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ORCIDPeter F. Stadler
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- affiliation: University of Leipzig, Department of Computer Science
- affiliation: University of Vienna, Institute for Theoretical Chemistry
- affiliation: Max Planck Institute for Biophysical Chemistry
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2020 – today
- 2024
[j245]Bruno J. Schmidt
, Tom Hartmann, Peter F. Stadler:
Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss. Adv. Appl. Math. 161: 102757 (2024)- [j244]Marcos E. González Laffitte, Peter F. Stadler:
Progressive Multiple Alignment of Graphs. Algorithms 17(3): 116 (2024) - [j243]Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler:
Transit functions and pyramid-like binary clustering systems. Discret. Appl. Math. 357: 365-384 (2024) - [j242]Sarah von Löhneysen, Mario Mörl, Peter F. Stadler:
Limits of experimental evidence in RNA secondary structure prediction. Frontiers Bioinform. 4 (2024) - [j241]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): 549-563 (2024) - [j240]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): 82 (2024) - [j239]John Anders, Peter F. Stadler:
RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions. J. Integr. Bioinform. 20(3) (2024) - [j238]Anahy Santiago Arguello, Guillaume E. Scholz, Peter F. Stadler:
Core Potentials: The Consensus Segmentation Conjecture. Math. Comput. Sci. 18(4): 19 (2024) - [j237]Marcos E. González Laffitte, Klaus Weinbauer, Tieu-Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, Peter F. Stadler:
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 16(9): 1217 (2024) - [c72]Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, Peter F. Stadler:
Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. CALDAM 2024: 148-161 - [c71]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: 89-109 - [i63]Manoj Changat, Ameera Vaheeda Shanavas, Peter F. Stadler:
Transit Functions and Clustering Systems. CoRR abs/2401.15662 (2024) - [i62]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 abs/2407.07741 (2024) - [i61]Carsten R. Seemann, Peter F. Stadler, Marc Hellmuth:
Nesting of Touching Polygons. CoRR abs/2409.13040 (2024) - [i60]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:
Democratising Artificial Intelligence for Pandemic Preparedness and Global Governance in Latin American and Caribbean Countries. CoRR abs/2409.14181 (2024) - 2023
- [j236]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): 8 (2023) - [j235]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): 16 (2023) - [j234]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) - [j233]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): 235 (2023) - [j232]Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth:
Planar median graphs and cubesquare-graphs. Discret. Appl. Math. 331: 38-58 (2023) - [j231]Annachiara Korchmaros, David Schaller, Marc Hellmuth, Peter F. Stadler:
Quasi-best match graphs. Discret. Appl. Math. 331: 104-125 (2023) - [j230]Paul Klemm, Peter F. Stadler, Marcus Lechner:
Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. Frontiers Bioinform. 3 (2023) - [j229]Marc Hellmuth, Katharina T. Huber, Vincent Moulton, Guillaume E. Scholz, Peter F. Stadler:
Injective Split Systems. Graphs Comb. 39(4): 65 (2023) - [j228]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): 2350016:1-2350016:19 (2023) - [j227]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): 2172-2207 (2023) - [j226]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): 232-242 (2023) - [j225]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Best Match Graphs With Binary Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 20(3): 1679-1690 (2023) - [j224]Marc Hellmuth, David Schaller, Peter F. Stadler:
Clustering systems of phylogenetic networks. Theory Biosci. 142(4): 301-358 (2023) - [c70]Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu:
Fitch Graph Completion. COCOON (2) 2023: 225-237 - [c69]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: 267-279 - [c68]Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
On the Realisability of Chemical Pathways. ISBRA 2023: 409-419 - [c67]Karl Käther, Steffen Lemke, Peter F. Stadler:
Annotation-Free Identification of Potential Synteny Anchors. IWBBIO (1) 2023: 217-230 - [d2]Christopher Klapproth, Siegfried Zöztsche, Felix Kühnl, Jörg Fallmann, Peter F. Stadler, Sven Findeiß:
Tailored machine learning models for functional RNA detection in genome-wide screens. Zenodo, 2023
- [i59]Konstantin Klemm, Anita Mehta, Peter F. Stadler:
Optimisation via encodings: a renormalisation group perspective. CoRR abs/2303.16258 (2023) - [i58]Marc Hellmuth, Peter F. Stadler:
The Theory of Gene Family Histories. CoRR abs/2304.11826 (2023) - [i57]Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu:
Fitch Graph Completion. CoRR abs/2306.06878 (2023) - [i56]Angel Garcia-Chung, Marisol Bermúdez-Montaña, Peter F. Stadler, Jürgen Jost, Guillermo Restrepo:
Chemically inspired Erdős-Rényi oriented hypergraphs. CoRR abs/2309.06351 (2023) - [i55]Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
On the Realisability of Chemical Pathways. CoRR abs/2309.10629 (2023) - [i54]Ameera Vaheeda Shanavas, Manoj Changat, Marc Hellmuth, Peter F. Stadler:
Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs. CoRR abs/2309.13634 (2023) - 2022
- [j223]Tom Hartmann, Max Bannach, Martin Middendorf, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Complete edge-colored permutation graphs. Adv. Appl. Math. 139: 102377 (2022) - [j222]Anahy Santiago Arguello, Peter F. Stadler:
Whitney's connectivity inequalities for directed hypergraphs. Art Discret. Appl. Math. 5(1) (2022) - [j221]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): 2 (2022) - [j220]Peter F. Stadler, Sebastian Will:
Bi-alignments with affine gaps costs. Algorithms Mol. Biol. 17(1): 10 (2022) - [j219]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) - [j218]Grover E. C. Guzman, Peter F. Stadler, André Fujita:
Efficient eigenvalue counts for tree-like networks. J. Complex Networks 10(5) (2022) - [j217]Carmen Bruckmann, Peter F. Stadler, Marc Hellmuth:
From modular decomposition trees to rooted median graphs. Discret. Appl. Math. 310: 1-9 (2022) - [j216]Marc Hellmuth, David Schaller, Peter F. Stadler:
Compatibility of partitions with trees, hierarchies, and split systems. Discret. Appl. Math. 314: 265-283 (2022) - [j215]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): 1398 (2022) - [j214]Stefan Müller, Christoph Flamm, Peter F. Stadler:
What makes a reaction network "chemical"? J. Cheminformatics 14(1): 63 (2022) - [j213]Franziska Reinhardt, Peter F. Stadler:
ExceS-A: an exon-centric split aligner. J. Integr. Bioinform. 19(1) (2022) - [j212]Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler:
Generic Context-Aware Group Contributions. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 429-442 (2022) - [c66]Dustyn Eggers, Christian Höner zu Siederdissen, Peter F. Stadler:
Accuracy of RNA Structure Prediction Depends on the Pseudoknot Grammar. BSB 2022: 20-31 - [i53]Marc Hellmuth, David Schaller, Peter F. Stadler:
Clustering Systems of Phylogenetic Networks. CoRR abs/2204.13466 (2022) - [i52]David Schaller, Tom Hartmann, Manuel Lafond, Nicolas Wieseke, Marc Hellmuth, Peter F. Stadler:
Relative Timing Information and Orthology in Evolutionary Scenarios. CoRR abs/2212.02201 (2022) - 2021
- [j211]Wilmer Leal, Guillermo Restrepo, Peter F. Stadler, Jürgen Jost:
Forman-Ricci Curvature for hypergraphs. Adv. Complex Syst. 24(1): 2150003:1-2150003:24 (2021) - [j210]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): 110 (2021) - [j209]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): 8 (2021) - [j208]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Heuristic algorithms for best match graph editing. Algorithms Mol. Biol. 16(1): 19 (2021) - [j207]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): 23 (2021) - [j206]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) - [j205]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) - [j204]Thomas Gatter, Peter F. Stadler:
Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more. Bioinform. 37(23): 4307-4313 (2021) - [j203]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): 277 (2021) - [j202]Halima Saker, Rainer Machné, Jörg Fallmann, Douglas B. Murray, Ahmad M. Shahin, Peter F. Stadler:
Weighted Consensus Segmentations. Comput. 9(2): 17 (2021) - [j201]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) - [j200]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Least resolved trees for two-colored best match graphs. J. Graph Algorithms Appl. 25(1): 397-416 (2021) - [j199]Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler:
Compositional Properties of Alignments. Math. Comput. Sci. 15(4): 609-630 (2021) - [j198]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): D743-D750 (2021) - [j197]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): 49-58 (2021) - [j196]Grover E. C. Guzman, Peter F. Stadler, André Fujita:
Efficient Laplacian spectral density computations for networks with arbitrary degree distributions. Netw. Sci. 9(3): 312-327 (2021) - [j195]David Schaller, Peter F. Stadler, Marc Hellmuth:
Complexity of modification problems for best match graphs. Theor. Comput. Sci. 865: 63-84 (2021) - [c65]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Best Match Graphs with Binary Trees. AlCoB 2021: 82-93 - [c64]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: 176-183 - [c63]Manoj Changat, Ferdoos Hossein Nezhad, Peter F. Stadler:
Cut Vertex Transit Functions of Hypergraphs. CALDAM 2021: 222-233 - [c62]Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard, David Schaller, Peter F. Stadler:
Combining Orthology and Xenology Data in a Common Phylogenetic Tree. BSB 2021: 53-64 - [e4]Peter F. Stadler, Maria Emília M. T. Walter, Maribel Hernandez-Rosales, Marcelo M. Brigido:
Advances in Bioinformatics and Computational Biology - 14th Brazilian Symposium on Bioinformatics, BSB 2021, Virtual Event, November 22-26, 2021, Proceedings. Lecture Notes in Computer Science 13063, Springer 2021, ISBN 978-3-030-91813-2 [contents] - [i51]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Least resolved trees for two-colored best match graphs. CoRR abs/2101.07000 (2021) - [i50]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs. CoRR abs/2103.06665 (2021) - [i49]Carmen Bruckmann, Peter F. Stadler, Marc Hellmuth:
From Modular Decomposition Trees to Rooted Median Graphs. CoRR abs/2103.06683 (2021) - [i48]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Heuristic Algorithms for Best Match Graph Editing. CoRR abs/2103.07280 (2021) - [i47]Marc Hellmuth, David Schaller, Peter F. Stadler:
Compatibility of Partitions, Hierarchies, and Split Systems. CoRR abs/2104.14146 (2021) - [i46]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 abs/2107.00072 (2021) - [i45]Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard, David Schaller, Peter F. Stadler:
Combining Orthology and Xenology Data in a Common Phylogenetic Tree. CoRR abs/2107.01893 (2021) - [i44]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Defining Autocatalysis in Chemical Reaction Networks. CoRR abs/2107.03086 (2021) - [i43]Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth:
Planar Median Graphs and Cubesquare-Graphs. CoRR abs/2110.09346 (2021) - [i42]David Schaller, Marc Hellmuth, Peter F. Stadler:
Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees. CoRR abs/2112.00403 (2021) - [i41]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 abs/2112.05876 (2021) - 2020
- [j194]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) - [j193]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): 519-533 (2020) - [j192]Peter F. Stadler, Manuela Geiß, David Schaller, Alitzel López Sánchez, Marcos E. 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): 5 (2020) - [j191]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): 75 (2020) - [j190]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: 495-511 (2020) - [j189]Yangjing Long, Peter F. Stadler:
Exact-2-relation graphs. Discret. Appl. Math. 285: 212-226 (2020) - [j188]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): 2050004:1-2050004:19 (2020) - [j187]Felipe Borim Corrêa, João Pedro Saraiva, Peter F. Stadler, Ulisses Nunes da Rocha:
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. Nucleic Acids Res. 48(Database-Issue): D626-D632 (2020) - [j186]Marc Hellmuth, Manuela Geiß, Peter F. Stadler:
Complexity of modification problems for reciprocal best match graphs. Theor. Comput. Sci. 809: 384-393 (2020) - [j185]Wim Hordijk, Stuart A. Kauffman, Peter F. Stadler:
Average Fitness Differences on NK Landscapes. Theory Biosci. 139(1): 1-7 (2020) - [j184]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): 349-359 (2020) - [c61]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS 2020: 23-31 - [c60]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) 2020: 193-214 - [c59]Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, Peter F. Stadler:
Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. WABI 2020: 10:1-10:22 - [c58]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: 180-191 - [c57]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: 247-258 - [d1]Sree Rohit Raj Kolora, Deisy Morselli Gysi, Stefan Schaffer, Rui Faria, Klaus Henle, Peter F. Stadler, Martin Schlegel, Katja Nowick, Marton Szablocs, Annegrett Grimm-Seyfarth:
Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards. Zenodo, 2020 - [i40]Fabian Gärtner, Felix Kühnl, Carsten R. Seemann, Christian Höner zu Siederdissen, Peter F. Stadler:
Superbubbles as an Empirical Characteristic of Directed Networks. CoRR abs/2001.03409 (2020) - [i39]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. CoRR abs/2001.05921 (2020) - [i38]Dulce I. Valdivia, Manuela Geiß, Maribel Hernández-Rosales, Peter F. Stadler, Marc Hellmuth:
Hierarchical and Modularly-Minimal Vertex Colorings. CoRR abs/2004.06340 (2020) - [i37]Tom Hartmann, Max Bannach, Martin Middendorf, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Complete Edge-Colored Permutation Graphs. CoRR abs/2004.07118 (2020) - [i36]David Schaller, Manuela Geiß, Peter F. Stadler, Marc Hellmuth:
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. CoRR abs/2006.02249 (2020) - [i35]David Schaller, Peter F. Stadler, Marc Hellmuth:
Complexity of Modification Problems for Best Match Graphs. CoRR abs/2006.16909 (2020) - [i34]David Schaller, Manuela Geiß, Marc Hellmuth, Peter F. Stadler:
Best Match Graphs with Binary Trees. CoRR abs/2011.00511 (2020) - [i33]David Schaller, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Indirect Identification of Horizontal Gene Transfer. CoRR abs/2012.08897 (2020)
2010 – 2019
- 2019
- [j183]Manoj Changat, Prasanth G. Narasimha-Shenoi, Peter F. Stadler:
Axiomatic characterization of transit functions of weak hierarchies. Art Discret. Appl. Math. 2(1): #P1.01 (2019) - [j182]Fabian Gärtner, Peter F. Stadler:
Direct Superbubble Detection. Algorithms 12(4): 81 (2019) - [j181]Daniel Wiegreffe, Daniel Alexander, Peter F. Stadler, Dirk Zeckzer:
RNApuzzler: efficient outerplanar drawing of RNA-secondary structures. Bioinform. 35(8): 1342-1349 (2019) - [j180]Ali M. Yazbeck, Peter F. Stadler, Kifah Tout, Jörg Fallmann:
Automatic curation of large comparative animal MicroRNA datasets. Bioinform. 35(22): 4553-4559 (2019) - [j179]Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjic, Peter F. Stadler, Katja Nowick:
SSS-test: a novel test for detecting positive selection on RNA secondary structure. BMC Bioinform. 20(1): 151:1-151:19 (2019) - [j178]Thomas Gatter, Peter F. Stadler:
Ryūtō: network-flow based transcriptome reconstruction. BMC Bioinform. 20(1): 190:1-190:14 (2019) - [j177]Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller:
flowEMMi: an automated model-based clustering tool for microbial cytometric data. BMC Bioinform. 20(1): 643 (2019) - [j176]Erhard Rahm, Wolfgang E. Nagel, Eric Peukert, René Jäkel, Fabian Gärtner, Peter F. Stadler, Daniel Wiegreffe, Dirk Zeckzer, Wolfgang Lehner:
Big Data Competence Center ScaDS Dresden/Leipzig: Overview and selected research activities. Datenbank-Spektrum 19(1): 5-16 (2019) - [j175]Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, Bérénice Batut, Maria A. Doyle, Tomas Klingström, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen, Björn A. Grüning:
The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Res. 47(Webserver-Issue): W511-W515 (2019) - [j174]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. IEEE ACM Trans. Comput. Biol. Bioinform. 16(2): 510-523 (2019) - [c56]Falco Kirchner, Nancy Retzlaff, Peter F. Stadler:
A General Framework for Exact Partially Local Alignments. BIOINFORMATICS 2019: 194-200 - [c55]Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, Peter F. Stadler:
Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. CIBB 2019: 159-170 - [i32]Manuela Geiß, Marcos González, Alitzel López Sánchez, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández-Rosales, Peter F. Stadler:
Best Match Graphs and Reconciliation of Gene Trees with Species Trees. CoRR abs/1904.12021 (2019) - [i31]Dulce I. Valdivia, Manuela Geiß, Marc Hellmuth, Maribel Hernández-Rosales, Peter F. Stadler:
Hierarchical Colorings of Cographs. CoRR abs/1906.10031 (2019) - [i30]Marc Hellmuth, Manuela Geiß, Peter F. Stadler:
Complexity of Modification Problems for Reciprocal Best Match Graphs. CoRR abs/1907.08865 (2019) - [i29]Marc Hellmuth, Carsten R. Seemann, Peter F. Stadler:
Generalized Fitch Relations II: Sets of Binary Relations that are explained by Edge-labeled Trees. CoRR abs/1911.07469 (2019) - 2018
- [j173]Marc Hellmuth, Yangjing Long, Manuela Geiß, Peter F. Stadler:
A short note on undirected Fitch graphs. Art Discret. Appl. Math. 1(1): #P1.08 (2018) - [j172]Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Time-consistent reconciliation maps and forbidden time travel. Algorithms Mol. Biol. 13(1): 2:1-2:17 (2018) - [j171]Alexander Donath, Peter F. Stadler:
Split-inducing indels in phylogenomic analysis. Algorithms Mol. Biol. 13(1): 12:1-12:12 (2018) - [j170]Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller, Peter F. Stadler:
Coordinate systems for supergenomes. Algorithms Mol. Biol. 13(1): 15:1-15:19 (2018) - [j169]Fabian Gärtner, Lydia Müller, Peter F. Stadler:
Superbubbles revisited. Algorithms Mol. Biol. 13(1): 16:1-16:17 (2018) - [j168]Manoj Changat, Ferdoos Hossein Nezhad, Peter F. Stadler:
Axiomatic characterization of transit functions of hierarchies. Ars Math. Contemp. 14(1): 117-128 (2018) - [j167]Alexandre Rossi Paschoal, Irma Lozada-Chávez, Douglas Silva Domingues, Peter F. Stadler:
ceRNAs in plants: computational approaches and associated challenges for target mimic research. Briefings Bioinform. 19(6): 1273-1289 (2018) - [j166]Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl, Peter F. Stadler, Fabian Amman:
Accurate mapping of tRNA reads. Bioinform. 34(7): 1116-1124 (2018) - [j165]Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl, Peter F. Stadler, Fabian Amman:
Accurate mapping of tRNA reads. Bioinform. 34(13): 2339 (2018) - [j164]Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler:
Finding the K best synthesis plans. J. Cheminformatics 10(1): 19:1-19:21 (2018) - [j163]Nancy Retzlaff, Peter F. Stadler:
Partially Local Multi-way Alignments. Math. Comput. Sci. 12(2): 207-234 (2018) - [j162]Haleh Ebadi, Michael Perry, Keith Short, Konstantin Klemm, Claude Desplan, Peter F. Stadler, Anita Mehta:
Patterning the insect eye: From stochastic to deterministic mechanisms. PLoS Comput. Biol. 14(11) (2018) - [j161]Nancy Retzlaff, Peter F. Stadler:
Phylogenetics beyond biology. Theory Biosci. 137(2): 133-143 (2018) - [i28]Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler:
Alignments as Compositional Structures. CoRR abs/1810.07800 (2018) - [i27]Wilmer Leal, Guillermo Restrepo, Peter F. Stadler, Jürgen Jost:
Forman-Ricci Curvature for Hypergraphs. CoRR abs/1811.07825 (2018) - 2017
- [j160]Sarah Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler:
Algebraic Dynamic Programming on Trees. Algorithms 10(4): 135 (2017) - [j159]Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler:
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. Algorithms Mol. Biol. 12(1): 22:1-22:11 (2017) - [j158]Felix Kühnl, Peter F. Stadler, Sebastian Will:
Tractable RNA-ligand interaction kinetics. BMC Bioinform. 18(S-12): 47-55 (2017) - [j157]Ali M. Yazbeck, Kifah R. Tout, Peter F. Stadler, Jana Hertel:
Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution. J. Integr. Bioinform. 14(1) (2017) - [j156]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:
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Res. 45(Webserver-Issue): W560-W566 (2017) - [j155]Sven Findeiß, Maja Etzel, Sebastian Will, Mario Mörl, Peter F. Stadler:
Design of Artificial Riboswitches as Biosensors. Sensors 17(9): 1990 (2017) - [c54]Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Graph Transformation with Stereo-Information. ICGT 2017: 54-69 - [c53]Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. WABI 2017: 17:1-17:12 - [i26]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
An Intermediate Level of Abstraction for Computational Systems Chemistry. CoRR abs/1701.09097 (2017) - [i25]Marc Hellmuth, Adrian Fritz, Nicolas Wieseke, Peter F. Stadler:
Merging Modules is equivalent to Editing P4's. CoRR abs/1702.07499 (2017) - [i24]Nikolai Nøjgaard, Manuela Geiß, Peter F. Stadler, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth:
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. CoRR abs/1705.02179 (2017) - [i23]Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler:
Local algorithms for the prime factorization of strong product graphs. CoRR abs/1705.03823 (2017) - [i22]Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler:
From event labeled gene trees to species trees. CoRR abs/1705.04190 (2017) - [i21]Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler:
A Survey on Hypergraph Products (Erratum). CoRR abs/1705.06037 (2017) - [i20]Manuela Geiß, John Anders, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth:
Reconstructing Gene Trees From Fitch's Xenology Relation. CoRR abs/1711.02152 (2017) - [i19]Manuela Geiß, Marc Hellmuth, Yangjing Long, Peter F. Stadler:
A Short Note on Undirected Fitch Graphs. CoRR abs/1712.01544 (2017) - [i18]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. CoRR abs/1712.02594 (2017) - [i17]Marc Hellmuth, Nicolas Wieseke, Marcus Lechner, Hans-Peter Lenhof, Martin Middendorf, Peter F. Stadler:
Phylogenomics with Paralogs. CoRR abs/1712.06442 (2017) - [i16]Manoj Changat, Prasanth G. Narasimha-Shenoi, Ferdoos Hossein Nezhad, Matjaz Kovse, Shilpa Mohandas, Abisha Ramachandran, Peter F. Stadler:
Topological Representation of the Transit Sets of k-Point Crossover Operators. CoRR abs/1712.09022 (2017) - [i15]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Algorithmic Cheminformatics (Dagstuhl Seminar 17452). Dagstuhl Reports 7(11): 28-45 (2017) - 2016
- [j154]Henrike Indrischek, Nicolas Wieseke, Peter F. Stadler, Sonja J. Prohaska:
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. Algorithms Mol. Biol. 11: 1 (2016) - [j153]Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler:
RNA folding with hard and soft constraints. Algorithms Mol. Biol. 11: 8 (2016) - [j152]Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger:
SHAPE directed RNA folding. Bioinform. 32(1): 145-147 (2016) - [j151]Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Pseudoknots in RNA folding landscapes. Bioinform. 32(2): 187-194 (2016) - [j150]João Victor de Araújo Oliveira, Fabrizio Costa, Rolf Backofen, Peter F. Stadler, Maria Emília Telles Walter, Jana Hertel:
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. BMC Bioinform. 17(S-18): 73-86 (2016) - [j149]Steve Hoffmann, Peter F. Stadler:
Read mapping. it Inf. Technol. 58(3): 119-125 (2016) - [j148]Richard H. Hammack, Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler:
Associativity and Non-Associativity of Some Hypergraph Products. Math. Comput. Sci. 10(3): 403-408 (2016) - [j147]Maik Riechert, Christian Höner zu Siederdissen, Peter F. Stadler:
Algebraic dynamic programming for multiple context-free grammars. Theor. Comput. Sci. 639: 91-109 (2016) - [j146]David C. Krakauer, Lydia Müller, Sonja J. Prohaska, Peter F. Stadler:
Design specifications for cellular regulation. Theory Biosci. 135(4): 231-240 (2016) - [c52]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
A Software Package for Chemically Inspired Graph Transformation. ICGT 2016: 73-88 - [c51]Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen:
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. ICGT 2016: 206-222 - [i14]Marc Hellmuth, Peter F. Stadler, Nicolas Wieseke:
The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations. CoRR abs/1603.02467 (2016) - [i13]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
A Software Package for Chemically Inspired Graph Transformation. CoRR abs/1603.02481 (2016) - [i12]Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen:
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. CoRR abs/1604.06379 (2016) - [i11]Marc Hellmuth, Maribel Hernandez-Rosales, Yangjing Long, Peter F. Stadler:
Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary Events. CoRR abs/1612.09093 (2016) - 2015
- [j145]Marc Hellmuth, Tilen Marc, Lydia Ostermeier, Peter F. Stadler:
The relaxed square property. Australas. J Comb. 62: 240- (2015) - [j144]Steve Hoffmann, Peter F. Stadler, Korbinian Strimmer:
A simple data-adaptive probabilistic variant calling model. Algorithms Mol. Biol. 10: 10 (2015) - [j143]Jan Engelhardt, Peter F. Stadler:
Evolution of 3'UTR-associated RNAs. BMC Bioinform. 16(S-8): A7 (2015) - [j142]Christian Höner zu Siederdissen, Sonja J. Prohaska, Peter F. Stadler:
Algebraic Dynamic Programming over general data structures. BMC Bioinform. 16(S19): S2 (2015) - [j141]Lydia Ostermeier, Peter F. Stadler:
The Grid Property and Product-Like Hypergraphs. Graphs Comb. 31(3): 757-770 (2015) - [j140]Wosley Arruda, Daniel S. Souza, Célia Ghedini Ralha, Maria Emília M. T. Walter, Tainá Raiol, Marcelo M. Brigido, Peter F. Stadler:
Knowledge-based reasoning to annotate noncoding RNA using multi-agent system. J. Bioinform. Comput. Biol. 13(6): 1550021:1-1550021:19 (2015) - [j139]Bärbel M. R. Stadler, Peter F. Stadler:
Connectivity Spaces. Math. Comput. Sci. 9(4): 409-436 (2015) - [j138]Sarah Berkemer, Ricardo Régis Cavalcante Chaves, Adrian Fritz, Marc Hellmuth, Maribel Hernandez-Rosales, Peter F. Stadler:
Spiders can be Recognized by Counting Their Legs. Math. Comput. Sci. 9(4): 437-441 (2015) - [j137]Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler:
Product Grammars for Alignment and Folding. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 507-519 (2015) - [j136]Manfred D. Laubichler, Peter F. Stadler, Sonja J. Prohaska, Katja Nowick:
The relativity of biological function. Theory Biosci. 134(3-4): 143-147 (2015) - [i10]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Support for Eschenmoser's Glyoxylate Scenario. CoRR abs/1502.07555 (2015) - [i9]Marc Hellmuth, Adrian Fritz, Nicolas Wieseke, Peter F. Stadler:
Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s. CoRR abs/1509.06983 (2015) - 2014
- [j135]Jing Qin, Markus Fricke, Manja Marz, Peter F. Stadler, Rolf Backofen:
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. Algorithms Mol. Biol. 9: 19 (2014) - [j134]Bernhard Misof, Karen Meusemann, Björn Marcus von Reumont, Patrick Kück, Sonja J. Prohaska, Peter F. Stadler:
A priori assessment of data quality in molecular phylogenetics. Algorithms Mol. Biol. 9: 22 (2014) - [j133]Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm:
Atom mapping with constraint programming. Algorithms Mol. Biol. 9: 23 (2014) - [j132]Marc Hellmuth, Josef Leydold, Peter F. Stadler:
Convex cycle bases. Ars Math. Contemp. 7(1): 123-140 (2014) - [j131]Sebastian Bartschat, Stephanie Kehr, Hakim Tafer, Peter F. Stadler, Jana Hertel:
snoStrip: a snoRNA annotation pipeline. Bioinform. 30(1): 115-116 (2014) - [j130]Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer:
Challenges in RNA virus bioinformatics. Bioinform. 30(13): 1793-1799 (2014) - [j129]Christian Otto, Peter F. Stadler, Steve Hoffmann:
Lacking alignments? The next-generation sequencing mapper segemehl revisited. Bioinform. 30(13): 1837-1843 (2014) - [j128]Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. Bioinform. 30(14): 2009-2017 (2014) - [j127]Fabian Amman, Michael T. Wolfinger, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler, Sven Findeiß:
TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinform. 15: 89 (2014) - [j126]Maribel Hernandez-Rosales, Nicolas Wieseke, Marc Hellmuth, Peter F. Stadler:
Simulation of gene family histories. BMC Bioinform. 15(S-3): A8 (2014) - [j125]Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler:
Unique square property, equitable partitions, and product-like graphs. Discret. Math. 320: 92-103 (2014) - [j124]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des. 7(2/3): 225-258 (2014) - [j123]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:
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Open. Nat. 505(7484): 546-549 (2014) - [c50]Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. FMMB 2014: 117-135 - [c49]Christian Höner zu Siederdissen, Sarah Berkemer, Fabian Amman, Axel Wintsche, Sebastian Will, Sonja J. Prohaska, Peter F. Stadler:
Comparative Detection of Processed Small RNAs in Archaea. IWBBIO 2014: 286-297 - [c48]Sebastian Will, Peter F. Stadler:
A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. WABI 2014: 135-147 - [c47]Christian Höner zu Siederdissen, Sonja J. Prohaska, Peter F. Stadler:
Dynamic Programming for Set Data Types. BSB 2014: 57-64 - [c46]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:
Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115. BSB 2014: 115-122 - [p2]Konstantin Klemm, Peter F. Stadler:
Rugged and Elementary Landscapes. Theory and Principled Methods for the Design of Metaheuristics 2014: 41-61 - [i8]Marc Hellmuth, Tilen Marc, Lydia Ostermeier, Peter F. Stadler:
The Relaxed Square Property. CoRR abs/1407.3164 (2014) - [i7]Sarah Berkemer, Ricardo Régis Cavalcante Chaves, Adrian Fritz, Marc Hellmuth, Maribel Hernandez-Rosales, Peter F. Stadler:
Spiders can be recognized by counting their legs. CoRR abs/1411.2105 (2014) - [i6]Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Algorithmic Cheminformatics (Dagstuhl Seminar 14452). Dagstuhl Reports 4(11): 22-39 (2014) - 2013
- [j122]Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen:
LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol. Biol. 8: 14 (2013) - [j121]Jan Hubicka, Jürgen Jost, Yangjing Long, Peter F. Stadler, Ling Yang:
Relations between graphs. Ars Math. Contemp. 6(2): 323-350 (2013) - [j120]Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, Peter F. Stadler:
Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy 15(10): 4066-4083 (2013) - [j119]Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler:
On the Complexity of Reconstructing Chemical Reaction Networks. Math. Comput. Sci. 7(3): 275-292 (2013) - [j118]Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin:
The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res. 41(Webserver-Issue): 475-479 (2013) - [j117]Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler:
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 10(4): 832-844 (2013) - [j116]Marcus Lechner, Manja Marz, Christian Ihling, Andrea Sinz, Peter F. Stadler, Veiko Krauss:
The correlation of genome size and DNA methylation rate in metazoans. Theory Biosci. 132(1): 47-60 (2013) - [c45]Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm:
Atom Mapping with Constraint Programming. CP 2013: 805-822 - [c44]Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, Peter F. Stadler:
Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures. WABI 2013: 112-125 - [c43]Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, Sebastian Will:
The Trouble with Long-Range Base Pairs in RNA Folding. BSB 2013: 1-11 - [c42]Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler:
How to Multiply Dynamic Programming Algorithms. BSB 2013: 82-93 - [c41]Wosley Arruda, Célia Ghedini Ralha, Tainá Raiol, Marcelo M. Brigido, Maria Emília M. T. Walter, Peter F. Stadler:
ncRNA-Agents: A Multiagent System for Non-coding RNA Annotation. BSB 2013: 136-147 - [i5]Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler:
Square Property, Equitable Partitions, and Product-like Graphs. CoRR abs/1301.6898 (2013) - [i4]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Generic Strategies for Chemical Space Exploration. CoRR abs/1302.4006 (2013) - [i3]Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler:
On the Complexity of Reconstructing Chemical Reaction Networks. CoRR abs/1309.7198 (2013) - 2012
- [j115]Marc Hellmuth, Philipp-Jens Ostermeier, Peter F. Stadler:
Minimum cycle bases of lexicographic products. Ars Math. Contemp. 5(2): 223-234 (2012) - [j114]David Langenberger, Sachin Pundhir, Claus Thorn Ekstrøm, Peter F. Stadler, Steve Hoffmann, Jan Gorodkin:
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinform. 28(1): 17-24 (2012) - [j113]Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel:
Addendum: topology and prediction of RNA pseudoknots. Bioinform. 28(2): 300 (2012) - [j112]Christian Otto, Peter F. Stadler, Steve Hoffmann:
Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinform. 28(13): 1698-1704 (2012) - [j111]Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler:
From event-labeled gene trees to species trees. BMC Bioinform. 13(S-19): S6 (2012) - [j110]Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler:
Diagonalized Cartesian products of s-prime graphs are s-prime. Discret. Math. 312(1): 74-80 (2012) - [j109]Ivo L. Hofacker, Christian M. Reidys, Peter F. Stadler:
Symmetric circular matchings and RNA folding. Discret. Math. 312(1): 100-112 (2012) - [j108]Lydia Ostermeier, Marc Hellmuth, Peter F. Stadler:
The Cartesian product of hypergraphs. J. Graph Theory 70(2): 180-196 (2012) - [j107]Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler:
A Survey on Hypergraph Products. Math. Comput. Sci. 6(1): 1-32 (2012) - [j106]Jan Engelhardt, Peter F. Stadler:
Hidden treasures in unspliced EST data. Theory Biosci. 131(1): 49-57 (2012) - [c40]Markus Rohrschneider, Peter F. Stadler, Gerik Scheuermann:
A Visual Cross-Database Comparison of Metabolic Networks. ISVC (2) 2012: 678-687 - [c39]Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker, Peter F. Stadler:
RNA Folding Algorithms with G-Quadruplexes. BSB 2012: 49-60 - [i2]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars. CoRR abs/1208.3153 (2012) - 2011
- [j105]Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, Christoph Flamm:
In Silico Evolution of Early Metabolism. Artif. Life 17(2): 87-108 (2011) - [j104]Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F. Stadler:
Fast local fragment chaining using sum-of-pair gap costs. Algorithms Mol. Biol. 6: 4 (2011) - [j103]Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker:
ViennaRNA Package 2.0. Algorithms Mol. Biol. 6: 26 (2011) - [j102]Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, Hakim Tafer:
PLEXY: efficient target prediction for box C/D snoRNAs. Bioinform. 27(2): 279-280 (2011) - [j101]Peter Menzel, Peter F. Stadler, Jan Gorodkin:
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinform. 27(3): 317-325 (2011) - [j100]Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen, Robert C. Penner, Peter F. Stadler, Markus E. Nebel:
Topology and prediction of RNA pseudoknots. Bioinform. 27(8): 1076-1085 (2011) - [j99]Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
A folding algorithm for extended RNA secondary structures. Bioinform. 27(13): 129-136 (2011) - [j98]Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, Peter F. Stadler:
Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinform. 27(14): 1894-1900 (2011) - [j97]Hakim Tafer, Fabian Amman, Florian Eggenhofer, Peter F. Stadler, Ivo L. Hofacker:
Fast accessibility-based prediction of RNA-RNA interactions. Bioinform. 27(14): 1934-1940 (2011) - [j96]Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F. Stadler, Sonja J. Prohaska:
Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinform. 12: 124 (2011) - [j95]Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, Steve Hoffmann:
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 39(Web-Server-Issue): 112-117 (2011) - [j94]Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker:
RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res. 39(Web-Server-Issue): 149-154 (2011) - [c38]Wolfgang Otto, Peter F. Stadler, Sonja J. Prohaska:
Phylogenetic Footprinting and Consistent Sets of Local Aligments. CPM 2011: 118-131 - [c37]David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, Peter F. Stadler:
MicroRNA or Not MicroRNA? BSB 2011: 1-9 - [i1]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete. CoRR abs/1110.6051 (2011) - 2010
- [j93]Christian Arnold, Peter F. Stadler:
Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Algorithms Mol. Biol. 5: 25 (2010) - [j92]Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler:
Target prediction and a statistical sampling algorithm for RNA-RNA interaction. Bioinform. 26(2): 175-181 (2010) - [j91]Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler:
RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinform. 26(5): 610-616 (2010) - [j90]Mario Fasold, Peter F. Stadler, Hans Binder:
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinform. 11: 207 (2010) - [j89]Manja Marz, Nathalie Vanzo, Peter F. Stadler:
Temperature-Dependent Structural Variability of RNAs: spliced Leader RNAs and their Evolutionary History. J. Bioinform. Comput. Biol. 8(1): 1-17 (2010) - [j88]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:
The primary transcriptome of the major human pathogen Helicobacter pylori. Nat. 464(7286): 250-255 (2010) - [j87]Stefan Jänicke, Christian Heine, Marc Hellmuth, Peter F. Stadler, Gerik Scheuermann:
Visualization of Graph Products. IEEE Trans. Vis. Comput. Graph. 16(6): 1082-1089 (2010) - [c36]Alexander Ullrich, Christoph Flamm, Markus Rohrschneider, Peter F. Stadler:
In Silico Evolution of Early Metabolism. ALIFE 2010: 57-64 - [c35]Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska:
Quantitative Comparison of Genomic-Wide Protein Domain Distributions. GCB 2010: 93-102 - [c34]Markus Rohrschneider, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, Gerik Scheuermann:
Visual Network Analysis of Dynamic Metabolic Pathways. ISVC (1) 2010: 316-327 - [c33]Rolf Backofen, Hamidreza Chitsaz, Ivo L. Hofacker, Süleyman Cenk Sahinalp, Peter F. Stadler:
Session Introduction. Pacific Symposium on Biocomputing 2010: 54-56 - [c32]Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler:
RNAz 2.0: Improved Noncoding RNA Detection. Pacific Symposium on Biocomputing 2010: 69-79 - [c31]David Langenberger, Clara Bermudez-Santana, Peter F. Stadler, Steve Hoffmann:
Identification and Classification of Small RNAs in Transcriptome Sequence Data. Pacific Symposium on Biocomputing 2010: 80-87 - [c30]Peter F. Stadler:
Evolution of the Long Non-coding RNAs MALAT1 and MENbeta/epsilon. BSB 2010: 1-12 - [c29]Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska:
Detection of Protein Domains in Eukaryotic Genome Sequences. BSB 2010: 71-74 - [e3]Carlos Eduardo Ferreira, Satoru Miyano, Peter F. Stadler:
Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics, BSB 2010, Rio de Janeiro, Brazil, August 31-September 3, 2010. Proceedings. Lecture Notes in Computer Science 6268, Springer 2010, ISBN 978-3-642-15059-3 [contents]
2000 – 2009
- 2009
- [j86]Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler:
A Topological Approach to Chemical Organizations. Artif. Life 15(1): 71-88 (2009) - [j85]Philipp-Jens Ostermeier, Marc Hellmuth, Josef Leydold, Konstantin Klemm, Peter F. Stadler:
A note on quasi-robust cycle bases. Ars Math. Contemp. 2(2): 231-240 (2009) - [j84]Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin:
Structural profiles of human miRNA families from pairwise clustering. Bioinform. 25(3): 291-294 (2009) - [j83]Markus Riester, Peter F. Stadler, Konstantin Klemm:
FRANz: reconstruction of wild multi-generation pedigrees. Bioinform. 25(16): 2134-2139 (2009) - [j82]David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovich, Peter F. Stadler:
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinform. 25(18): 2298-2301 (2009) - [j81]Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler:
Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinform. 25(20): 2646-2654 (2009) - [j80]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:
Sequence assembly. Comput. Biol. Chem. 33(2): 121-136 (2009) - [j79]Andreas W. M. Dress, Bülent Karasözen, Peter F. Stadler, Gerhard-Wilhelm Weber:
Preface. Discret. Appl. Math. 157(10): 2217-2220 (2009) - [j78]Konstantin Klemm, Peter F. Stadler:
A note on fundamental, non-fundamental, and robust cycle bases. Discret. Appl. Math. 157(10): 2432-2438 (2009) - [j77]Axel Mosig, Türker Bíyíkoglu, Sonja J. Prohaska, Peter F. Stadler:
Discovering cis-regulatory modules by optimizing barbecues. Discret. Appl. Math. 157(10): 2458-2468 (2009) - [j76]Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler:
Approximate graph products. Eur. J. Comb. 30(5): 1119-1133 (2009) - [j75]Marc Hellmuth, Wilfried Imrich, Werner Klöckl, Peter F. Stadler:
Local Algorithms for the Prime Factorization of Strong Product Graphs. Math. Comput. Sci. 2(4): 653-682 (2009) - [j74]Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz:
tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37(Database-Issue): 159-162 (2009) - [j73]Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller:
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures. PLoS Comput. Biol. 5(9) (2009) - [j72]Karen E. Chambers, Ryan McDaniell, Jeremy D. Raincrow, Maya Deshmukh, Peter F. Stadler, Chi-hua Chiu:
Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory Biosci. 128(2): 109-120 (2009) - [j71]Peter F. Stadler, Sonja J. Prohaska, Christian V. Forst, David C. Krakauer:
Defining genes: a computational framework. Theory Biosci. 128(3): 165-170 (2009) - [c28]Andreas Heffel, Sonja J. Prohaska, Peter F. Stadler, Gerhard Kauer, Jens-Peer Kuska:
Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns. Bildverarbeitung für die Medizin 2009: 415-419 - [c27]Peter Menzel, Jan Gorodkin, Peter F. Stadler:
Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search. GCB 2009: 211-220 - [e2]Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, Peter F. Stadler:
German Conference on Bioinformatics 2009, 28th to 30th September 2009, Martin Luther University Halle-Wittenberg, Germany. LNI P-157, GI 2009, ISBN 978-3-88579-251-2 [contents] - 2008
- [j70]Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler:
Noisy: Identification of problematic columns in multiple sequence alignments. Algorithms Mol. Biol. 3 (2008) - [j69]Jana Hertel, Ivo L. Hofacker, Peter F. Stadler:
SnoReport: computational identification of snoRNAs with unknown targets. Bioinform. 24(2): 158-164 (2008) - [j68]Stephan H. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler:
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinform. 9 (2008) - [j67]Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska:
SynBlast: Assisting the analysis of conserved synteny information. BMC Bioinform. 9 (2008) - [j66]Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler:
Duplicated RNA genes in teleost Fish genomes. J. Bioinform. Comput. Biol. 6(6): 1157-1175 (2008) - [j65]Sonja J. Prohaska, Peter F. Stadler:
"Genes". Theory Biosci. 127(3): 215-221 (2008) - [c26]Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker:
Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. BIRD 2008: 114-127 - [c25]Markus Riester, Peter F. Stadler, Konstantin Klemm:
FRANz: Fast Reconstruction of Wild Pedigrees. German Conference on Bioinformatics 2008: 168-177 - [c24]Andreas Heffel, Peter F. Stadler, Sonja J. Prohaska, Gerhard Kauer, Jens-Peer Kuska:
Process flow for classification and clustering of fruit fly gene expression patterns. ICIP 2008: 721-724 - [p1]Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Visualization of Barrier Tree Sequences Revisited. Visualization in Medicine and Life Sciences 2008: 275-290 - 2007
- [j64]Kristin Reiche, Peter F. Stadler:
RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol. Biol. 2 (2007) - [j63]Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf:
CREx: inferring genomic rearrangements based on common intervals. Bioinform. 23(21): 2957-2958 (2007) - [j62]Matthias Kruspe, Peter F. Stadler:
Progressive multiple sequence alignments from triplets. BMC Bioinform. 8 (2007) - [j61]Manja Marz, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler:
U7 snRNAs: A Computational Survey. Genom. Proteom. Bioinform. 5(3-4): 187-195 (2007) - [j60]Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen:
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering. PLoS Comput. Biol. 3(4) (2007) - [j59]Olaf Breidbach, Jürgen Jost, Peter F. Stadler:
Towards theoretical formalisms. Theory Biosci. 126(1): 1-2 (2007) - [j58]Axel Mosig, Guofeng Meng, Bärbel M. R. Stadler, Peter F. Stadler:
Evolution of the vertebrate Y RNA cluster. Theory Biosci. 126(1): 9-14 (2007) - [j57]Marleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelsson, Detlef Bernhard, Martin Schlegel:
The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. Theory Biosci. 126(1): 35-42 (2007) - [c23]Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler:
Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA 2007: 194-212 - [c22]Axel Mosig, Peter Menzel, Peter F. Stadler:
Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. German Conference on Bioinformatics 2007: 68-77 - [c21]Axel Mosig, Julian J.-L. Chen, Peter F. Stadler:
Homology Search with Fragmented Nucleic Acid Sequence Patterns. WABI 2007: 335-345 - [e1]Christopher R. Stephens, Marc Toussaint, L. Darrell Whitley, Peter F. Stadler:
Foundations of Genetic Algorithms, 9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers. Lecture Notes in Computer Science 4436, Springer 2007, ISBN 978-3-540-73479-6 [contents] - 2006
- [j56]Stephan H. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker:
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol. 1 (2006) - [j55]Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler:
Multiple sequence alignment with user-defined anchor points. Algorithms Mol. Biol. 1 (2006) - [j54]Burkhard Morgenstern, Peter F. Stadler:
New journal: Algorithms for Molecular Biology. Algorithms Mol. Biol. 1 (2006) - [j53]Stephan H. Bernhart, Ivo L. Hofacker, Peter F. Stadler:
Local RNA base pairing probabilities in large sequences. Bioinform. 22(5): 614-615 (2006) - [j52]Ivo L. Hofacker, Peter F. Stadler:
Memory efficient folding algorithms for circular RNA secondary structures. Bioinform. 22(10): 1172-1176 (2006) - [j51]Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
Thermodynamics of RNA-RNA binding. Bioinform. 22(10): 1177-1182 (2006) - [j50]Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinform. 7: 67 (2006) - [j49]Wilfried Imrich, Peter F. Stadler:
A prime factor theorem for a generalized direct product. Discuss. Math. Graph Theory 26(1): 135-140 (2006) - [j48]Axel Mosig, Katrin Sameith, Peter F. Stadler:
Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences. Genom. Proteom. Bioinform. 4(1): 56-60 (2006) - [j47]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:
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res. 34(Database-Issue): 135-139 (2006) - [j46]Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12(5): 781-788 (2006) - [c20]Axel Mosig, Ivo L. Hofacker, Peter F. Stadler:
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs. German Conference on Bioinformatics 2006: 93-102 - [c19]Jana Hertel, Peter F. Stadler:
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. ISMB (Supplement of Bioinformatics) 2006: 197-202 - [c18]Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm:
Visualization of Lattice-Based Protein Folding Simulations. IV 2006: 89-94 - 2005
- [j45]Camille Stephan-Otto Attolini, Peter F. Stadler:
Neutral Networks of Interacting RNA Secondary Structures. Adv. Complex Syst. 8(2-3): 275-283 (2005) - [j44]Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran Ramaswami Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff:
Multiple sequence alignment with user-defined constraints at GOBICS. Bioinform. 21(7): 1271-1273 (2005) - [j43]Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler:
Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinform. 6: 160 (2005) - [j42]Petra M. Gleiss, Josef Leydold, Peter F. Stadler:
Minimum path bases and relevant paths. Networks 46(3): 119-123 (2005) - [j41]Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler:
Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 102(7): 2454-2459 (2005) - [j40]Ante Graovac, Peter F. Stadler:
MATH/CHEM/COMP 2004 Contributions. Theory Biosci. 123(4): 263-264 (2005) - [j39]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:
Evolutionary patterns of non-coding RNAs. Theory Biosci. 123(4): 301-369 (2005) - [j38]Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson:
Erratum to "Aggregation of variables and system decomposability: Applications to fitness landscape analysis. Theory Biosci. 124(1): 87-88 (2005) - [c17]Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm:
CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL 2005: 500-509 - [c16]Gil Benkö, Christoph Flamm, Peter F. Stadler:
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL 2005: 725-733 - [c15]Kristin Missal, Dominic Rose, Peter F. Stadler:
Non-coding RNAs in Ciona intestinalis. ECCB/JBI 2005: 78 - [c14]Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker:
Thermodynamics of RNA-RNA Binding. German Conference on Bioinformatics 2005: 3-13 - [c13]Ivo L. Hofacker, Peter F. Stadler:
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics 2005: 15-25 - 2004
- [j37]Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler:
Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinform. 20(2): 186-190 (2004) - [j36]Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits:
Conserved RNA secondary structures in viral genomes: a survey. Bioinform. 20(10): 1495-1499 (2004) - [j35]Ivo L. Hofacker, Stephan H. Bernhart, Peter F. Stadler:
Alignment of RNA base pairing probability matrices. Bioinform. 20(14): 2222-2227 (2004) - [j34]Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler:
Counterexamples in Chemical Ring Perception. J. Chem. Inf. Model. 44(2): 323-331 (2004) - [j33]Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler:
The Footprint Sorting Problem. J. Chem. Inf. Model. 44(2): 332-338 (2004) - [j32]Christina Witwer, Ivo L. Hofacker, Peter F. Stadler:
Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE ACM Trans. Comput. Biol. Bioinform. 1(2): 66-77 (2004) - [j31]Olaf Breidbach, Jürgen Jost, Peter F. Stadler, Michael S. Weingarten:
Editorial. Theory Biosci. 123(1): 1-2 (2004) - [j30]Max Shpak, Peter F. Stadler, Günter P. Wagner, Joachim Hermisson:
Aggregation of variables and system decomposition: Applications to fitness landscape analysis. Theory Biosci. 123(1): 33-68 (2004) - [j29]Sonja J. Prohaska, Peter F. Stadler:
The duplication of the Hox gene clusters in teleost fishes. Theory Biosci. 123(1): 89-110 (2004) - [j28]Max Shpak, Peter F. Stadler, Günter P. Wagner, Lee Altenberg:
Simon-Ando decomposability and fitness landscapes. Theory Biosci. 123(2): 139-180 (2004) - [c12]Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran Ramaswami Subramanian, Peter F. Stadler:
Multiple sequence alignment with user-defined constraints. German Conference on Bioinformatics 2004: 25-36 - [c11]C. Thurner, Ivo L. Hofacker, Peter F. Stadler:
Conserved RNA Pseudoknots. German Conference on Bioinformatics 2004: 207-216 - [c10]Ivo L. Hofacker, Peter F. Stadler:
The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science 2004: 728-735 - 2003
- [j27]Bärbel M. R. Stadler, Peter F. Stadler:
Molecular Replicator Dynamics. Adv. Complex Syst. 6(1): 47-78 (2003) - [j26]Petra M. Gleiss, Josef Leydold, Peter F. Stadler:
Circuit bases of strongly connected digraphs. Discuss. Math. Graph Theory 23(2): 241-260 (2003) - [j25]Peter F. Stadler, Christoph Flamm:
Barrier Trees on Poset-Valued Landscapes. Genet. Program. Evolvable Mach. 4(1): 7-20 (2003) - [j24]Gil Benkö, Christoph Flamm, Peter F. Stadler:
A Graph-Based Toy Model of Chemistry. J. Chem. Inf. Comput. Sci. 43(4): 1085-1093 (2003) - [j23]Peter F. Stadler:
Minimum cycle bases of Halin graphs. J. Graph Theory 43(2): 150-155 (2003) - [c9]Gil Benkö, Christoph Flamm, Peter F. Stadler:
Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL 2003: 10-19 - [c8]Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler:
Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics 2003: 1-7 - [c7]Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits:
Conserved RNA secondary structures in viral genomes: A survey. German Conference on Bioinformatics 2003: 57-62 - 2002
- [j22]Wilfried Imrich, Peter F. Stadler:
Minimum cycle bases of product graphs. Australas. J Comb. 26: 233-244 (2002) - [j21]Oliver Bastert, Daniel N. Rockmore, Peter F. Stadler, Gottfried Tinhofer:
Landscapes on spaces of trees. Appl. Math. Comput. 131(2-3): 439-459 (2002) - [j20]Bärbel M. R. Stadler, Peter F. Stadler:
Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry. J. Chem. Inf. Comput. Sci. 42(3): 577-585 (2002) - [j19]Christian M. Reidys, Peter F. Stadler:
Combinatorial Landscapes. SIAM Rev. 44(1): 3-54 (2002) - [c6]Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler:
Stochastic pairwise alignments. ECCB 2002: 153-160 - 2001
- [j18]Petra M. Gleiss, Peter F. Stadler, Andreas Wagner, David A. Fell:
Relevant cycles in Chemical reaction Networks. Adv. Complex Syst. 4(2-3): 207-226 (2001) - [j17]Peter F. Stadler, Anita Mehta, Jean-Marc Luck:
Glassy States in a shaken Sandbox. Adv. Complex Syst. 4(4): 429-440 (2001) - [j16]Christian M. Reidys, Peter F. Stadler:
Neutrality in fitness landscapes. Appl. Math. Comput. 117(2-3): 321-350 (2001) - 2000
- [j15]Jan Cupal, Stephan Kopp, Peter F. Stadler:
RNA Shape Space Topology. Artif. Life 6(1): 3-23 (2000) - [j14]Petra M. Gleiss, Josef Leydold, Peter F. Stadler:
Interchangeability of Relevant Cycles in Graphs. Electron. J. Comb. 7 (2000) - [j13]Martin Fekete, Ivo L. Hofacker, Peter F. Stadler:
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. J. Comput. Biol. 7(1-2): 171-182 (2000)
1990 – 1999
- 1999
- [j12]Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
RNA In Silico The Computational Biology of RNA Secondary Structures. Adv. Complex Syst. 2(1): 65-100 (1999) - [j11]Eric Bonabeau, Peter F. Stadler:
Call for proposals. Adv. Complex Syst. 2(3): 195-196 (1999) - [j10]Ivo L. Hofacker, Peter F. Stadler:
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Comput. Chem. 23(3-4): 401-414 (1999) - [c5]Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler:
Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics 1999: 73-79 - [c4]G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler:
An efficient potential for protein sequence design. German Conference on Bioinformatics 1999: 107-112 - 1998
- [j9]Wim Hordijk, Peter F. Stadler:
Amplitude Spectra of Fitness Landscapes. Adv. Complex Syst. 1(1): 39-66 (1998) - [j8]Josef Leydold, Peter F. Stadler:
Minimal Cycle Bases of Outerplanar Graphs. Electron. J. Comb. 5 (1998) - [j7]Ivo L. Hofacker, Peter Schuster, Peter F. Stadler:
Combinatorics of RNA Secondary Structures. Discret. Appl. Math. 88(1-3): 207-237 (1998) - 1997
- [j6]Peter F. Stadler, Günter P. Wagner:
Algebraic Theory of Recombination Spaces. Evol. Comput. 5(3): 241-275 (1997) - [c3]Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler:
Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. ISMB 1997: 88-91 - 1996
- [j5]Christian M. Reidys, Peter F. Stadler:
Bio-molecular Shapes and Algebraic Structures. Comput. Chem. 20(1): 85-94 (1996) - [j4]Robert Happel, Peter F. Stadler:
Canonical approximation of fitness landscapes. Complex. 2(1): 53-58 (1996) - [j3]Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler:
Base Pairing Probabilities in a Complete HIV-1 RNA. J. Comput. Biol. 3(2): 253-274 (1996) - [c2]Jan Cupal, Ivo L. Hofacker, Peter F. Stadler:
Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. German Conference on Bioinformatics 1996: 184-186 - [c1]Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz:
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. KDD 1996: 20-25 - 1995
- [j2]Peter F. Stadler:
Random walks and orthogonal functions associated with highly symmetric graphs. Discret. Math. 145(1-3): 229-237 (1995) - 1994
- [j1]Peter Schuster, Peter F. Stadler:
Landscapes: Complex Optimization Problems and Biopolymer Structures. Comput. Chem. 18(3): 295-324 (1994)
Coauthor Index
Jakob L. Andersen
aka: Jakob Lykke Andersen
aka: Jakob Lykke Andersen
André C. P. L. F. de Carvalho
aka: André Carlos Ponce de Leon Ferreira de Carvalho
aka: André Carlos Ponce de Leon Ferreira de Carvalho
[j237] [c68] [i55] [j214] [j212] [i44] [c61] [c60] [c57] [j174] [j164] [c54] [i26] [i18] [i15] [c52] [c51] [i13] [i12] [i10] [j133] [j124] [c50] [i6] [j120] [j119] [c45] [i4] [i3] [i2] [j105] [j103] [i1] [c36] [j86] [j70] [p1] [c23] [j56] [j50] [j46] [c18] [j39] [c17] [c16] [j34] [j25] [j24] [c9] [c8] [j12] [c3]
[c72] [c71] [i61] [j235] [j232] [j231] [j229] [j227] [j225] [j224] [c70] [i58] [i57] [i54] [j223] [j221] [j217] [j216] [j212] [i53] [i52] [j210] [j208] [j207] [j201] [j200] [j195] [c65] [c62] [i51] [i50] [i49] [i48] [i47] [i46] [i45] [i43] [i42] [j194] [j192] [j190] [j186] [i39] [i38] [i37] [i36] [i35] [i34] [i33] [i32] [i31] [i30] [i29] [j173] [j172] [c53] [i25] [i24] [i23] [i22] [i21] [i20] [i19] [i17] [j148] [i14] [i11] [j145] [j138] [i9] [j132] [j126] [j125] [i8] [i7] [i5] [j115] [j111] [j110] [j108] [j107] [j87] [j85] [j76] [j75]
Maribel Hernandez-Rosales
aka: Maribel Hernández-Rosales
aka: Maribel Hernández-Rosales
[j241] [j236] [j228] [c69] [c61] [c60] [c55] [j153] [j152] [j151] [j137] [j130] [j128] [j127] [j118] [j117] [c43] [c42] [j109] [c39] [j103] [j99] [j97] [j94] [j91] [c33] [c32] [j69] [j68] [c26] [p1] [j60] [c23] [j56] [j53] [j52] [j51] [j50] [j47] [j46] [c20] [j43] [j41] [j39] [c14] [c13] [j37] [j36] [j35] [j32] [c11] [c10] [c7] [c6] [j13] [j12] [j10] [c5] [c4] [j7] [c2] [c1]
Maria Emília M. T. Walter
aka: Maria Emília Telles Walter
aka: Maria Emília Telles Walter
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