
2005	—	`conf`	Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL Gil Benkö, Christoph Flamm, Peter F. Stadler
2005	J	`jnl`	Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler
2005	J	`jnl`	MATH/CHEM/COMP 2004 Contributions. Theory Biosci. Ante Graovac, Peter F. Stadler
2005	—	`conf`	Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics Ivo L. Hofacker, Peter F. Stadler
2005	J	`jnl`	Minimum path bases and relevant paths. Networks Petra M. Gleiss, Josef Leydold, Peter F. Stadler
2005	J	`jnl`	Multiple sequence alignment with user-defined constraints at GOBICS. Bioinform. Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran Ramaswami Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff
2005	J	`jnl`	Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinform. Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
2005	J	`jnl`	Neutral Networks of Interacting RNA Secondary Structures. Adv. Complex Syst. Camille Stephan-Otto Attolini, Peter F. Stadler
2005	—	`conf`	Non-coding RNAs in ECCB/JBI Kristin Missal, Dominic Rose, Peter F. Stadler
2005	—	`conf`	Thermodynamics of RNA-RNA Binding. German Conference on Bioinformatics Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker
2004	J	`jnl`	Aggregation of variables and system decomposition: Applications to fitness landscape analysis. Theory Biosci. Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson
2004	J	`jnl`	Alignment of RNA base pairing probability matrices. Bioinform. Ivo L. Hofacker, Stephan H. Bernhart, Peter F. Stadler
2004	—	`conf`	Conserved RNA Pseudoknots. German Conference on Bioinformatics C. Thurner, Ivo L. Hofacker, Peter F. Stadler
2004	J	`jnl`	Conserved RNA secondary structures in viral genomes: a survey. Bioinform. Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
2004	J	`jnl`	Counterexamples in Chemical Ring Perception. J. Chem. Inf. Model. Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler
2004	J	`jnl`	Editorial. Theory Biosci. Olaf Breidbach, Jürgen Jost, Peter F. Stadler, Michael S. Weingarten
2004	—	`conf`	Multiple sequence alignment with user-defined constraints. German Conference on Bioinformatics Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran Ramaswami Subramanian, Peter F. Stadler
2004	J	`jnl`	Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE ACM Trans. Comput. Biol. Bioinform. Christina Witwer, Ivo L. Hofacker, Peter F. Stadler
2004	J	`jnl`	Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinform. Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler
2004	J	`jnl`	Simon-Ando decomposability and fitness landscapes. Theory Biosci. Max Shpak, Peter F. Stadler, Günter P. Wagner, Lee Altenberg
2004	J	`jnl`	The Footprint Sorting Problem. J. Chem. Inf. Model. Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler
2004	Misc	`conf`	The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science Ivo L. Hofacker, Peter F. Stadler
2004	J	`jnl`	The duplication of the Theory Biosci. Sonja J. Prohaska, Peter F. Stadler
2003	J	`jnl`	A Graph-Based Toy Model of Chemistry. J. Chem. Inf. Comput. Sci. Gil Benkö, Christoph Flamm, Peter F. Stadler
2003	J	`jnl`	Barrier Trees on Poset-Valued Landscapes. Genet. Program. Evolvable Mach. Peter F. Stadler, Christoph Flamm
2003	J	`jnl`	Circuit bases of strongly connected digraphs. Discuss. Math. Graph Theory Petra M. Gleiss, Josef Leydold, Peter F. Stadler
2003	—	`conf`	Conserved RNA secondary structures in viral genomes: A survey. German Conference on Bioinformatics Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits
2003	—	`conf`	Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler
2003	—	`conf`	Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL Gil Benkö, Christoph Flamm, Peter F. Stadler
2003	J	`jnl`	Minimum cycle bases of Halin graphs. J. Graph Theory Peter F. Stadler
2003	J	`jnl`	Molecular Replicator Dynamics. Adv. Complex Syst. Bärbel M. R. Stadler, Peter F. Stadler
2002	J	`jnl`	Combinatorial Landscapes. SIAM Rev. Christian M. Reidys, Peter F. Stadler
2002	J	`jnl`	Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry. J. Chem. Inf. Comput. Sci. Bärbel M. R. Stadler, Peter F. Stadler
2002	J	`jnl`	Landscapes on spaces of trees. Appl. Math. Comput. Oliver Bastert, Daniel N. Rockmore, Peter F. Stadler, Gottfried Tinhofer
2002	J	`jnl`	Minimum cycle bases of product graphs. Australas. J Comb. Wilfried Imrich, Peter F. Stadler
2002	C	`conf`	Stochastic pairwise alignments. ECCB Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler
2001	J	`jnl`	Glassy States in a shaken Sandbox. Adv. Complex Syst. Peter F. Stadler, Anita Mehta, Jean-Marc Luck
2001	J	`jnl`	Neutrality in fitness landscapes. Appl. Math. Comput. Christian M. Reidys, Peter F. Stadler
2001	J	`jnl`	Relevant cycles in Chemical reaction Networks. Adv. Complex Syst. Petra M. Gleiss, Peter F. Stadler, Andreas Wagner, David A. Fell
2000	J	`jnl`	Interchangeability of Relevant Cycles in Graphs. Electron. J. Comb. Petra M. Gleiss, Josef Leydold, Peter F. Stadler
2000	J	`jnl`	Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. J. Comput. Biol. Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
2000	J	`jnl`	RNA Shape Space Topology. Artif. Life Jan Cupal, Stephan Kopp, Peter F. Stadler
1999	—	`conf`	An efficient potential for protein sequence design. German Conference on Bioinformatics G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler
1999	J	`jnl`	Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Comput. Chem. Ivo L. Hofacker, Peter F. Stadler
1999	J	`jnl`	Call for proposals. Adv. Complex Syst. Eric Bonabeau, Peter F. Stadler
1999	—	`conf`	Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler
1999	J	`jnl`	RNA Adv. Complex Syst. Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
1998	J	`jnl`	Amplitude Spectra of Fitness Landscapes. Adv. Complex Syst. Wim Hordijk, Peter F. Stadler
1998	J	`jnl`	Combinatorics of RNA Secondary Structures. Discret. Appl. Math. Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
1998	J	`jnl`	Minimal Cycle Bases of Outerplanar Graphs. Electron. J. Comb. Josef Leydold, Peter F. Stadler
1997	J	`jnl`	Algebraic Theory of Recombination Spaces. Evol. Comput. Peter F. Stadler, Günter P. Wagner
1997	A	`conf`	Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. ISMB Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler
1996	J	`jnl`	Base Pairing Probabilities in a Complete HIV-1 RNA. J. Comput. Biol. Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler
1996	J	`jnl`	Bio-molecular Shapes and Algebraic Structures. Comput. Chem. Christian M. Reidys, Peter F. Stadler
1996	J	`jnl`	Canonical approximation of fitness landscapes. Complex. Robert Happel, Peter F. Stadler
1996	—	`conf`	Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. German Conference on Bioinformatics Jan Cupal, Ivo L. Hofacker, Peter F. Stadler
1996	A*	`conf`	Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. KDD Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
1995	J	`jnl`	Random walks and orthogonal functions associated with highly symmetric graphs. Discret. Math. Peter F. Stadler
1994	J	`jnl`	Landscapes: Complex Optimization Problems and Biopolymer Structures. Comput. Chem. Peter Schuster, Peter F. Stadler