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ORCIDBibTeX records: Peter F. Stadler
@article{DBLP:journals/algorithms/LaffitteS24,
author = {Marcos E. Gonz{\'{a}}lez Laffitte and
Peter F. Stadler},
title = {Progressive Multiple Alignment of Graphs},
journal = {Algorithms},
volume = {17},
number = {3},
pages = {116},
year = {2024},
url = {https://doi.org/10.3390/a17030116},
doi = {10.3390/A17030116},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/LaffitteS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/AndersS24,
author = {John Anders and
Peter F. Stadler},
title = {RNAcode{\_}Web - Convenient identification of evolutionary conserved
protein coding regions},
journal = {J. Integr. Bioinform.},
volume = {20},
number = {3},
year = {2024},
url = {https://doi.org/10.1515/jib-2022-0046},
doi = {10.1515/JIB-2022-0046},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/AndersS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/caldam/ShanavasCHS24,
author = {Ameera Vaheeda Shanavas and
Manoj Changat and
Marc Hellmuth and
Peter F. Stadler},
editor = {Subrahmanyam Kalyanasundaram and
Anil Maheshwari},
title = {Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs},
booktitle = {Algorithms and Discrete Applied Mathematics - 10th International Conference,
{CALDAM} 2024, Bhilai, India, February 15-17, 2024, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14508},
pages = {148--161},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-3-031-52213-0\_11},
doi = {10.1007/978-3-031-52213-0\_11},
timestamp = {Fri, 26 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/caldam/ShanavasCHS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2401-15662,
author = {Manoj Changat and
Ameera Vaheeda Shanavas and
Peter F. Stadler},
title = {Transit Functions and Clustering Systems},
journal = {CoRR},
volume = {abs/2401.15662},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.15662},
doi = {10.48550/ARXIV.2401.15662},
eprinttype = {arXiv},
eprint = {2401.15662},
timestamp = {Tue, 06 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-15662.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/YaoLHS23,
author = {Hua{-}Ting Yao and
Ronny Lorenz and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Mono-valent salt corrections for {RNA} secondary structures in the
ViennaRNA package},
journal = {Algorithms Mol. Biol.},
volume = {18},
number = {1},
pages = {8},
year = {2023},
url = {https://doi.org/10.1186/s13015-023-00236-0},
doi = {10.1186/S13015-023-00236-0},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/YaoLHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SchallerHLSWH23,
author = {David Schaller and
Tom Hartmann and
Manuel Lafond and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
title = {Relative timing information and orthology in evolutionary scenarios},
journal = {Algorithms Mol. Biol.},
volume = {18},
number = {1},
pages = {16},
year = {2023},
url = {https://doi.org/10.1186/s13015-023-00240-4},
doi = {10.1186/S13015-023-00240-4},
timestamp = {Mon, 20 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/SchallerHLSWH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchaferRSSHBFV23,
author = {Richard A. Sch{\"{a}}fer and
Dominik Rabsch and
Guillaume E. Scholz and
Peter F. Stadler and
Wolfgang R. Hess and
Rolf Backofen and
J{\"{o}}rg Fallmann and
Bj{\"{o}}rn Vo{\ss}},
title = {{RNA} interaction format: a general data format for {RNA} interactions},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad665},
doi = {10.1093/BIOINFORMATICS/BTAD665},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchaferRSSHBFV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FiedlerBMS23,
author = {Lisa Fiedler and
Matthias Bernt and
Martin Middendorf and
Peter F. Stadler},
title = {Detecting gene breakpoints in noisy genome sequences using position-annotated
colored de-Bruijn graphs},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {235},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05371-4},
doi = {10.1186/S12859-023-05371-4},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FiedlerBMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/SeemannMSH23,
author = {Carsten R. Seemann and
Vincent Moulton and
Peter F. Stadler and
Marc Hellmuth},
title = {Planar median graphs and cubesquare-graphs},
journal = {Discret. Appl. Math.},
volume = {331},
pages = {38--58},
year = {2023},
url = {https://doi.org/10.1016/j.dam.2023.01.022},
doi = {10.1016/J.DAM.2023.01.022},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/SeemannMSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/KorchmarosSHS23,
author = {Annachiara Korchmaros and
David Schaller and
Marc Hellmuth and
Peter F. Stadler},
title = {Quasi-best match graphs},
journal = {Discret. Appl. Math.},
volume = {331},
pages = {104--125},
year = {2023},
url = {https://doi.org/10.1016/j.dam.2023.01.015},
doi = {10.1016/J.DAM.2023.01.015},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/KorchmarosSHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gc/HellmuthHMSS23,
author = {Marc Hellmuth and
Katharina T. Huber and
Vincent Moulton and
Guillaume E. Scholz and
Peter F. Stadler},
title = {Injective Split Systems},
journal = {Graphs Comb.},
volume = {39},
number = {4},
pages = {65},
year = {2023},
url = {https://doi.org/10.1007/s00373-023-02660-w},
doi = {10.1007/S00373-023-02660-W},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/gc/HellmuthHMSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/WaldlSLBHLS23,
author = {Maria Waldl and
Thomas Spicher and
Ronny Lorenz and
Irene K. Beckmann and
Ivo L. Hofacker and
Sarah von L{\"{o}}hneysen and
Peter F. Stadler},
title = {Local {RNA} folding revisited},
journal = {J. Bioinform. Comput. Biol.},
volume = {21},
number = {4},
pages = {2350016:1--2350016:19},
year = {2023},
url = {https://doi.org/10.1142/S0219720023500166},
doi = {10.1142/S0219720023500166},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbcb/WaldlSLBHLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamdm/SchallerHS23,
author = {David Schaller and
Marc Hellmuth and
Peter F. Stadler},
title = {Orientation of Fitch Graphs and Reconciliation-Free Inference of Horizontal
Gene Transfer in Gene Trees},
journal = {{SIAM} J. Discret. Math.},
volume = {37},
number = {3},
pages = {2172--2207},
year = {2023},
url = {https://doi.org/10.1137/22m150736x},
doi = {10.1137/22M150736X},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/siamdm/SchallerHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/0001GHS23,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Best Match Graphs With Binary Trees},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {20},
number = {3},
pages = {1679--1690},
year = {2023},
url = {https://doi.org/10.1109/TCBB.2022.3143870},
doi = {10.1109/TCBB.2022.3143870},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/0001GHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/HellmuthSS23,
author = {Marc Hellmuth and
David Schaller and
Peter F. Stadler},
title = {Clustering systems of phylogenetic networks},
journal = {Theory Biosci.},
volume = {142},
number = {4},
pages = {301--358},
year = {2023},
url = {https://doi.org/10.1007/s12064-023-00398-w},
doi = {10.1007/S12064-023-00398-W},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tib/HellmuthSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/HellmuthSP23,
author = {Marc Hellmuth and
Peter F. Stadler and
Sandhya Thekkumpadan Puthiyaveedu},
editor = {Weili Wu and
Guangmo Tong},
title = {Fitch Graph Completion},
booktitle = {Computing and Combinatorics - 29th International Conference, {COCOON}
2023, Hawaii, HI, USA, December 15-17, 2023, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {14423},
pages = {225--237},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-49193-1\_17},
doi = {10.1007/978-3-031-49193-1\_17},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cocoon/HellmuthSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/LohneysenSVYLHS23,
author = {Sarah von L{\"{o}}hneysen and
Thomas Spicher and
Yuliia Varenyk and
Hua{-}Ting Yao and
Ronny Lorenz and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {Phylogenetic Information as Soft Constraints in {RNA} Secondary Structure
Prediction},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {267--279},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_21},
doi = {10.1007/978-981-99-7074-2\_21},
timestamp = {Fri, 27 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/LohneysenSVYLHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AndersenBFFMS23,
author = {Jakob L. Andersen and
Sissel Banke and
Rolf Fagerberg and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
editor = {Xuan Guo and
Serghei Mangul and
Murray Patterson and
Alexander Zelikovsky},
title = {On the Realisability of Chemical Pathways},
booktitle = {Bioinformatics Research and Applications - 19th International Symposium,
{ISBRA} 2023, Wroc{\l}aw, Poland, October 9-12, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14248},
pages = {409--419},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-7074-2\_32},
doi = {10.1007/978-981-99-7074-2\_32},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/isbra/AndersenBFFMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/KatherLS23,
author = {Karl K{\"{a}}ther and
Steffen Lemke and
Peter F. Stadler},
editor = {Ignacio Rojas and
Olga Valenzuela and
Fernando Rojas Ruiz and
Luis Javier Herrera and
Francisco M. Ortu{\~{n}}o},
title = {Annotation-Free Identification of Potential Synteny Anchors},
booktitle = {Bioinformatics and Biomedical Engineering - 10th International Work-Conference,
{IWBBIO} 2023, Meloneras, Gran Canaria, Spain, July 12-14, 2023 Proceedings,
Part {I}},
series = {Lecture Notes in Computer Science},
volume = {13919},
pages = {217--230},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-34953-9\_17},
doi = {10.1007/978-3-031-34953-9\_17},
timestamp = {Tue, 26 Dec 2023 17:13:20 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/KatherLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2303-16258,
author = {Konstantin Klemm and
Anita Mehta and
Peter F. Stadler},
title = {Optimisation via encodings: a renormalisation group perspective},
journal = {CoRR},
volume = {abs/2303.16258},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2303.16258},
doi = {10.48550/ARXIV.2303.16258},
eprinttype = {arXiv},
eprint = {2303.16258},
timestamp = {Fri, 14 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2303-16258.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-11826,
author = {Marc Hellmuth and
Peter F. Stadler},
title = {The Theory of Gene Family Histories},
journal = {CoRR},
volume = {abs/2304.11826},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.11826},
doi = {10.48550/ARXIV.2304.11826},
eprinttype = {arXiv},
eprint = {2304.11826},
timestamp = {Wed, 03 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-11826.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-06878,
author = {Marc Hellmuth and
Peter F. Stadler and
Sandhya Thekkumpadan Puthiyaveedu},
title = {Fitch Graph Completion},
journal = {CoRR},
volume = {abs/2306.06878},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.06878},
doi = {10.48550/ARXIV.2306.06878},
eprinttype = {arXiv},
eprint = {2306.06878},
timestamp = {Fri, 16 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-06878.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-06351,
author = {Angel Garcia{-}Chung and
Marisol Berm{\'{u}}dez{-}Monta{\~{n}}a and
Peter F. Stadler and
J{\"{u}}rgen Jost and
Guillermo Restrepo},
title = {Chemically inspired Erd{\H{o}}s-R{\'{e}}nyi oriented hypergraphs},
journal = {CoRR},
volume = {abs/2309.06351},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.06351},
doi = {10.48550/ARXIV.2309.06351},
eprinttype = {arXiv},
eprint = {2309.06351},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-06351.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-10629,
author = {Jakob L. Andersen and
Sissel Banke and
Rolf Fagerberg and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {On the Realisability of Chemical Pathways},
journal = {CoRR},
volume = {abs/2309.10629},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.10629},
doi = {10.48550/ARXIV.2309.10629},
eprinttype = {arXiv},
eprint = {2309.10629},
timestamp = {Tue, 26 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-10629.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-13634,
author = {Ameera Vaheeda Shanavas and
Manoj Changat and
Marc Hellmuth and
Peter F. Stadler},
title = {Unique Least Common Ancestors and Clusters in Directed Acyclic Graphs},
journal = {CoRR},
volume = {abs/2309.13634},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.13634},
doi = {10.48550/ARXIV.2309.13634},
eprinttype = {arXiv},
eprint = {2309.13634},
timestamp = {Wed, 27 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-13634.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/aam/HartmannBMSWH22,
author = {Tom Hartmann and
Max Bannach and
Martin Middendorf and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
title = {Complete edge-colored permutation graphs},
journal = {Adv. Appl. Math.},
volume = {139},
pages = {102377},
year = {2022},
url = {https://doi.org/10.1016/j.aam.2022.102377},
doi = {10.1016/J.AAM.2022.102377},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/aam/HartmannBMSWH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/adam/ArguelloS22,
author = {Anahy Santiago Arguello and
Peter F. Stadler},
title = {Whitney's connectivity inequalities for directed hypergraphs},
journal = {Art Discret. Appl. Math.},
volume = {5},
number = {1},
year = {2022},
url = {https://doi.org/10.26493/2590-9770.1380.1c9},
doi = {10.26493/2590-9770.1380.1C9},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/adam/ArguelloS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/adam/ValdiviaHGSH22,
author = {Dulce I. Valdivia and
Maribel Hern{\'{a}}ndez{-}Rosales and
Manuela Gei{\ss} and
Peter F. Stadler and
Marc Hellmuth},
title = {Hierarchical and modularly-minimal vertex colorings},
journal = {Art Discret. Appl. Math.},
volume = {6},
number = {2},
pages = {2},
year = {2022},
url = {https://doi.org/10.26493/2590-9770.1422.9b6},
doi = {10.26493/2590-9770.1422.9B6},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/adam/ValdiviaHGSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/StadlerW22,
author = {Peter F. Stadler and
Sebastian Will},
title = {Bi-alignments with affine gaps costs},
journal = {Algorithms Mol. Biol.},
volume = {17},
number = {1},
pages = {10},
year = {2022},
url = {https://doi.org/10.1186/s13015-022-00219-7},
doi = {10.1186/S13015-022-00219-7},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/StadlerW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BonidiaAASRSC22,
author = {Robson Bonidia and
Anderson P. Avila{-}Santos and
Breno L{\'{\i}}vio Silva de Almeida and
Peter F. Stadler and
Ulisses Nunes da Rocha and
Danilo Sipoli Sanches and
Andr{\'{e}} C. P. L. F. de Carvalho},
title = {BioAutoML: automated feature engineering and metalearning to predict
noncoding RNAs in bacteria},
journal = {Briefings Bioinform.},
volume = {23},
number = {4},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac218},
doi = {10.1093/BIB/BBAC218},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/BonidiaAASRSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/compnet/GuzmanSF22,
author = {Grover E. C. Guzman and
Peter F. Stadler and
Andr{\'{e}} Fujita},
title = {Efficient eigenvalue counts for tree-like networks},
journal = {J. Complex Networks},
volume = {10},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/comnet/cnac040},
doi = {10.1093/COMNET/CNAC040},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/compnet/GuzmanSF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/BruckmannSH22,
author = {Carmen Bruckmann and
Peter F. Stadler and
Marc Hellmuth},
title = {From modular decomposition trees to rooted median graphs},
journal = {Discret. Appl. Math.},
volume = {310},
pages = {1--9},
year = {2022},
url = {https://doi.org/10.1016/j.dam.2021.12.017},
doi = {10.1016/J.DAM.2021.12.017},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/BruckmannSH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/HellmuthSS22,
author = {Marc Hellmuth and
David Schaller and
Peter F. Stadler},
title = {Compatibility of partitions with trees, hierarchies, and split systems},
journal = {Discret. Appl. Math.},
volume = {314},
pages = {265--283},
year = {2022},
url = {https://doi.org/10.1016/j.dam.2022.03.014},
doi = {10.1016/J.DAM.2022.03.014},
timestamp = {Wed, 18 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/HellmuthSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/entropy/BonidiaAASRSC22,
author = {Robson Parmezan Bonidia and
Anderson P. Avila{-}Santos and
Breno L{\'{\i}}vio Silva de Almeida and
Peter F. Stadler and
Ulisses Nunes da Rocha and
Danilo Sipoli Sanches and
Andr{\'{e}} C. P. L. F. de Carvalho},
title = {Information Theory for Biological Sequence Classification: {A} Novel
Feature Extraction Technique Based on Tsallis Entropy},
journal = {Entropy},
volume = {24},
number = {10},
pages = {1398},
year = {2022},
url = {https://doi.org/10.3390/e24101398},
doi = {10.3390/E24101398},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/entropy/BonidiaAASRSC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/MullerFS22,
author = {Stefan M{\"{u}}ller and
Christoph Flamm and
Peter F. Stadler},
title = {What makes a reaction network "chemical"?},
journal = {J. Cheminformatics},
volume = {14},
number = {1},
pages = {63},
year = {2022},
url = {https://doi.org/10.1186/s13321-022-00621-8},
doi = {10.1186/S13321-022-00621-8},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/MullerFS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/ReinhardtS22,
author = {Franziska Reinhardt and
Peter F. Stadler},
title = {ExceS-A: an exon-centric split aligner},
journal = {J. Integr. Bioinform.},
volume = {19},
number = {1},
year = {2022},
url = {https://doi.org/10.1515/jib-2021-0040},
doi = {10.1515/JIB-2021-0040},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/ReinhardtS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/FlammHMNS22,
author = {Christoph Flamm and
Marc Hellmuth and
Daniel Merkle and
Nikolai N{\o}jgaard and
Peter F. Stadler},
title = {Generic Context-Aware Group Contributions},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {19},
number = {1},
pages = {429--442},
year = {2022},
url = {https://doi.org/10.1109/TCBB.2020.2998948},
doi = {10.1109/TCBB.2020.2998948},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/FlammHMNS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/EggersSS22,
author = {Dustyn Eggers and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
editor = {Nicole M. Scherer and
Raquel Cardoso de Melo Minardi},
title = {Accuracy of {RNA} Structure Prediction Depends on the Pseudoknot Grammar},
booktitle = {Advances in Bioinformatics and Computational Biology - 15th Brazilian
Symposium on Bioinformatics, {BSB} 2022, Buzios, Brazil, September
21-23, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13523},
pages = {20--31},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-21175-1\_3},
doi = {10.1007/978-3-031-21175-1\_3},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/EggersSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-13466,
author = {Marc Hellmuth and
David Schaller and
Peter F. Stadler},
title = {Clustering Systems of Phylogenetic Networks},
journal = {CoRR},
volume = {abs/2204.13466},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.13466},
doi = {10.48550/ARXIV.2204.13466},
eprinttype = {arXiv},
eprint = {2204.13466},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-13466.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2212-02201,
author = {David Schaller and
Tom Hartmann and
Manuel Lafond and
Nicolas Wieseke and
Marc Hellmuth and
Peter F. Stadler},
title = {Relative Timing Information and Orthology in Evolutionary Scenarios},
journal = {CoRR},
volume = {abs/2212.02201},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2212.02201},
doi = {10.48550/ARXIV.2212.02201},
eprinttype = {arXiv},
eprint = {2212.02201},
timestamp = {Thu, 08 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2212-02201.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/LealRSJ21,
author = {Wilmer Leal and
Guillermo Restrepo and
Peter F. Stadler and
J{\"{u}}rgen Jost},
title = {Forman-Ricci Curvature for hypergraphs},
journal = {Adv. Complex Syst.},
volume = {24},
number = {1},
pages = {2150003:1--2150003:24},
year = {2021},
url = {https://doi.org/10.1142/S021952592150003X},
doi = {10.1142/S021952592150003X},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/LealRSJ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/SchallerGHS21,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable
Best Match Graphs},
journal = {Algorithms},
volume = {14},
number = {4},
pages = {110},
year = {2021},
url = {https://doi.org/10.3390/a14040110},
doi = {10.3390/A14040110},
timestamp = {Sun, 16 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/SchallerGHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GatterLFDHS21,
author = {Thomas Gatter and
Sarah von L{\"{o}}hneysen and
J{\"{o}}rg Fallmann and
Polina Drozdova and
Tom Hartmann and
Peter F. Stadler},
title = {LazyB: fast and cheap genome assembly},
journal = {Algorithms Mol. Biol.},
volume = {16},
number = {1},
pages = {8},
year = {2021},
url = {https://doi.org/10.1186/s13015-021-00186-5},
doi = {10.1186/S13015-021-00186-5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/GatterLFDHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SchallerGHS21,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Heuristic algorithms for best match graph editing},
journal = {Algorithms Mol. Biol.},
volume = {16},
number = {1},
pages = {19},
year = {2021},
url = {https://doi.org/10.1186/s13015-021-00196-3},
doi = {10.1186/S13015-021-00196-3},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/SchallerGHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SchallerHS21,
author = {David Schaller and
Marc Hellmuth and
Peter F. Stadler},
title = {A simpler linear-time algorithm for the common refinement of rooted
phylogenetic trees on a common leaf set},
journal = {Algorithms Mol. Biol.},
volume = {16},
number = {1},
pages = {23},
year = {2021},
url = {https://doi.org/10.1186/s13015-021-00202-8},
doi = {10.1186/S13015-021-00202-8},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/SchallerHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NunnOSL21,
author = {Adam Nunn and
Christian Otto and
Peter F. Stadler and
David Langenberger},
title = {Comprehensive benchmarking of software for mapping whole genome bisulfite
data: from read alignment to {DNA} methylation analysis},
journal = {Briefings Bioinform.},
volume = {22},
number = {5},
year = {2021},
url = {https://doi.org/10.1093/bib/bbab021},
doi = {10.1093/BIB/BBAB021},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NunnOSL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NunnOSL21a,
author = {Adam Nunn and
Christian Otto and
Peter F. Stadler and
David Langenberger},
title = {Erratum to: Comprehensive benchmarking of software for mapping whole
genome bisulfite data: from read alignment to {DNA} methylation analysis},
journal = {Briefings Bioinform.},
volume = {22},
number = {5},
year = {2021},
url = {https://doi.org/10.1093/bib/bbab183},
doi = {10.1093/BIB/BBAB183},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/NunnOSL21a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GatterS21,
author = {Thomas Gatter and
Peter F. Stadler},
title = {Ry{\={u}}t{\={o}}: improved multi-sample transcript assembly for differential
transcript expression analysis and more},
journal = {Bioinform.},
volume = {37},
number = {23},
pages = {4307--4313},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab494},
doi = {10.1093/BIOINFORMATICS/BTAB494},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GatterS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AndersPJHBS21,
author = {John Anders and
Hannes Petruschke and
Nico Jehmlich and
Sven{-}Bastiaan Haange and
Martin von Bergen and
Peter F. Stadler},
title = {A workflow to identify novel proteins based on the direct mapping
of peptide-spectrum-matches to genomic locations},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {277},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04159-8},
doi = {10.1186/S12859-021-04159-8},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AndersPJHBS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/computation/SakerMFMSS21,
author = {Halima Saker and
Rainer Machn{\'{e}} and
J{\"{o}}rg Fallmann and
Douglas B. Murray and
Ahmad M. Shahin and
Peter F. Stadler},
title = {Weighted Consensus Segmentations},
journal = {Comput.},
volume = {9},
number = {2},
pages = {17},
year = {2021},
url = {https://doi.org/10.3390/computation9020017},
doi = {10.3390/COMPUTATION9020017},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/computation/SakerMFMSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dmtcs/HellmuthSS21,
author = {Marc Hellmuth and
Carsten R. Seemann and
Peter F. Stadler},
title = {Generalized Fitch Graphs {III:} Symmetrized Fitch maps and Sets of
Symmetric Binary Relations that are explained by Unrooted Edge-labeled
Trees},
journal = {Discret. Math. Theor. Comput. Sci.},
volume = {23},
number = {1},
year = {2021},
url = {https://doi.org/10.46298/dmtcs.6040},
doi = {10.46298/DMTCS.6040},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dmtcs/HellmuthSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jgaa/SchallerGHS21,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Least resolved trees for two-colored best match graphs},
journal = {J. Graph Algorithms Appl.},
volume = {25},
number = {1},
pages = {397--416},
year = {2021},
url = {https://doi.org/10.7155/jgaa.00564},
doi = {10.7155/JGAA.00564},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jgaa/SchallerGHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/BerkemerSS21,
author = {Sarah J. Berkemer and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
title = {Compositional Properties of Alignments},
journal = {Math. Comput. Sci.},
volume = {15},
number = {4},
pages = {609--630},
year = {2021},
url = {https://doi.org/10.1007/s11786-020-00496-8},
doi = {10.1007/S11786-020-00496-8},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/BerkemerSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KasmanasBCTJHBS21,
author = {Jonas Coelho Kasmanas and
Alexander Bartholom{\"{a}}us and
Felipe Borim Corr{\^{e}}a and
Tamara L. Tal and
Nico Jehmlich and
Gunda Herberth and
Martin von Bergen and
Peter F. Stadler and
Andr{\'{e}} Carlos Ponce de Leon Ferreira de Carvalho and
Ulisses Nunes da Rocha},
title = {HumanMetagenomeDB: a public repository of curated and standardized
metadata for human metagenomes},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D743--D750},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1031},
doi = {10.1093/NAR/GKAA1031},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KasmanasBCTJHBS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netsci/GartnerKSSSL21,
author = {Fabian G{\"{a}}rtner and
Felix K{\"{u}}hnl and
Carsten R. Seemann and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
title = {Superbubbles as an empirical characteristic of directed networks},
journal = {Netw. Sci.},
volume = {9},
number = {1},
pages = {49--58},
year = {2021},
url = {https://doi.org/10.1017/nws.2020.32},
doi = {10.1017/NWS.2020.32},
timestamp = {Wed, 07 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/netsci/GartnerKSSSL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netsci/GuzmanSF21,
author = {Grover E. C. Guzman and
Peter F. Stadler and
Andr{\'{e}} Fujita},
title = {Efficient Laplacian spectral density computations for networks with
arbitrary degree distributions},
journal = {Netw. Sci.},
volume = {9},
number = {3},
pages = {312--327},
year = {2021},
url = {https://doi.org/10.1017/nws.2021.10},
doi = {10.1017/NWS.2021.10},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/netsci/GuzmanSF21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/SchallerSH21,
author = {David Schaller and
Peter F. Stadler and
Marc Hellmuth},
title = {Complexity of modification problems for best match graphs},
journal = {Theor. Comput. Sci.},
volume = {865},
pages = {63--84},
year = {2021},
url = {https://doi.org/10.1016/j.tcs.2021.02.037},
doi = {10.1016/J.TCS.2021.02.037},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/SchallerSH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/0001GHS21,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
editor = {Carlos Mart{\'{\i}}n{-}Vide and
Miguel A. Vega{-}Rodr{\'{\i}}guez and
Travis J. Wheeler},
title = {Best Match Graphs with Binary Trees},
booktitle = {Algorithms for Computational Biology - 8th International Conference,
AlCoB 2021, Missoula, MT, USA, June 7-11, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12715},
pages = {82--93},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-74432-8\_6},
doi = {10.1007/978-3-030-74432-8\_6},
timestamp = {Tue, 15 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alcob/0001GHS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/CostaOSSFSW21,
author = {Mirele C. S. F. Costa and
Jo{\~{a}}o Victor de Ara{\'{u}}jo Oliveira and
Waldeyr M. C. Silva and
Rituparno Sen and
J{\"{o}}rg Fallmann and
Peter F. Stadler and
Maria Em{\'{\i}}lia M. T. Walter},
editor = {Ronny Lorenz and
Ana L. N. Fred and
Hugo Gamboa},
title = {Machine Learning Studies of Non-coding RNAs based on Artificially
Constructed Training Data},
booktitle = {Proceedings of the 14th International Joint Conference on Biomedical
Engineering Systems and Technologies, {BIOSTEC} 2021, Volume 3: BIOINFORMATICS,
Online Streaming, February 11-13, 2021},
pages = {176--183},
publisher = {{SCITEPRESS}},
year = {2021},
url = {https://doi.org/10.5220/0010346001760183},
doi = {10.5220/0010346001760183},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/biostec/CostaOSSFSW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/caldam/ChangatNS21,
author = {Manoj Changat and
Ferdoos Hossein Nezhad and
Peter F. Stadler},
editor = {Apurva Mudgal and
C. R. Subramanian},
title = {Cut Vertex Transit Functions of Hypergraphs},
booktitle = {Algorithms and Discrete Applied Mathematics - 7th International Conference,
{CALDAM} 2021, Rupnagar, India, February 11-13, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12601},
pages = {222--233},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-67899-9\_17},
doi = {10.1007/978-3-030-67899-9\_17},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/caldam/ChangatNS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/HellmuthMNSS21,
author = {Marc Hellmuth and
Mira Michel and
Nikolai N. N{\o}jgaard and
David Schaller and
Peter F. Stadler},
editor = {Peter F. Stadler and
Maria Em{\'{\i}}lia M. T. Walter and
Maribel Hernandez{-}Rosales and
Marcelo M. Brigido},
title = {Combining Orthology and Xenology Data in a Common Phylogenetic Tree},
booktitle = {Advances in Bioinformatics and Computational Biology - 14th Brazilian
Symposium on Bioinformatics, {BSB} 2021, Virtual Event, November 22-26,
2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13063},
pages = {53--64},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-91814-9\_5},
doi = {10.1007/978-3-030-91814-9\_5},
timestamp = {Wed, 15 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/HellmuthMNSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wob/2021,
editor = {Peter F. Stadler and
Maria Em{\'{\i}}lia M. T. Walter and
Maribel Hernandez{-}Rosales and
Marcelo M. Brigido},
title = {Advances in Bioinformatics and Computational Biology - 14th Brazilian
Symposium on Bioinformatics, {BSB} 2021, Virtual Event, November 22-26,
2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13063},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-91814-9},
doi = {10.1007/978-3-030-91814-9},
isbn = {978-3-030-91813-2},
timestamp = {Fri, 03 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/2021.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2101-07000,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Least resolved trees for two-colored best match graphs},
journal = {CoRR},
volume = {abs/2101.07000},
year = {2021},
url = {https://arxiv.org/abs/2101.07000},
eprinttype = {arXiv},
eprint = {2101.07000},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2101-07000.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2103-06665,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable
Best Match Graphs},
journal = {CoRR},
volume = {abs/2103.06665},
year = {2021},
url = {https://arxiv.org/abs/2103.06665},
eprinttype = {arXiv},
eprint = {2103.06665},
timestamp = {Tue, 13 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2103-06665.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2103-06683,
author = {Carmen Bruckmann and
Peter F. Stadler and
Marc Hellmuth},
title = {From Modular Decomposition Trees to Rooted Median Graphs},
journal = {CoRR},
volume = {abs/2103.06683},
year = {2021},
url = {https://arxiv.org/abs/2103.06683},
eprinttype = {arXiv},
eprint = {2103.06683},
timestamp = {Tue, 16 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2103-06683.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2103-07280,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Heuristic Algorithms for Best Match Graph Editing},
journal = {CoRR},
volume = {abs/2103.07280},
year = {2021},
url = {https://arxiv.org/abs/2103.07280},
eprinttype = {arXiv},
eprint = {2103.07280},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2103-07280.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2104-14146,
author = {Marc Hellmuth and
David Schaller and
Peter F. Stadler},
title = {Compatibility of Partitions, Hierarchies, and Split Systems},
journal = {CoRR},
volume = {abs/2104.14146},
year = {2021},
url = {https://arxiv.org/abs/2104.14146},
eprinttype = {arXiv},
eprint = {2104.14146},
timestamp = {Tue, 04 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2104-14146.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2107-00072,
author = {David Schaller and
Marc Hellmuth and
Peter F. Stadler},
title = {A Linear-Time Algorithm for the Common Refinement of Rooted Phylogenetic
Trees on a Common Leaf Set},
journal = {CoRR},
volume = {abs/2107.00072},
year = {2021},
url = {https://arxiv.org/abs/2107.00072},
eprinttype = {arXiv},
eprint = {2107.00072},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2107-00072.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2107-01893,
author = {Marc Hellmuth and
Mira Michel and
Nikolai N. N{\o}jgaard and
David Schaller and
Peter F. Stadler},
title = {Combining Orthology and Xenology Data in a Common Phylogenetic Tree},
journal = {CoRR},
volume = {abs/2107.01893},
year = {2021},
url = {https://arxiv.org/abs/2107.01893},
eprinttype = {arXiv},
eprint = {2107.01893},
timestamp = {Wed, 07 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2107-01893.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2107-03086,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Defining Autocatalysis in Chemical Reaction Networks},
journal = {CoRR},
volume = {abs/2107.03086},
year = {2021},
url = {https://arxiv.org/abs/2107.03086},
eprinttype = {arXiv},
eprint = {2107.03086},
timestamp = {Thu, 22 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2107-03086.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-09346,
author = {Carsten R. Seemann and
Vincent Moulton and
Peter F. Stadler and
Marc Hellmuth},
title = {Planar Median Graphs and Cubesquare-Graphs},
journal = {CoRR},
volume = {abs/2110.09346},
year = {2021},
url = {https://arxiv.org/abs/2110.09346},
eprinttype = {arXiv},
eprint = {2110.09346},
timestamp = {Mon, 25 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-09346.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2112-00403,
author = {David Schaller and
Marc Hellmuth and
Peter F. Stadler},
title = {Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer
in Gene Trees},
journal = {CoRR},
volume = {abs/2112.00403},
year = {2021},
url = {https://arxiv.org/abs/2112.00403},
eprinttype = {arXiv},
eprint = {2112.00403},
timestamp = {Tue, 07 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2112-00403.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2112-05876,
author = {David H. Wolpert and
Michael H. Price and
Stefani A. Crabtree and
Timothy A. Kohler and
J{\"{u}}rgen Jost and
James Evans and
Peter F. Stadler and
Hajime Shimao and
Manfred D. Laubichler},
title = {The Past as a Stochastic Process},
journal = {CoRR},
volume = {abs/2112.05876},
year = {2021},
url = {https://arxiv.org/abs/2112.05876},
eprinttype = {arXiv},
eprint = {2112.05876},
timestamp = {Wed, 05 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2112-05876.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/adam/FritzHSW20,
author = {Adrian Fritz and
Marc Hellmuth and
Peter F. Stadler and
Nicolas Wieseke},
title = {Cograph editing: Merging modules is equivalent to editing P{\_}4s},
journal = {Art Discret. Appl. Math.},
volume = {3},
number = {2},
year = {2020},
url = {https://doi.org/10.26493/2590-9770.1252.e71},
doi = {10.26493/2590-9770.1252.E71},
timestamp = {Fri, 19 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/adam/FritzHSW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/akcej/ChangatNNKMRS20,
author = {Manoj Changat and
Prasanth G. Narasimha{-}Shenoi and
Ferdoos Hossein Nezhad and
Matjaz Kovse and
Shilpa Mohandas and
Abisha Ramachandran and
Peter F. Stadler},
title = {Transit sets of -point crossover operators},
journal = {{AKCE} Int. J. Graphs Comb.},
volume = {17},
number = {1},
pages = {519--533},
year = {2020},
url = {https://doi.org/10.1016/j.akcej.2019.03.019},
doi = {10.1016/J.AKCEJ.2019.03.019},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/akcej/ChangatNNKMRS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/StadlerGSLLVHH20,
author = {Peter F. Stadler and
Manuela Gei{\ss} and
David Schaller and
Alitzel L{\'{o}}pez and
Marcos E. Gonz{\'{a}}lez Laffitte and
Dulce I. Valdivia and
Marc Hellmuth and
Maribel Hernandez{-}Rosales},
title = {From pairs of most similar sequences to phylogenetic best matches},
journal = {Algorithms Mol. Biol.},
volume = {15},
number = {1},
pages = {5},
year = {2020},
url = {https://doi.org/10.1186/s13015-020-00165-2},
doi = {10.1186/S13015-020-00165-2},
timestamp = {Mon, 22 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/StadlerGSLLVHH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/computation/Rodriguez-Fernandez20,
author = {Angel E. Rodriguez{-}Fernandez and
Bernardo A. Gonzalez{-}Torres and
Ricardo Menchaca{-}Mendez and
Peter F. Stadler},
title = {Clustering Improves the Goemans-Williamson Approximation for the Max-Cut
Problem},
journal = {Comput.},
volume = {8},
number = {3},
pages = {75},
year = {2020},
url = {https://doi.org/10.3390/computation8030075},
doi = {10.3390/COMPUTATION8030075},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/computation/Rodriguez-Fernandez20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/HellmuthSS20,
author = {Marc Hellmuth and
Carsten R. Seemann and
Peter F. Stadler},
title = {Generalized Fitch graphs {II:} Sets of binary relations that are explained
by edge-labeled trees},
journal = {Discret. Appl. Math.},
volume = {283},
pages = {495--511},
year = {2020},
url = {https://doi.org/10.1016/j.dam.2020.01.036},
doi = {10.1016/J.DAM.2020.01.036},
timestamp = {Thu, 06 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/HellmuthSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/LongS20,
author = {Yangjing Long and
Peter F. Stadler},
title = {Exact-2-relation graphs},
journal = {Discret. Appl. Math.},
volume = {285},
pages = {212--226},
year = {2020},
url = {https://doi.org/10.1016/j.dam.2020.05.015},
doi = {10.1016/J.DAM.2020.05.015},
timestamp = {Tue, 20 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/LongS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/BaloghBSS20,
author = {G{\'{a}}bor Balogh and
Stephan H. Bernhart and
Peter F. Stadler and
Jana Schor},
title = {A probabilistic version of Sankoff's maximum parsimony algorithm},
journal = {J. Bioinform. Comput. Biol.},
volume = {18},
number = {1},
pages = {2050004:1--2050004:19},
year = {2020},
url = {https://doi.org/10.1142/S0219720020500043},
doi = {10.1142/S0219720020500043},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/BaloghBSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CorreaSSR20,
author = {Felipe Borim Corr{\^{e}}a and
Jo{\~{a}}o Pedro Saraiva and
Peter F. Stadler and
Ulisses Nunes da Rocha},
title = {TerrestrialMetagenomeDB: a public repository of curated and standardized
metadata for terrestrial metagenomes},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D626--D632},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz994},
doi = {10.1093/NAR/GKZ994},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CorreaSSR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/HellmuthGS20,
author = {Marc Hellmuth and
Manuela Gei{\ss} and
Peter F. Stadler},
title = {Complexity of modification problems for reciprocal best match graphs},
journal = {Theor. Comput. Sci.},
volume = {809},
pages = {384--393},
year = {2020},
url = {https://doi.org/10.1016/j.tcs.2019.12.033},
doi = {10.1016/J.TCS.2019.12.033},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/HellmuthGS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/HordijkKS20,
author = {Wim Hordijk and
Stuart A. Kauffman and
Peter F. Stadler},
title = {Average Fitness Differences on {NK} Landscapes},
journal = {Theory Biosci.},
volume = {139},
number = {1},
pages = {1--7},
year = {2020},
url = {https://doi.org/10.1007/s12064-019-00296-0},
doi = {10.1007/S12064-019-00296-0},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/HordijkKS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/SenFWS20,
author = {Rituparno Sen and
J{\"{o}}rg Fallmann and
Maria Em{\'{\i}}lia M. T. Walter and
Peter F. Stadler},
title = {Are spliced ncRNA host genes distinct classes of lncRNAs?},
journal = {Theory Biosci.},
volume = {139},
number = {4},
pages = {349--359},
year = {2020},
url = {https://doi.org/10.1007/s12064-020-00330-6},
doi = {10.1007/S12064-020-00330-6},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/SenFWS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/LorenzFHS20,
author = {Ronny Lorenz and
Christoph Flamm and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Elisabetta De Maria and
Ana L. N. Fred and
Hugo Gamboa},
title = {Efficient Computation of Base-pairing Probabilities in Multi-strand
{RNA} Folding},
booktitle = {Proceedings of the 13th International Joint Conference on Biomedical
Engineering Systems and Technologies {(BIOSTEC} 2020) - Volume 3:
BIOINFORMATICS, Valletta, Malta, February 24-26, 2020},
pages = {23--31},
publisher = {{SCITEPRESS}},
year = {2020},
url = {https://doi.org/10.5220/0008916600230031},
doi = {10.5220/0008916600230031},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/biostec/LorenzFHS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/LorenzFHS20a,
author = {Ronny Lorenz and
Christoph Flamm and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Xuesong Ye and
Filipe Soares and
Elisabetta De Maria and
Pedro G{\'{o}}mez Vilda and
Federico Cabitza and
Ana L. N. Fred and
Hugo Gamboa},
title = {Efficient Algorithms for Co-folding of Multiple RNAs},
booktitle = {Biomedical Engineering Systems and Technologies - 13th International
Joint Conference, {BIOSTEC} 2020, Valletta, Malta, February 24-26,
2020, Revised Selected Papers},
series = {Communications in Computer and Information Science},
volume = {1400},
pages = {193--214},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-72379-8\_10},
doi = {10.1007/978-3-030-72379-8\_10},
timestamp = {Sat, 09 Apr 2022 12:35:18 +0200},
biburl = {https://dblp.org/rec/conf/biostec/LorenzFHS20a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/GatterLDHS20,
author = {Thomas Gatter and
Sarah von L{\"{o}}hneysen and
Polina Drozdova and
Tom Hartmann and
Peter F. Stadler},
editor = {Carl Kingsford and
Nadia Pisanti},
title = {Economic Genome Assembly from Low Coverage Illumina and Nanopore Data},
booktitle = {20th International Workshop on Algorithms in Bioinformatics, {WABI}
2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)},
series = {LIPIcs},
volume = {172},
pages = {10:1--10:22},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2020},
url = {https://doi.org/10.4230/LIPIcs.WABI.2020.10},
doi = {10.4230/LIPICS.WABI.2020.10},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/GatterLDHS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/AlmoSSGSHMB20,
author = {Manuela M. do Almo and
Isabel G. Sousa and
Waldeyr Mendes Cordeiro da Silva and
Thomas Gatter and
Peter F. Stadler and
Steve Hoffmann and
Andrea Queiroz Maranh{\~{a}}o and
Marcelo M. Brigido},
editor = {Jo{\~{a}}o C. Setubal and
Waldeyr M. C. Silva},
title = {Anti-CD3 Stimulated {T} Cell Transcriptome Reveals Novel ncRNAs and
Correlates with a Suppressive Profile},
booktitle = {Advances in Bioinformatics and Computational Biology - 13th Brazilian
Symposium on Bioinformatics, {BSB} 2020, S{\~{a}}o Paulo, Brazil,
November 23-27, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12558},
pages = {180--191},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-65775-8\_17},
doi = {10.1007/978-3-030-65775-8\_17},
timestamp = {Sat, 09 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/AlmoSSGSHMB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/SilvaAAWBSF20,
author = {Waldeyr Mendes Cordeiro da Silva and
Daniela P. de Andrade and
Jakob L. Andersen and
Maria Em{\'{\i}}lia Telles Walter and
Marcelo M. Brigido and
Peter F. Stadler and
Christoph Flamm},
editor = {Jo{\~{a}}o C. Setubal and
Waldeyr M. C. Silva},
title = {Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene
Synthases},
booktitle = {Advances in Bioinformatics and Computational Biology - 13th Brazilian
Symposium on Bioinformatics, {BSB} 2020, S{\~{a}}o Paulo, Brazil,
November 23-27, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12558},
pages = {247--258},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-65775-8\_23},
doi = {10.1007/978-3-030-65775-8\_23},
timestamp = {Tue, 02 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/SilvaAAWBSF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2001-03409,
author = {Fabian G{\"{a}}rtner and
Felix K{\"{u}}hnl and
Carsten R. Seemann and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
title = {Superbubbles as an Empirical Characteristic of Directed Networks},
journal = {CoRR},
volume = {abs/2001.03409},
year = {2020},
url = {https://arxiv.org/abs/2001.03409},
eprinttype = {arXiv},
eprint = {2001.03409},
timestamp = {Wed, 24 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2001-03409.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2001-05921,
author = {Marc Hellmuth and
Carsten R. Seemann and
Peter F. Stadler},
title = {Generalized Fitch Graphs {III:} Symmetrized Fitch maps and Sets of
Symmetric Binary Relations that are explained by Unrooted Edge-labeled
Trees},
journal = {CoRR},
volume = {abs/2001.05921},
year = {2020},
url = {https://arxiv.org/abs/2001.05921},
eprinttype = {arXiv},
eprint = {2001.05921},
timestamp = {Fri, 17 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2001-05921.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-06340,
author = {Dulce I. Valdivia and
Manuela Gei{\ss} and
Maribel Hern{\'{a}}ndez{-}Rosales and
Peter F. Stadler and
Marc Hellmuth},
title = {Hierarchical and Modularly-Minimal Vertex Colorings},
journal = {CoRR},
volume = {abs/2004.06340},
year = {2020},
url = {https://arxiv.org/abs/2004.06340},
eprinttype = {arXiv},
eprint = {2004.06340},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-06340.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-07118,
author = {Tom Hartmann and
Max Bannach and
Martin Middendorf and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
title = {Complete Edge-Colored Permutation Graphs},
journal = {CoRR},
volume = {abs/2004.07118},
year = {2020},
url = {https://arxiv.org/abs/2004.07118},
eprinttype = {arXiv},
eprint = {2004.07118},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-07118.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-02249,
author = {David Schaller and
Manuela Gei{\ss} and
Peter F. Stadler and
Marc Hellmuth},
title = {Complete Characterization of Incorrect Orthology Assignments in Best
Match Graphs},
journal = {CoRR},
volume = {abs/2006.02249},
year = {2020},
url = {https://arxiv.org/abs/2006.02249},
eprinttype = {arXiv},
eprint = {2006.02249},
timestamp = {Tue, 13 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-02249.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-16909,
author = {David Schaller and
Peter F. Stadler and
Marc Hellmuth},
title = {Complexity of Modification Problems for Best Match Graphs},
journal = {CoRR},
volume = {abs/2006.16909},
year = {2020},
url = {https://arxiv.org/abs/2006.16909},
eprinttype = {arXiv},
eprint = {2006.16909},
timestamp = {Tue, 13 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-16909.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2011-00511,
author = {David Schaller and
Manuela Gei{\ss} and
Marc Hellmuth and
Peter F. Stadler},
title = {Best Match Graphs with Binary Trees},
journal = {CoRR},
volume = {abs/2011.00511},
year = {2020},
url = {https://arxiv.org/abs/2011.00511},
eprinttype = {arXiv},
eprint = {2011.00511},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2011-00511.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2012-08897,
author = {David Schaller and
Manuel Lafond and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
title = {Indirect Identification of Horizontal Gene Transfer},
journal = {CoRR},
volume = {abs/2012.08897},
year = {2020},
url = {https://arxiv.org/abs/2012.08897},
eprinttype = {arXiv},
eprint = {2012.08897},
timestamp = {Tue, 13 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2012-08897.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/adam/ChangatNS19,
author = {Manoj Changat and
Prasanth G. Narasimha{-}Shenoi and
Peter F. Stadler},
title = {Axiomatic characterization of transit functions of weak hierarchies},
journal = {Art Discret. Appl. Math.},
volume = {2},
number = {1},
pages = {{\#}P1.01},
year = {2019},
url = {https://doi.org/10.26493/2590-9770.1260.989},
doi = {10.26493/2590-9770.1260.989},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/adam/ChangatNS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/GartnerS19,
author = {Fabian G{\"{a}}rtner and
Peter F. Stadler},
title = {Direct Superbubble Detection},
journal = {Algorithms},
volume = {12},
number = {4},
pages = {81},
year = {2019},
url = {https://doi.org/10.3390/a12040081},
doi = {10.3390/A12040081},
timestamp = {Fri, 31 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/GartnerS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WiegreffeASZ19,
author = {Daniel Wiegreffe and
Daniel Alexander and
Peter F. Stadler and
Dirk Zeckzer},
title = {RNApuzzler: efficient outerplanar drawing of RNA-secondary structures},
journal = {Bioinform.},
volume = {35},
number = {8},
pages = {1342--1349},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty817},
doi = {10.1093/BIOINFORMATICS/BTY817},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WiegreffeASZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YazbeckSTF19,
author = {Ali M. Yazbeck and
Peter F. Stadler and
Kifah Tout and
J{\"{o}}rg Fallmann},
title = {Automatic curation of large comparative animal MicroRNA datasets},
journal = {Bioinform.},
volume = {35},
number = {22},
pages = {4553--4559},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz271},
doi = {10.1093/BIOINFORMATICS/BTZ271},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YazbeckSTF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CostaSDSN19,
author = {Maria Beatriz Walter Costa and
Christian H{\"{o}}ner zu Siederdissen and
Marko Dunjic and
Peter F. Stadler and
Katja Nowick},
title = {SSS-test: a novel test for detecting positive selection on {RNA} secondary
structure},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {151:1--151:19},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2711-y},
doi = {10.1186/S12859-019-2711-Y},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CostaSDSN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GatterS19,
author = {Thomas Gatter and
Peter F. Stadler},
title = {Ry{\={u}}t{\={o}}: network-flow based transcriptome reconstruction},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {190:1--190:14},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2786-5},
doi = {10.1186/S12859-019-2786-5},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GatterS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LudwigSLSM19,
author = {Joachim Ludwig and
Christian H{\"{o}}ner zu Siederdissen and
Zishu Liu and
Peter F. Stadler and
Susann M{\"{u}}ller},
title = {flowEMMi: an automated model-based clustering tool for microbial cytometric
data},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {643},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-3152-3},
doi = {10.1186/S12859-019-3152-3},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LudwigSLSM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dbsk/RahmNPJGSWZL19,
author = {Erhard Rahm and
Wolfgang E. Nagel and
Eric Peukert and
Ren{\'{e}} J{\"{a}}kel and
Fabian G{\"{a}}rtner and
Peter F. Stadler and
Daniel Wiegreffe and
Dirk Zeckzer and
Wolfgang Lehner},
title = {Big Data Competence Center ScaDS Dresden/Leipzig: Overview and selected
research activities},
journal = {Datenbank-Spektrum},
volume = {19},
number = {1},
pages = {5--16},
year = {2019},
url = {https://doi.org/10.1007/s13222-018-00303-6},
doi = {10.1007/S13222-018-00303-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dbsk/RahmNPJGSWZL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FallmannVBBDKES19,
author = {J{\"{o}}rg Fallmann and
Pavankumar Videm and
Andrea Bagnacani and
B{\'{e}}r{\'{e}}nice Batut and
Maria A. Doyle and
Tomas Klingstr{\"{o}}m and
Florian Eggenhofer and
Peter F. Stadler and
Rolf Backofen and
Bj{\"{o}}rn A. Gr{\"{u}}ning},
title = {The {RNA} workbench 2.0: next generation {RNA} data analysis},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Webserver-Issue},
pages = {W511--W515},
year = {2019},
url = {https://doi.org/10.1093/nar/gkz353},
doi = {10.1093/NAR/GKZ353},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/FallmannVBBDKES19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/AndersenFMS19,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {2},
pages = {510--523},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2017.2781724},
doi = {10.1109/TCBB.2017.2781724},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/AndersenFMS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/KirchnerRS19,
author = {Falco Kirchner and
Nancy Retzlaff and
Peter F. Stadler},
editor = {Elisabetta De Maria and
Ana L. N. Fred and
Hugo Gamboa},
title = {A General Framework for Exact Partially Local Alignments},
booktitle = {Proceedings of the 12th International Joint Conference on Biomedical
Engineering Systems and Technologies {(BIOSTEC} 2019) - Volume 3:
BIOINFORMATICS, Prague, Czech Republic, February 22-24, 2019},
pages = {194--200},
publisher = {SciTePress},
year = {2019},
url = {https://doi.org/10.5220/0007380001940200},
doi = {10.5220/0007380001940200},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/biostec/KirchnerRS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/WaldlWWHS19,
author = {Maria Waldl and
Sebastian Will and
Michael T. Wolfinger and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Paolo Cazzaniga and
Daniela Besozzi and
Ivan Merelli and
Luca Manzoni},
title = {Bi-alignments as Models of Incongruent Evolution of {RNA} Sequence
and Secondary Structure},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics
- 16th International Meeting, {CIBB} 2019, Bergamo, Italy, September
4-6, 2019, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {12313},
pages = {159--170},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-63061-4\_15},
doi = {10.1007/978-3-030-63061-4\_15},
timestamp = {Thu, 17 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cibb/WaldlWWHS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1904-12021,
author = {Manuela Gei{\ss} and
Marcos Gonz{\'{a}}lez and
Alitzel L{\'{o}}pez and
Dulce I. Valdivia and
Marc Hellmuth and
Maribel Hern{\'{a}}ndez{-}Rosales and
Peter F. Stadler},
title = {Best Match Graphs and Reconciliation of Gene Trees with Species Trees},
journal = {CoRR},
volume = {abs/1904.12021},
year = {2019},
url = {http://arxiv.org/abs/1904.12021},
eprinttype = {arXiv},
eprint = {1904.12021},
timestamp = {Sat, 23 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1904-12021.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1906-10031,
author = {Dulce I. Valdivia and
Manuela Gei{\ss} and
Marc Hellmuth and
Maribel Hern{\'{a}}ndez{-}Rosales and
Peter F. Stadler},
title = {Hierarchical Colorings of Cographs},
journal = {CoRR},
volume = {abs/1906.10031},
year = {2019},
url = {http://arxiv.org/abs/1906.10031},
eprinttype = {arXiv},
eprint = {1906.10031},
timestamp = {Fri, 28 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1906-10031.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1907-08865,
author = {Marc Hellmuth and
Manuela Gei{\ss} and
Peter F. Stadler},
title = {Complexity of Modification Problems for Reciprocal Best Match Graphs},
journal = {CoRR},
volume = {abs/1907.08865},
year = {2019},
url = {http://arxiv.org/abs/1907.08865},
eprinttype = {arXiv},
eprint = {1907.08865},
timestamp = {Tue, 30 Jul 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1907-08865.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1911-07469,
author = {Marc Hellmuth and
Carsten R. Seemann and
Peter F. Stadler},
title = {Generalized Fitch Relations {II:} Sets of Binary Relations that are
explained by Edge-labeled Trees},
journal = {CoRR},
volume = {abs/1911.07469},
year = {2019},
url = {http://arxiv.org/abs/1911.07469},
eprinttype = {arXiv},
eprint = {1911.07469},
timestamp = {Mon, 02 Dec 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1911-07469.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/adam/HellmuthLGS18,
author = {Marc Hellmuth and
Yangjing Long and
Manuela Gei{\ss} and
Peter F. Stadler},
title = {A short note on undirected Fitch graphs},
journal = {Art Discret. Appl. Math.},
volume = {1},
number = {1},
pages = {{\#}P1.08},
year = {2018},
url = {https://doi.org/10.26493/2590-9770.1245.98c},
doi = {10.26493/2590-9770.1245.98C},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/adam/HellmuthLGS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NojgaardGMSWH18,
author = {Nikolai N{\o}jgaard and
Manuela Gei{\ss} and
Daniel Merkle and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
title = {Time-consistent reconciliation maps and forbidden time travel},
journal = {Algorithms Mol. Biol.},
volume = {13},
number = {1},
pages = {2:1--2:17},
year = {2018},
url = {https://doi.org/10.1186/s13015-018-0121-8},
doi = {10.1186/S13015-018-0121-8},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/NojgaardGMSWH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DonathS18,
author = {Alexander Donath and
Peter F. Stadler},
title = {Split-inducing indels in phylogenomic analysis},
journal = {Algorithms Mol. Biol.},
volume = {13},
number = {1},
pages = {12:1--12:12},
year = {2018},
url = {https://doi.org/10.1186/s13015-018-0130-7},
doi = {10.1186/S13015-018-0130-7},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/DonathS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GartnerSMS18,
author = {Fabian G{\"{a}}rtner and
Christian H{\"{o}}ner zu Siederdissen and
Lydia M{\"{u}}ller and
Peter F. Stadler},
title = {Coordinate systems for supergenomes},
journal = {Algorithms Mol. Biol.},
volume = {13},
number = {1},
pages = {15:1--15:19},
year = {2018},
url = {https://doi.org/10.1186/s13015-018-0133-4},
doi = {10.1186/S13015-018-0133-4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/GartnerSMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GartnerMS18,
author = {Fabian G{\"{a}}rtner and
Lydia M{\"{u}}ller and
Peter F. Stadler},
title = {Superbubbles revisited},
journal = {Algorithms Mol. Biol.},
volume = {13},
number = {1},
pages = {16:1--16:17},
year = {2018},
url = {https://doi.org/10.1186/s13015-018-0134-3},
doi = {10.1186/S13015-018-0134-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/GartnerMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/arsmc/ChangatNS18,
author = {Manoj Changat and
Ferdoos Hossein Nezhad and
Peter F. Stadler},
title = {Axiomatic characterization of transit functions of hierarchies},
journal = {Ars Math. Contemp.},
volume = {14},
number = {1},
pages = {117--128},
year = {2018},
url = {https://doi.org/10.26493/1855-3974.831.e12},
doi = {10.26493/1855-3974.831.E12},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/arsmc/ChangatNS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/PaschoalLDS18,
author = {Alexandre Rossi Paschoal and
Irma Lozada{-}Ch{\'{a}}vez and
Douglas Silva Domingues and
Peter F. Stadler},
title = {ceRNAs in plants: computational approaches and associated challenges
for target mimic research},
journal = {Briefings Bioinform.},
volume = {19},
number = {6},
pages = {1273--1289},
year = {2018},
url = {https://doi.org/10.1093/bib/bbx058},
doi = {10.1093/BIB/BBX058},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/PaschoalLDS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoffmannFVMSA18,
author = {Anne Hoffmann and
J{\"{o}}rg Fallmann and
Elisa Vilardo and
Mario M{\"{o}}rl and
Peter F. Stadler and
Fabian Amman},
title = {Accurate mapping of tRNA reads},
journal = {Bioinform.},
volume = {34},
number = {7},
pages = {1116--1124},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx756},
doi = {10.1093/BIOINFORMATICS/BTX756},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoffmannFVMSA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HoffmannFVMSA18a,
author = {Anne Hoffmann and
J{\"{o}}rg Fallmann and
Elisa Vilardo and
Mario M{\"{o}}rl and
Peter F. Stadler and
Fabian Amman},
title = {Accurate mapping of tRNA reads},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {2339},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty118},
doi = {10.1093/BIOINFORMATICS/BTY118},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoffmannFVMSA18a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/FagerbergFKMS18,
author = {Rolf Fagerberg and
Christoph Flamm and
Rojin Kianian and
Daniel Merkle and
Peter F. Stadler},
title = {Finding the {K} best synthesis plans},
journal = {J. Cheminformatics},
volume = {10},
number = {1},
pages = {19:1--19:21},
year = {2018},
url = {https://doi.org/10.1186/s13321-018-0273-z},
doi = {10.1186/S13321-018-0273-Z},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/FagerbergFKMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/RetzlaffS18,
author = {Nancy Retzlaff and
Peter F. Stadler},
title = {Partially Local Multi-way Alignments},
journal = {Math. Comput. Sci.},
volume = {12},
number = {2},
pages = {207--234},
year = {2018},
url = {https://doi.org/10.1007/s11786-018-0338-4},
doi = {10.1007/S11786-018-0338-4},
timestamp = {Wed, 12 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/RetzlaffS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/EbadiPSKDSM18,
author = {Haleh Ebadi and
Michael Perry and
Keith Short and
Konstantin Klemm and
Claude Desplan and
Peter F. Stadler and
Anita Mehta},
title = {Patterning the insect eye: From stochastic to deterministic mechanisms},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {11},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006363},
doi = {10.1371/JOURNAL.PCBI.1006363},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/EbadiPSKDSM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/RetzlaffS18,
author = {Nancy Retzlaff and
Peter F. Stadler},
title = {Phylogenetics beyond biology},
journal = {Theory Biosci.},
volume = {137},
number = {2},
pages = {133--143},
year = {2018},
url = {https://doi.org/10.1007/s12064-018-0264-7},
doi = {10.1007/S12064-018-0264-7},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/RetzlaffS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1810-07800,
author = {Sarah J. Berkemer and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
title = {Alignments as Compositional Structures},
journal = {CoRR},
volume = {abs/1810.07800},
year = {2018},
url = {http://arxiv.org/abs/1810.07800},
eprinttype = {arXiv},
eprint = {1810.07800},
timestamp = {Thu, 01 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1810-07800.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1811-07825,
author = {Wilmer Leal and
Guillermo Restrepo and
Peter F. Stadler and
J{\"{u}}rgen Jost},
title = {Forman-Ricci Curvature for Hypergraphs},
journal = {CoRR},
volume = {abs/1811.07825},
year = {2018},
url = {http://arxiv.org/abs/1811.07825},
eprinttype = {arXiv},
eprint = {1811.07825},
timestamp = {Mon, 26 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1811-07825.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/BerkemerSS17,
author = {Sarah Berkemer and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
title = {Algebraic Dynamic Programming on Trees},
journal = {Algorithms},
volume = {10},
number = {4},
pages = {135},
year = {2017},
url = {https://doi.org/10.3390/a10040135},
doi = {10.3390/A10040135},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithms/BerkemerSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ArabBSTS17,
author = {Marwa Al Arab and
Matthias Bernt and
Christian H{\"{o}}ner zu Siederdissen and
Kifah Tout and
Peter F. Stadler},
title = {Partially local three-way alignments and the sequence signatures of
mitochondrial genome rearrangements},
journal = {Algorithms Mol. Biol.},
volume = {12},
number = {1},
pages = {22:1--22:11},
year = {2017},
url = {https://doi.org/10.1186/s13015-017-0113-0},
doi = {10.1186/S13015-017-0113-0},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/ArabBSTS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KuhnlSW17,
author = {Felix K{\"{u}}hnl and
Peter F. Stadler and
Sebastian Will},
title = {Tractable RNA-ligand interaction kinetics},
journal = {{BMC} Bioinform.},
volume = {18},
number = {{S-12}},
pages = {47--55},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1823-5},
doi = {10.1186/S12859-017-1823-5},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KuhnlSW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/YazbeckTSH17,
author = {Ali M. Yazbeck and
Kifah R. Tout and
Peter F. Stadler and
Jana Hertel},
title = {Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution},
journal = {J. Integr. Bioinform.},
volume = {14},
number = {1},
year = {2017},
url = {https://doi.org/10.1515/jib-2016-0013},
doi = {10.1515/JIB-2016-0013},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/YazbeckTSH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GruningFYWEEHBV17,
author = {Bj{\"{o}}rn A. Gr{\"{u}}ning and
J{\"{o}}rg Fallmann and
Dilmurat Yusuf and
Sebastian Will and
Anika Erxleben and
Florian Eggenhofer and
Torsten Houwaart and
B{\'{e}}r{\'{e}}nice Batut and
Pavankumar Videm and
Andrea Bagnacani and
Markus Wolfien and
Steffen Lott and
Youri Hoogstrate and
Wolfgang R. Hess and
Olaf Wolkenhauer and
Steve Hoffmann and
Altuna Akalin and
Uwe Ohler and
Peter F. Stadler and
Rolf Backofen},
title = {The {RNA} workbench: best practices for {RNA} and high-throughput
sequencing bioinformatics in Galaxy},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Webserver-Issue},
pages = {W560--W566},
year = {2017},
url = {https://doi.org/10.1093/nar/gkx409},
doi = {10.1093/NAR/GKX409},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GruningFYWEEHBV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sensors/FindeissEWMS17,
author = {Sven Findei{\ss} and
Maja Etzel and
Sebastian Will and
Mario M{\"{o}}rl and
Peter F. Stadler},
title = {Design of Artificial Riboswitches as Biosensors},
journal = {Sensors},
volume = {17},
number = {9},
pages = {1990},
year = {2017},
url = {https://doi.org/10.3390/s17091990},
doi = {10.3390/S17091990},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/sensors/FindeissEWMS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gg/AndersenFMS17,
author = {Jakob Lykke Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
editor = {Juan de Lara and
Detlef Plump},
title = {Chemical Graph Transformation with Stereo-Information},
booktitle = {Graph Transformation - 10th International Conference, {ICGT} 2017,
Held as Part of {STAF} 2017, Marburg, Germany, July 18-19, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10373},
pages = {54--69},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-61470-0\_4},
doi = {10.1007/978-3-319-61470-0\_4},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gg/AndersenFMS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/NojgaardGMSWH17,
author = {Nikolai N{\o}jgaard and
Manuela Gei{\ss} and
Daniel Merkle and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
editor = {Russell Schwartz and
Knut Reinert},
title = {Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation
Maps},
booktitle = {17th International Workshop on Algorithms in Bioinformatics, {WABI}
2017, August 21-23, 2017, Boston, MA, {USA}},
series = {LIPIcs},
volume = {88},
pages = {17:1--17:12},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2017},
url = {https://doi.org/10.4230/LIPIcs.WABI.2017.17},
doi = {10.4230/LIPICS.WABI.2017.17},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/NojgaardGMSWH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AndersenFMS17,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {An Intermediate Level of Abstraction for Computational Systems Chemistry},
journal = {CoRR},
volume = {abs/1701.09097},
year = {2017},
url = {http://arxiv.org/abs/1701.09097},
eprinttype = {arXiv},
eprint = {1701.09097},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/AndersenFMS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthFWS17,
author = {Marc Hellmuth and
Adrian Fritz and
Nicolas Wieseke and
Peter F. Stadler},
title = {Merging Modules is equivalent to Editing P4's},
journal = {CoRR},
volume = {abs/1702.07499},
year = {2017},
url = {http://arxiv.org/abs/1702.07499},
eprinttype = {arXiv},
eprint = {1702.07499},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthFWS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/NojgaardGSMWH17,
author = {Nikolai N{\o}jgaard and
Manuela Gei{\ss} and
Peter F. Stadler and
Daniel Merkle and
Nicolas Wieseke and
Marc Hellmuth},
title = {Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation
Maps},
journal = {CoRR},
volume = {abs/1705.02179},
year = {2017},
url = {http://arxiv.org/abs/1705.02179},
eprinttype = {arXiv},
eprint = {1705.02179},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/NojgaardGSMWH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthIKS17,
author = {Marc Hellmuth and
Wilfried Imrich and
Werner Kl{\"{o}}ckl and
Peter F. Stadler},
title = {Local algorithms for the prime factorization of strong product graphs},
journal = {CoRR},
volume = {abs/1705.03823},
year = {2017},
url = {http://arxiv.org/abs/1705.03823},
eprinttype = {arXiv},
eprint = {1705.03823},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthIKS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/Hernandez-Rosales17,
author = {Maribel Hernandez{-}Rosales and
Marc Hellmuth and
Nicolas Wieseke and
Katharina T. Huber and
Vincent Moulton and
Peter F. Stadler},
title = {From event labeled gene trees to species trees},
journal = {CoRR},
volume = {abs/1705.04190},
year = {2017},
url = {http://arxiv.org/abs/1705.04190},
eprinttype = {arXiv},
eprint = {1705.04190},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/Hernandez-Rosales17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthOS17,
author = {Marc Hellmuth and
Lydia Ostermeier and
Peter F. Stadler},
title = {A Survey on Hypergraph Products (Erratum)},
journal = {CoRR},
volume = {abs/1705.06037},
year = {2017},
url = {http://arxiv.org/abs/1705.06037},
eprinttype = {arXiv},
eprint = {1705.06037},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthOS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1711-02152,
author = {Manuela Gei{\ss} and
John Anders and
Peter F. Stadler and
Nicolas Wieseke and
Marc Hellmuth},
title = {Reconstructing Gene Trees From Fitch's Xenology Relation},
journal = {CoRR},
volume = {abs/1711.02152},
year = {2017},
url = {http://arxiv.org/abs/1711.02152},
eprinttype = {arXiv},
eprint = {1711.02152},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1711-02152.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-01544,
author = {Manuela Gei{\ss} and
Marc Hellmuth and
Yangjing Long and
Peter F. Stadler},
title = {A Short Note on Undirected Fitch Graphs},
journal = {CoRR},
volume = {abs/1712.01544},
year = {2017},
url = {http://arxiv.org/abs/1712.01544},
eprinttype = {arXiv},
eprint = {1712.01544},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-01544.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-02594,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows},
journal = {CoRR},
volume = {abs/1712.02594},
year = {2017},
url = {http://arxiv.org/abs/1712.02594},
eprinttype = {arXiv},
eprint = {1712.02594},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-02594.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-06442,
author = {Marc Hellmuth and
Nicolas Wieseke and
Marcus Lechner and
Hans{-}Peter Lenhof and
Martin Middendorf and
Peter F. Stadler},
title = {Phylogenomics with Paralogs},
journal = {CoRR},
volume = {abs/1712.06442},
year = {2017},
url = {http://arxiv.org/abs/1712.06442},
eprinttype = {arXiv},
eprint = {1712.06442},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-06442.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-09022,
author = {Manoj Changat and
Prasanth G. Narasimha{-}Shenoi and
Ferdoos Hossein Nezhad and
Matjaz Kovse and
Shilpa Mohandas and
Abisha Ramachandran and
Peter F. Stadler},
title = {Topological Representation of the Transit Sets of k-Point Crossover
Operators},
journal = {CoRR},
volume = {abs/1712.09022},
year = {2017},
url = {http://arxiv.org/abs/1712.09022},
eprinttype = {arXiv},
eprint = {1712.09022},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-09022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dagstuhl-reports/AndersenFMS17,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Algorithmic Cheminformatics (Dagstuhl Seminar 17452)},
journal = {Dagstuhl Reports},
volume = {7},
number = {11},
pages = {28--45},
year = {2017},
url = {https://doi.org/10.4230/DagRep.7.11.28},
doi = {10.4230/DAGREP.7.11.28},
timestamp = {Thu, 29 Mar 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dagstuhl-reports/AndersenFMS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/IndrischekWSP16,
author = {Henrike Indrischek and
Nicolas Wieseke and
Peter F. Stadler and
Sonja J. Prohaska},
title = {The paralog-to-contig assignment problem: high quality gene models
from fragmented assemblies},
journal = {Algorithms Mol. Biol.},
volume = {11},
pages = {1},
year = {2016},
url = {https://doi.org/10.1186/s13015-016-0063-y},
doi = {10.1186/S13015-016-0063-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/IndrischekWSP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LorenzHS16,
author = {Ronny Lorenz and
Ivo L. Hofacker and
Peter F. Stadler},
title = {{RNA} folding with hard and soft constraints},
journal = {Algorithms Mol. Biol.},
volume = {11},
pages = {8},
year = {2016},
url = {https://doi.org/10.1186/s13015-016-0070-z},
doi = {10.1186/S13015-016-0070-Z},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/LorenzHS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LorenzLHSW16,
author = {Ronny Lorenz and
Dominik Luntzer and
Ivo L. Hofacker and
Peter F. Stadler and
Michael T. Wolfinger},
title = {{SHAPE} directed {RNA} folding},
journal = {Bioinform.},
volume = {32},
number = {1},
pages = {145--147},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv523},
doi = {10.1093/BIOINFORMATICS/BTV523},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LorenzLHSW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KucharikHSQ16,
author = {Marcel Kuchar{\'{\i}}k and
Ivo L. Hofacker and
Peter F. Stadler and
Jing Qin},
title = {Pseudoknots in {RNA} folding landscapes},
journal = {Bioinform.},
volume = {32},
number = {2},
pages = {187--194},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv572},
doi = {10.1093/BIOINFORMATICS/BTV572},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KucharikHSQ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OliveiraCBSWH16,
author = {Jo{\~{a}}o Victor de Ara{\'{u}}jo Oliveira and
Fabrizio Costa and
Rolf Backofen and
Peter F. Stadler and
Maria Em{\'{\i}}lia Telles Walter and
Jana Hertel},
title = {SnoReport 2.0: new features and a refined Support Vector Machine to
improve snoRNA identification},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-18}},
pages = {73--86},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1345-6},
doi = {10.1186/S12859-016-1345-6},
timestamp = {Tue, 02 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/OliveiraCBSWH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/it/HoffmannS16,
author = {Steve Hoffmann and
Peter F. Stadler},
title = {Read mapping},
journal = {it Inf. Technol.},
volume = {58},
number = {3},
pages = {119--125},
year = {2016},
url = {https://doi.org/10.1515/itit-2015-0046},
doi = {10.1515/ITIT-2015-0046},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/it/HoffmannS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/HammackHOS16,
author = {Richard H. Hammack and
Marc Hellmuth and
Lydia Ostermeier and
Peter F. Stadler},
title = {Associativity and Non-Associativity of Some Hypergraph Products},
journal = {Math. Comput. Sci.},
volume = {10},
number = {3},
pages = {403--408},
year = {2016},
url = {https://doi.org/10.1007/s11786-016-0276-y},
doi = {10.1007/S11786-016-0276-Y},
timestamp = {Sun, 22 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/HammackHOS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/RiechertSS16,
author = {Maik Riechert and
Christian H{\"{o}}ner zu Siederdissen and
Peter F. Stadler},
title = {Algebraic dynamic programming for multiple context-free grammars},
journal = {Theor. Comput. Sci.},
volume = {639},
pages = {91--109},
year = {2016},
url = {https://doi.org/10.1016/j.tcs.2016.05.032},
doi = {10.1016/J.TCS.2016.05.032},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/RiechertSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/KrakauerMPS16,
author = {David C. Krakauer and
Lydia M{\"{u}}ller and
Sonja J. Prohaska and
Peter F. Stadler},
title = {Design specifications for cellular regulation},
journal = {Theory Biosci.},
volume = {135},
number = {4},
pages = {231--240},
year = {2016},
url = {https://doi.org/10.1007/s12064-016-0239-5},
doi = {10.1007/S12064-016-0239-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/KrakauerMPS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gg/AndersenFMS16,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
editor = {Rachid Echahed and
Mark Minas},
title = {A Software Package for Chemically Inspired Graph Transformation},
booktitle = {Graph Transformation - 9th International Conference, {ICGT} 2016,
in Memory of Hartmut Ehrig, Held as Part of {STAF} 2016, Vienna, Austria,
July 5-6, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9761},
pages = {73--88},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-40530-8\_5},
doi = {10.1007/978-3-319-40530-8\_5},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gg/AndersenFMS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gg/FlammMST16,
author = {Christoph Flamm and
Daniel Merkle and
Peter F. Stadler and
Uffe Thorsen},
editor = {Rachid Echahed and
Mark Minas},
title = {Automatic Inference of Graph Transformation Rules Using the Cyclic
Nature of Chemical Reactions},
booktitle = {Graph Transformation - 9th International Conference, {ICGT} 2016,
in Memory of Hartmut Ehrig, Held as Part of {STAF} 2016, Vienna, Austria,
July 5-6, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9761},
pages = {206--222},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-40530-8\_13},
doi = {10.1007/978-3-319-40530-8\_13},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gg/FlammMST16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthSW16,
author = {Marc Hellmuth and
Peter F. Stadler and
Nicolas Wieseke},
title = {The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures
and Tree-representable Systems of Binary Relations},
journal = {CoRR},
volume = {abs/1603.02467},
year = {2016},
url = {http://arxiv.org/abs/1603.02467},
eprinttype = {arXiv},
eprint = {1603.02467},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthSW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AndersenFMS16,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {A Software Package for Chemically Inspired Graph Transformation},
journal = {CoRR},
volume = {abs/1603.02481},
year = {2016},
url = {http://arxiv.org/abs/1603.02481},
eprinttype = {arXiv},
eprint = {1603.02481},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/AndersenFMS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/FlammMST16,
author = {Christoph Flamm and
Daniel Merkle and
Peter F. Stadler and
Uffe Thorsen},
title = {Automatic Inference of Graph Transformation Rules Using the Cyclic
Nature of Chemical Reactions},
journal = {CoRR},
volume = {abs/1604.06379},
year = {2016},
url = {http://arxiv.org/abs/1604.06379},
eprinttype = {arXiv},
eprint = {1604.06379},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/FlammMST16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthHLS16,
author = {Marc Hellmuth and
Maribel Hernandez{-}Rosales and
Yangjing Long and
Peter F. Stadler},
title = {Inference of Phylogenetic Trees from the Knowledge of Rare Evolutionary
Events},
journal = {CoRR},
volume = {abs/1612.09093},
year = {2016},
url = {http://arxiv.org/abs/1612.09093},
eprinttype = {arXiv},
eprint = {1612.09093},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthHLS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ajc/HellmuthMOS15,
author = {Marc Hellmuth and
Tilen Marc and
Lydia Ostermeier and
Peter F. Stadler},
title = {The relaxed square property},
journal = {Australas. {J} Comb.},
volume = {62},
pages = {240},
year = {2015},
url = {http://ajc.maths.uq.edu.au/pdf/62/ajc\_v62\_p240.pdf},
timestamp = {Wed, 11 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ajc/HellmuthMOS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HoffmannSS15,
author = {Steve Hoffmann and
Peter F. Stadler and
Korbinian Strimmer},
title = {A simple data-adaptive probabilistic variant calling model},
journal = {Algorithms Mol. Biol.},
volume = {10},
pages = {10},
year = {2015},
url = {https://doi.org/10.1186/s13015-015-0037-5},
doi = {10.1186/S13015-015-0037-5},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/HoffmannSS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EngelhardtS15,
author = {Jan Engelhardt and
Peter F. Stadler},
title = {Evolution of 3'UTR-associated RNAs},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S-8}},
pages = {A7},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-S8-A7},
doi = {10.1186/1471-2105-16-S8-A7},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/EngelhardtS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SiederdissenPS15,
author = {Christian H{\"{o}}ner zu Siederdissen and
Sonja J. Prohaska and
Peter F. Stadler},
title = {Algebraic Dynamic Programming over general data structures},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S19}},
pages = {S2},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-s19-s2},
doi = {10.1186/1471-2105-16-S19-S2},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SiederdissenPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gc/OstermeierS15,
author = {Lydia Ostermeier and
Peter F. Stadler},
title = {The Grid Property and Product-Like Hypergraphs},
journal = {Graphs Comb.},
volume = {31},
number = {3},
pages = {757--770},
year = {2015},
url = {https://doi.org/10.1007/s00373-013-1392-y},
doi = {10.1007/S00373-013-1392-Y},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/gc/OstermeierS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/ArrudaSRWRBS15,
author = {Wosley Arruda and
Daniel S. Souza and
C{\'{e}}lia Ghedini Ralha and
Maria Em{\'{\i}}lia M. T. Walter and
Tain{\'{a}} Raiol and
Marcelo M. Brigido and
Peter F. Stadler},
title = {Knowledge-based reasoning to annotate noncoding {RNA} using multi-agent
system},
journal = {J. Bioinform. Comput. Biol.},
volume = {13},
number = {6},
pages = {1550021:1--1550021:19},
year = {2015},
url = {https://doi.org/10.1142/S0219720015500213},
doi = {10.1142/S0219720015500213},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/ArrudaSRWRBS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/StadlerS15,
author = {B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
title = {Connectivity Spaces},
journal = {Math. Comput. Sci.},
volume = {9},
number = {4},
pages = {409--436},
year = {2015},
url = {https://doi.org/10.1007/s11786-015-0241-1},
doi = {10.1007/S11786-015-0241-1},
timestamp = {Wed, 12 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/StadlerS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/BerkemerCFHHS15,
author = {Sarah Berkemer and
Ricardo R{\'{e}}gis Cavalcante Chaves and
Adrian Fritz and
Marc Hellmuth and
Maribel Hernandez{-}Rosales and
Peter F. Stadler},
title = {Spiders can be Recognized by Counting Their Legs},
journal = {Math. Comput. Sci.},
volume = {9},
number = {4},
pages = {437--441},
year = {2015},
url = {https://doi.org/10.1007/s11786-015-0233-1},
doi = {10.1007/S11786-015-0233-1},
timestamp = {Wed, 12 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/BerkemerCFHHS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SiederdissenHS15,
author = {Christian H{\"{o}}ner zu Siederdissen and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Product Grammars for Alignment and Folding},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {12},
number = {3},
pages = {507--519},
year = {2015},
url = {https://doi.org/10.1109/TCBB.2014.2326155},
doi = {10.1109/TCBB.2014.2326155},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SiederdissenHS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/LaubichlerSPN15,
author = {Manfred D. Laubichler and
Peter F. Stadler and
Sonja J. Prohaska and
Katja Nowick},
title = {The relativity of biological function},
journal = {Theory Biosci.},
volume = {134},
number = {3-4},
pages = {143--147},
year = {2015},
url = {https://doi.org/10.1007/s12064-015-0215-5},
doi = {10.1007/S12064-015-0215-5},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tib/LaubichlerSPN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AndersenFMS15,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Support for Eschenmoser's Glyoxylate Scenario},
journal = {CoRR},
volume = {abs/1502.07555},
year = {2015},
url = {http://arxiv.org/abs/1502.07555},
eprinttype = {arXiv},
eprint = {1502.07555},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/AndersenFMS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthFWS15,
author = {Marc Hellmuth and
Adrian Fritz and
Nicolas Wieseke and
Peter F. Stadler},
title = {Techniques for the Cograph Editing Problem: Module Merge is equivalent
to Editing P4s},
journal = {CoRR},
volume = {abs/1509.06983},
year = {2015},
url = {http://arxiv.org/abs/1509.06983},
eprinttype = {arXiv},
eprint = {1509.06983},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthFWS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/QinFMSB14,
author = {Jing Qin and
Markus Fricke and
Manja Marz and
Peter F. Stadler and
Rolf Backofen},
title = {Graph-distance distribution of the Boltzmann ensemble of {RNA} secondary
structures},
journal = {Algorithms Mol. Biol.},
volume = {9},
pages = {19},
year = {2014},
url = {https://doi.org/10.1186/1748-7188-9-19},
doi = {10.1186/1748-7188-9-19},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/QinFMSB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MisofMRKPS14,
author = {Bernhard Misof and
Karen Meusemann and
Bj{\"{o}}rn Marcus von Reumont and
Patrick K{\"{u}}ck and
Sonja J. Prohaska and
Peter F. Stadler},
title = {A priori assessment of data quality in molecular phylogenetics},
journal = {Algorithms Mol. Biol.},
volume = {9},
pages = {22},
year = {2014},
url = {https://doi.org/10.1186/s13015-014-0022-4},
doi = {10.1186/S13015-014-0022-4},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/MisofMRKPS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MannNSBSF14,
author = {Martin Mann and
Feras Nahar and
Norah Schnorr and
Rolf Backofen and
Peter F. Stadler and
Christoph Flamm},
title = {Atom mapping with constraint programming},
journal = {Algorithms Mol. Biol.},
volume = {9},
pages = {23},
year = {2014},
url = {https://doi.org/10.1186/s13015-014-0023-3},
doi = {10.1186/S13015-014-0023-3},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/MannNSBSF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/arsmc/HellmuthLS14,
author = {Marc Hellmuth and
Josef Leydold and
Peter F. Stadler},
title = {Convex cycle bases},
journal = {Ars Math. Contemp.},
volume = {7},
number = {1},
pages = {123--140},
year = {2014},
url = {https://doi.org/10.26493/1855-3974.226.0a2},
doi = {10.26493/1855-3974.226.0A2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/arsmc/HellmuthLS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BartschatKTSH14,
author = {Sebastian Bartschat and
Stephanie Kehr and
Hakim Tafer and
Peter F. Stadler and
Jana Hertel},
title = {snoStrip: a snoRNA annotation pipeline},
journal = {Bioinform.},
volume = {30},
number = {1},
pages = {115--116},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt604},
doi = {10.1093/BIOINFORMATICS/BTT604},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BartschatKTSH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarzBDFFHHMRST14,
author = {Manja Marz and
Niko Beerenwinkel and
Christian Drosten and
Markus Fricke and
Dmitrij Frishman and
Ivo L. Hofacker and
Dieter Hoffmann and
Martin Middendorf and
Thomas Rattei and
Peter F. Stadler and
Armin T{\"{o}}pfer},
title = {Challenges in {RNA} virus bioinformatics},
journal = {Bioinform.},
volume = {30},
number = {13},
pages = {1793--1799},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu105},
doi = {10.1093/BIOINFORMATICS/BTU105},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarzBDFFHHMRST14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OttoSH14,
author = {Christian Otto and
Peter F. Stadler and
Steve Hoffmann},
title = {Lacking alignments? The next-generation sequencing mapper segemehl
revisited},
journal = {Bioinform.},
volume = {30},
number = {13},
pages = {1837--1843},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu146},
doi = {10.1093/BIOINFORMATICS/BTU146},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OttoSH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KucharikHSQ14,
author = {Marcel Kuchar{\'{\i}}k and
Ivo L. Hofacker and
Peter F. Stadler and
Jing Qin},
title = {Basin Hopping Graph: a computational framework to characterize {RNA}
folding landscapes},
journal = {Bioinform.},
volume = {30},
number = {14},
pages = {2009--2017},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu156},
doi = {10.1093/BIOINFORMATICS/BTU156},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KucharikHSQ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AmmanWLHSF14,
author = {Fabian Amman and
Michael T. Wolfinger and
Ronny Lorenz and
Ivo L. Hofacker and
Peter F. Stadler and
Sven Findei{\ss}},
title = {{TSSAR:} {TSS} annotation regime for dRNA-seq data},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {89},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-89},
doi = {10.1186/1471-2105-15-89},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AmmanWLHSF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Hernandez-RosalesWHS14,
author = {Maribel Hernandez{-}Rosales and
Nicolas Wieseke and
Marc Hellmuth and
Peter F. Stadler},
title = {Simulation of gene family histories},
journal = {{BMC} Bioinform.},
volume = {15},
number = {{S-3}},
pages = {A8},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-S3-A8},
doi = {10.1186/1471-2105-15-S3-A8},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Hernandez-RosalesWHS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dm/HellmuthOS14,
author = {Marc Hellmuth and
Lydia Ostermeier and
Peter F. Stadler},
title = {Unique square property, equitable partitions, and product-like graphs},
journal = {Discret. Math.},
volume = {320},
pages = {92--103},
year = {2014},
url = {https://doi.org/10.1016/j.disc.2013.12.012},
doi = {10.1016/J.DISC.2013.12.012},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dm/HellmuthOS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/AndersenFMS14,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Generic strategies for chemical space exploration},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {7},
number = {2/3},
pages = {225--258},
year = {2014},
url = {https://doi.org/10.1504/IJCBDD.2014.061649},
doi = {10.1504/IJCBDD.2014.061649},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/AndersenFMS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/DohmMHCZTRSSRGK14,
author = {Juliane C. Dohm and
Andr{\'{e}} E. Minoche and
Daniela Holtgr{\"{a}}we and
Salvador Capella{-}Guti{\'{e}}rrez and
Falk Zakrzewski and
Hakim Tafer and
Oliver Rupp and
Thomas Rosleff S{\"{o}}rensen and
Ralf Stracke and
Richard Reinhardt and
Alexander Goesmann and
Thomas Kraft and
Britta Schulz and
Peter F. Stadler and
Thomas Schmidt and
Toni Gabald{\'{o}}n and
Hans Lehrach and
Bernd Weisshaar and
Heinz Himmelbauer},
title = {The genome of the recently domesticated crop plant sugar beet (\emph{Beta
vulgaris}) Open},
journal = {Nat.},
volume = {505},
number = {7484},
pages = {546--549},
year = {2014},
url = {https://doi.org/10.1038/nature12817},
doi = {10.1038/NATURE12817},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/DohmMHCZTRSSRGK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fmmb/AndersenFMS14,
author = {Jakob Lykke Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
editor = {Fran{\c{c}}ois Fages and
Carla Piazza},
title = {50 Shades of Rule Composition - From Chemical Reactions to Higher
Levels of Abstraction},
booktitle = {Formal Methods in Macro-Biology - First International Conference,
{FMMB} 2014, Noum{\'{e}}a, New Caledonia, September 22-24, 2014.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8738},
pages = {117--135},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-10398-3\_9},
doi = {10.1007/978-3-319-10398-3\_9},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/fmmb/AndersenFMS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/SiederdissenBAW14,
author = {Christian H{\"{o}}ner zu Siederdissen and
Sarah Berkemer and
Fabian Amman and
Axel Wintsche and
Sebastian Will and
Sonja J. Prohaska and
Peter F. Stadler},
editor = {Ignacio Rojas and
Francisco M. Ortu{\~{n}}o Guzman},
title = {Comparative Detection of Processed Small RNAs in Archaea},
booktitle = {International Work-Conference on Bioinformatics and Biomedical Engineering,
{IWBBIO} 2014, Granada, Spain, April 7-9, 2014},
pages = {286--297},
publisher = {Copicentro Editorial},
year = {2014},
url = {http://iwbbio.ugr.es/2014/papers/IWBBIO\_2014\_paper\_33.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/SiederdissenBAW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/WillS14,
author = {Sebastian Will and
Peter F. Stadler},
editor = {Daniel G. Brown and
Burkhard Morgenstern},
title = {A Common Framework for Linear and Cyclic Multiple Sequence Alignment
Problems},
booktitle = {Algorithms in Bioinformatics - 14th International Workshop, {WABI}
2014, Wroclaw, Poland, September 8-10, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8701},
pages = {135--147},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-662-44753-6\_11},
doi = {10.1007/978-3-662-44753-6\_11},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/WillS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/SiederdissenPS14,
author = {Christian H{\"{o}}ner zu Siederdissen and
Sonja J. Prohaska and
Peter F. Stadler},
editor = {S{\'{e}}rgio Vale Aguiar Campos},
title = {Dynamic Programming for Set Data Types},
booktitle = {Advances in Bioinformatics and Computational Biology - 9th Brazilian
Symposium on Bioinformatics, {BSB} 2014, Belo Horizonte, Brazil, October
28-30, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8826},
pages = {57--64},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-12418-6\_8},
doi = {10.1007/978-3-319-12418-6\_8},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/SiederdissenPS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/SchneiderBDMPBTWRBWS14,
author = {Hugo W. Schneider and
Sebastian Bartschat and
Gero Doose and
Lucas Maciel and
Erick Pizani and
Marcelo Bassani and
Fernando Araripe Torres and
Sebastian Will and
Tain{\'{a}} Raiol and
Marcelo M. Brigido and
Maria Em{\'{\i}}lia Telles Walter and
Peter F. Stadler},
editor = {S{\'{e}}rgio Vale Aguiar Campos},
title = {Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris
str. {GS115}},
booktitle = {Advances in Bioinformatics and Computational Biology - 9th Brazilian
Symposium on Bioinformatics, {BSB} 2014, Belo Horizonte, Brazil, October
28-30, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8826},
pages = {115--122},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-12418-6\_15},
doi = {10.1007/978-3-319-12418-6\_15},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/SchneiderBDMPBTWRBWS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/ncs/KlemmS14,
author = {Konstantin Klemm and
Peter F. Stadler},
editor = {Yossi Borenstein and
Alberto Moraglio},
title = {Rugged and Elementary Landscapes},
booktitle = {Theory and Principled Methods for the Design of Metaheuristics},
series = {Natural Computing Series},
pages = {41--61},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-642-33206-7\_3},
doi = {10.1007/978-3-642-33206-7\_3},
timestamp = {Mon, 26 Oct 2020 08:19:22 +0100},
biburl = {https://dblp.org/rec/series/ncs/KlemmS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HellmuthMOS14,
author = {Marc Hellmuth and
Tilen Marc and
Lydia Ostermeier and
Peter F. Stadler},
title = {The Relaxed Square Property},
journal = {CoRR},
volume = {abs/1407.3164},
year = {2014},
url = {http://arxiv.org/abs/1407.3164},
eprinttype = {arXiv},
eprint = {1407.3164},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HellmuthMOS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BerkemerCFHHS14,
author = {Sarah Berkemer and
Ricardo R{\'{e}}gis Cavalcante Chaves and
Adrian Fritz and
Marc Hellmuth and
Maribel Hernandez{-}Rosales and
Peter F. Stadler},
title = {Spiders can be recognized by counting their legs},
journal = {CoRR},
volume = {abs/1411.2105},
year = {2014},
url = {http://arxiv.org/abs/1411.2105},
eprinttype = {arXiv},
eprint = {1411.2105},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BerkemerCFHHS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dagstuhl-reports/BanzhafFMS14,
author = {Wolfgang Banzhaf and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Algorithmic Cheminformatics (Dagstuhl Seminar 14452)},
journal = {Dagstuhl Reports},
volume = {4},
number = {11},
pages = {22--39},
year = {2014},
url = {https://doi.org/10.4230/DagRep.4.11.22},
doi = {10.4230/DAGREP.4.11.22},
timestamp = {Wed, 07 Jun 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dagstuhl-reports/BanzhafFMS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WillSHESRB13,
author = {Sebastian Will and
Michael F. Siebauer and
Steffen Heyne and
Jan Engelhardt and
Peter F. Stadler and
Kristin Reiche and
Rolf Backofen},
title = {LocARNAscan: Incorporating thermodynamic stability in sequence and
structure-based {RNA} homology search},
journal = {Algorithms Mol. Biol.},
volume = {8},
pages = {14},
year = {2013},
url = {https://doi.org/10.1186/1748-7188-8-14},
doi = {10.1186/1748-7188-8-14},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/WillSHESRB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/arsmc/HubickaJLSY13,
author = {Jan Hubicka and
J{\"{u}}rgen Jost and
Yangjing Long and
Peter F. Stadler and
Ling Yang},
title = {Relations between graphs},
journal = {Ars Math. Contemp.},
volume = {6},
number = {2},
pages = {323--350},
year = {2013},
url = {https://doi.org/10.26493/1855-3974.335.d57},
doi = {10.26493/1855-3974.335.D57},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/arsmc/HubickaJLSY13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/entropy/AndersenAFHMS13,
author = {Jakob L. Andersen and
Tommy Andersen and
Christoph Flamm and
Martin M. Hanczyc and
Daniel Merkle and
Peter F. Stadler},
title = {Navigating the Chemical Space of {HCN} Polymerization and Hydrolysis:
Guiding Graph Grammars by Mass Spectrometry Data},
journal = {Entropy},
volume = {15},
number = {10},
pages = {4066--4083},
year = {2013},
url = {https://doi.org/10.3390/e15104066},
doi = {10.3390/E15104066},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/entropy/AndersenAFHMS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/FagerbergFMPS13,
author = {Rolf Fagerberg and
Christoph Flamm and
Daniel Merkle and
Philipp Peters and
Peter F. Stadler},
title = {On the Complexity of Reconstructing Chemical Reaction Networks},
journal = {Math. Comput. Sci.},
volume = {7},
number = {3},
pages = {275--292},
year = {2013},
url = {https://doi.org/10.1007/s11786-013-0160-y},
doi = {10.1007/S11786-013-0160-Y},
timestamp = {Wed, 12 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/FagerbergFMPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SabarinathanTSHSG13,
author = {Radhakrishnan Sabarinathan and
Hakim Tafer and
Stefan E. Seemann and
Ivo L. Hofacker and
Peter F. Stadler and
Jan Gorodkin},
title = {The RNAsnp web server: predicting {SNP} effects on local {RNA} secondary
structure},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Webserver-Issue},
pages = {475--479},
year = {2013},
url = {https://doi.org/10.1093/nar/gkt291},
doi = {10.1093/NAR/GKT291},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SabarinathanTSHSG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LorenzBQSTAHS13,
author = {Ronny Lorenz and
Stephan H. Bernhart and
Jing Qin and
Christian H{\"{o}}ner zu Siederdissen and
Andrea Tanzer and
Fabian Amman and
Ivo L. Hofacker and
Peter F. Stadler},
title = {2D Meets 4G: G-Quadruplexes in {RNA} Secondary Structure Prediction},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {10},
number = {4},
pages = {832--844},
year = {2013},
url = {https://doi.org/10.1109/TCBB.2013.7},
doi = {10.1109/TCBB.2013.7},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LorenzBQSTAHS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/LechnerMISSK13,
author = {Marcus Lechner and
Manja Marz and
Christian Ihling and
Andrea Sinz and
Peter F. Stadler and
Veiko Krauss},
title = {The correlation of genome size and {DNA} methylation rate in metazoans},
journal = {Theory Biosci.},
volume = {132},
number = {1},
pages = {47--60},
year = {2013},
url = {https://doi.org/10.1007/s12064-012-0167-y},
doi = {10.1007/S12064-012-0167-Y},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/LechnerMISSK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cp/MannNEBSF13,
author = {Martin Mann and
Feras Nahar and
Heinz Ekker and
Rolf Backofen and
Peter F. Stadler and
Christoph Flamm},
editor = {Christian Schulte},
title = {Atom Mapping with Constraint Programming},
booktitle = {Principles and Practice of Constraint Programming - 19th International
Conference, {CP} 2013, Uppsala, Sweden, September 16-20, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8124},
pages = {805--822},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-40627-0\_59},
doi = {10.1007/978-3-642-40627-0\_59},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/cp/MannNEBSF13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BackofenFMQS13,
author = {Rolf Backofen and
Markus Fricke and
Manja Marz and
Jing Qin and
Peter F. Stadler},
editor = {Aaron E. Darling and
Jens Stoye},
title = {Distribution of Graph-Distances in Boltzmann Ensembles of {RNA} Secondary
Structures},
booktitle = {Algorithms in Bioinformatics - 13th International Workshop, {WABI}
2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8126},
pages = {112--125},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-40453-5\_10},
doi = {10.1007/978-3-642-40453-5\_10},
timestamp = {Tue, 21 Mar 2023 21:00:29 +0100},
biburl = {https://dblp.org/rec/conf/wabi/BackofenFMQS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/AmmanBDHQSW13,
author = {Fabian Amman and
Stephan H. Bernhart and
Gero Doose and
Ivo L. Hofacker and
Jing Qin and
Peter F. Stadler and
Sebastian Will},
editor = {Jo{\~{a}}o C. Setubal and
Nalvo F. Almeida},
title = {The Trouble with Long-Range Base Pairs in {RNA} Folding},
booktitle = {Advances in Bioinformatics and Computational Biology - 8th Brazilian
Symposium on Bioinformatics, {BSB} 2013, Recife, Brazil, November
3-7, 2013, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8213},
pages = {1--11},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-319-02624-4\_1},
doi = {10.1007/978-3-319-02624-4\_1},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/AmmanBDHQSW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/SiederdissenHS13,
author = {Christian H{\"{o}}ner zu Siederdissen and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Jo{\~{a}}o C. Setubal and
Nalvo F. Almeida},
title = {How to Multiply Dynamic Programming Algorithms},
booktitle = {Advances in Bioinformatics and Computational Biology - 8th Brazilian
Symposium on Bioinformatics, {BSB} 2013, Recife, Brazil, November
3-7, 2013, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8213},
pages = {82--93},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-319-02624-4\_8},
doi = {10.1007/978-3-319-02624-4\_8},
timestamp = {Wed, 25 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/SiederdissenHS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/ArrudaRRBWS13,
author = {Wosley Arruda and
C{\'{e}}lia Ghedini Ralha and
Tain{\'{a}} Raiol and
Marcelo M. Brigido and
Maria Em{\'{\i}}lia M. T. Walter and
Peter F. Stadler},
editor = {Jo{\~{a}}o C. Setubal and
Nalvo F. Almeida},
title = {ncRNA-Agents: {A} Multiagent System for Non-coding {RNA} Annotation},
booktitle = {Advances in Bioinformatics and Computational Biology - 8th Brazilian
Symposium on Bioinformatics, {BSB} 2013, Recife, Brazil, November
3-7, 2013, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8213},
pages = {136--147},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-319-02624-4\_13},
doi = {10.1007/978-3-319-02624-4\_13},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/ArrudaRRBWS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1301-6898,
author = {Marc Hellmuth and
Lydia Ostermeier and
Peter F. Stadler},
title = {Square Property, Equitable Partitions, and Product-like Graphs},
journal = {CoRR},
volume = {abs/1301.6898},
year = {2013},
url = {http://arxiv.org/abs/1301.6898},
eprinttype = {arXiv},
eprint = {1301.6898},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1301-6898.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1302-4006,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Generic Strategies for Chemical Space Exploration},
journal = {CoRR},
volume = {abs/1302.4006},
year = {2013},
url = {http://arxiv.org/abs/1302.4006},
eprinttype = {arXiv},
eprint = {1302.4006},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1302-4006.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/FagerbergFMPS13,
author = {Rolf Fagerberg and
Christoph Flamm and
Daniel Merkle and
Philipp Peters and
Peter F. Stadler},
title = {On the Complexity of Reconstructing Chemical Reaction Networks},
journal = {CoRR},
volume = {abs/1309.7198},
year = {2013},
url = {http://arxiv.org/abs/1309.7198},
eprinttype = {arXiv},
eprint = {1309.7198},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/FagerbergFMPS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/arsmc/HellmuthOS12,
author = {Marc Hellmuth and
Philipp{-}Jens Ostermeier and
Peter F. Stadler},
title = {Minimum cycle bases of lexicographic products},
journal = {Ars Math. Contemp.},
volume = {5},
number = {2},
pages = {223--234},
year = {2012},
url = {https://doi.org/10.26493/1855-3974.172.8a7},
doi = {10.26493/1855-3974.172.8A7},
timestamp = {Wed, 27 Mar 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/arsmc/HellmuthOS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LangenbergerPESHG12,
author = {David Langenberger and
Sachin Pundhir and
Claus Thorn Ekstr{\o}m and
Peter F. Stadler and
Steve Hoffmann and
Jan Gorodkin},
title = {deepBlockAlign: a tool for aligning RNA-seq profiles of read block
patterns},
journal = {Bioinform.},
volume = {28},
number = {1},
pages = {17--24},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/btr598},
doi = {10.1093/BIOINFORMATICS/BTR598},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LangenbergerPESHG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReidysHAPSN12,
author = {Christian M. Reidys and
Fenix W. D. Huang and
J{\o}rgen E. Andersen and
Robert C. Penner and
Peter F. Stadler and
Markus E. Nebel},
title = {Addendum: topology and prediction of {RNA} pseudoknots},
journal = {Bioinform.},
volume = {28},
number = {2},
pages = {300},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/btr643},
doi = {10.1093/BIOINFORMATICS/BTR643},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReidysHAPSN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OttoSH12,
author = {Christian Otto and
Peter F. Stadler and
Steve Hoffmann},
title = {Fast and sensitive mapping of bisulfite-treated sequencing data},
journal = {Bioinform.},
volume = {28},
number = {13},
pages = {1698--1704},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts254},
doi = {10.1093/BIOINFORMATICS/BTS254},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OttoSH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Hernandez-RosalesHWHMS12,
author = {Maribel Hernandez{-}Rosales and
Marc Hellmuth and
Nicolas Wieseke and
Katharina T. Huber and
Vincent Moulton and
Peter F. Stadler},
title = {From event-labeled gene trees to species trees},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-19}},
pages = {S6},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S19-S6},
doi = {10.1186/1471-2105-13-S19-S6},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Hernandez-RosalesHWHMS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dm/HellmuthOS12,
author = {Marc Hellmuth and
Lydia Ostermeier and
Peter F. Stadler},
title = {Diagonalized Cartesian products of s-prime graphs are s-prime},
journal = {Discret. Math.},
volume = {312},
number = {1},
pages = {74--80},
year = {2012},
url = {https://doi.org/10.1016/j.disc.2011.03.033},
doi = {10.1016/J.DISC.2011.03.033},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dm/HellmuthOS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dm/HofackerRS12,
author = {Ivo L. Hofacker and
Christian M. Reidys and
Peter F. Stadler},
title = {Symmetric circular matchings and {RNA} folding},
journal = {Discret. Math.},
volume = {312},
number = {1},
pages = {100--112},
year = {2012},
url = {https://doi.org/10.1016/j.disc.2011.06.004},
doi = {10.1016/J.DISC.2011.06.004},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dm/HofackerRS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jgt/OstermeierHS12,
author = {Lydia Ostermeier and
Marc Hellmuth and
Peter F. Stadler},
title = {The Cartesian product of hypergraphs},
journal = {J. Graph Theory},
volume = {70},
number = {2},
pages = {180--196},
year = {2012},
url = {https://doi.org/10.1002/jgt.20609},
doi = {10.1002/JGT.20609},
timestamp = {Fri, 02 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jgt/OstermeierHS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/HellmuthOS12,
author = {Marc Hellmuth and
Lydia Ostermeier and
Peter F. Stadler},
title = {A Survey on Hypergraph Products},
journal = {Math. Comput. Sci.},
volume = {6},
number = {1},
pages = {1--32},
year = {2012},
url = {https://doi.org/10.1007/s11786-012-0109-6},
doi = {10.1007/S11786-012-0109-6},
timestamp = {Wed, 12 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/HellmuthOS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/EngelhardtS12,
author = {Jan Engelhardt and
Peter F. Stadler},
title = {Hidden treasures in unspliced {EST} data},
journal = {Theory Biosci.},
volume = {131},
number = {1},
pages = {49--57},
year = {2012},
url = {https://doi.org/10.1007/s12064-012-0151-6},
doi = {10.1007/S12064-012-0151-6},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/EngelhardtS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isvc/RohrschneiderSS12,
author = {Markus Rohrschneider and
Peter F. Stadler and
Gerik Scheuermann},
editor = {George Bebis and
Richard Boyle and
Bahram Parvin and
Darko Koracin and
Charless C. Fowlkes and
Sen Wang and
Min{-}Hyung Choi and
Stephan Mantler and
J{\"{u}}rgen P. Schulze and
Daniel Acevedo and
Klaus Mueller and
Michael E. Papka},
title = {A Visual Cross-Database Comparison of Metabolic Networks},
booktitle = {Advances in Visual Computing - 8th International Symposium, {ISVC}
2012, Rethymnon, Crete, Greece, July 16-18, 2012, Revised Selected
Papers, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {7432},
pages = {678--687},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33191-6\_67},
doi = {10.1007/978-3-642-33191-6\_67},
timestamp = {Fri, 04 Nov 2022 09:06:17 +0100},
biburl = {https://dblp.org/rec/conf/isvc/RohrschneiderSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/LorenzBEQSAHS12,
author = {Ronny Lorenz and
Stephan H. Bernhart and
Fabian Externbrink and
Jing Qin and
Christian H{\"{o}}ner zu Siederdissen and
Fabian Amman and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Marc{\'{\i}}lio Carlos Pereira de Souto and
Maricel G. Kann},
title = {{RNA} Folding Algorithms with G-Quadruplexes},
booktitle = {Advances in Bioinformatics and Computational Biology - 7th Brazilian
Symposium on Bioinformatics, {BSB} 2012, Campo Grande, Brazil, August
15-17, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7409},
pages = {49--60},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31927-3\_5},
doi = {10.1007/978-3-642-31927-3\_5},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/LorenzBEQSAHS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1208-3153,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Inferring Chemical Reaction Patterns Using Rule Composition in Graph
Grammars},
journal = {CoRR},
volume = {abs/1208.3153},
year = {2012},
url = {http://arxiv.org/abs/1208.3153},
eprinttype = {arXiv},
eprint = {1208.3153},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1208-3153.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/alife/UllrichRSSF11,
author = {Alexander Ullrich and
Markus Rohrschneider and
Gerik Scheuermann and
Peter F. Stadler and
Christoph Flamm},
title = {In Silico Evolution of Early Metabolism},
journal = {Artif. Life},
volume = {17},
number = {2},
pages = {87--108},
year = {2011},
url = {https://doi.org/10.1162/artl\_a\_00021},
doi = {10.1162/ARTL\_A\_00021},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/alife/UllrichRSSF11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/OttoHGS11,
author = {Christian Otto and
Steve Hoffmann and
Jan Gorodkin and
Peter F. Stadler},
title = {Fast local fragment chaining using sum-of-pair gap costs},
journal = {Algorithms Mol. Biol.},
volume = {6},
pages = {4},
year = {2011},
url = {https://doi.org/10.1186/1748-7188-6-4},
doi = {10.1186/1748-7188-6-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/OttoHGS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LorenzBSTFSH11,
author = {Ronny Lorenz and
Stephan H. Bernhart and
Christian H{\"{o}}ner zu Siederdissen and
Hakim Tafer and
Christoph Flamm and
Peter F. Stadler and
Ivo L. Hofacker},
title = {ViennaRNA Package 2.0},
journal = {Algorithms Mol. Biol.},
volume = {6},
pages = {26},
year = {2011},
url = {https://doi.org/10.1186/1748-7188-6-26},
doi = {10.1186/1748-7188-6-26},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/LorenzBSTFSH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KehrBST11,
author = {Stephanie Kehr and
Sebastian Bartschat and
Peter F. Stadler and
Hakim Tafer},
title = {{PLEXY:} efficient target prediction for box {C/D} snoRNAs},
journal = {Bioinform.},
volume = {27},
number = {2},
pages = {279--280},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq642},
doi = {10.1093/BIOINFORMATICS/BTQ642},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KehrBST11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MenzelSG11,
author = {Peter Menzel and
Peter F. Stadler and
Jan Gorodkin},
title = {maxAlike: maximum likelihood-based sequence reconstruction with application
to improved primer design for unknown sequences},
journal = {Bioinform.},
volume = {27},
number = {3},
pages = {317--325},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq651},
doi = {10.1093/BIOINFORMATICS/BTQ651},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MenzelSG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReidysHAPSN11,
author = {Christian M. Reidys and
Fenix W. D. Huang and
J{\o}rgen E. Andersen and
Robert C. Penner and
Peter F. Stadler and
Markus E. Nebel},
title = {Topology and prediction of {RNA} pseudoknots},
journal = {Bioinform.},
volume = {27},
number = {8},
pages = {1076--1085},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr090},
doi = {10.1093/BIOINFORMATICS/BTR090},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReidysHAPSN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SiederdissenBSH11,
author = {Christian H{\"{o}}ner zu Siederdissen and
Stephan H. Bernhart and
Peter F. Stadler and
Ivo L. Hofacker},
title = {A folding algorithm for extended {RNA} secondary structures},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {129--136},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr220},
doi = {10.1093/BIOINFORMATICS/BTR220},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SiederdissenBSH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoseHSHBS11,
author = {Dominic Rose and
Michael Hiller and
Katharina Schutt and
J{\"{o}}rg Hackerm{\"{u}}ller and
Rolf Backofen and
Peter F. Stadler},
title = {Computational discovery of human coding and non-coding transcripts
with conserved splice sites},
journal = {Bioinform.},
volume = {27},
number = {14},
pages = {1894--1900},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr314},
doi = {10.1093/BIOINFORMATICS/BTR314},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoseHSHBS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TaferAESH11,
author = {Hakim Tafer and
Fabian Amman and
Florian Eggenhofer and
Peter F. Stadler and
Ivo L. Hofacker},
title = {Fast accessibility-based prediction of {RNA-RNA} interactions},
journal = {Bioinform.},
volume = {27},
number = {14},
pages = {1934--1940},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr281},
doi = {10.1093/BIOINFORMATICS/BTR281},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TaferAESH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LechnerFSMSP11,
author = {Marcus Lechner and
Sven Findei{\ss} and
Lydia Steiner and
Manja Marz and
Peter F. Stadler and
Sonja J. Prohaska},
title = {Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {124},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-124},
doi = {10.1186/1471-2105-12-124},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LechnerFSMSP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FasoldLBSH11,
author = {Mario Fasold and
David Langenberger and
Hans Binder and
Peter F. Stadler and
Steve Hoffmann},
title = {{DARIO:} a ncRNA detection and analysis tool for next-generation sequencing
experiments},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Web-Server-Issue},
pages = {112--117},
year = {2011},
url = {https://doi.org/10.1093/nar/gkr357},
doi = {10.1093/NAR/GKR357},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/FasoldLBSH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/EggenhoferTSH11,
author = {Florian Eggenhofer and
Hakim Tafer and
Peter F. Stadler and
Ivo L. Hofacker},
title = {RNApredator: fast accessibility-based prediction of sRNA targets},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Web-Server-Issue},
pages = {149--154},
year = {2011},
url = {https://doi.org/10.1093/nar/gkr467},
doi = {10.1093/NAR/GKR467},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/EggenhoferTSH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/OttoSP11,
author = {Wolfgang Otto and
Peter F. Stadler and
Sonja J. Prohaska},
editor = {Raffaele Giancarlo and
Giovanni Manzini},
title = {Phylogenetic Footprinting and Consistent Sets of Local Aligments},
booktitle = {Combinatorial Pattern Matching - 22nd Annual Symposium, {CPM} 2011,
Palermo, Italy, June 27-29, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6661},
pages = {118--131},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21458-5\_12},
doi = {10.1007/978-3-642-21458-5\_12},
timestamp = {Thu, 13 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/OttoSP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/LangenbergerBHHTS11,
author = {David Langenberger and
Sebastian Bartschat and
Jana Hertel and
Steve Hoffmann and
Hakim Tafer and
Peter F. Stadler},
editor = {Osmar Norberto de Souza and
Guilherme P. Telles and
Mathew J. Palakal},
title = {MicroRNA or Not MicroRNA?},
booktitle = {Advances in Bioinformatics and Computational Biology - 6th Brazilian
Symposium on Bioinformatics, {BSB} 2011, Brasilia, Brazil, August
10-12, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6832},
pages = {1--9},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-22825-4\_1},
doi = {10.1007/978-3-642-22825-4\_1},
timestamp = {Tue, 14 May 2019 10:00:50 +0200},
biburl = {https://dblp.org/rec/conf/wob/LangenbergerBHHTS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1110-6051,
author = {Jakob L. Andersen and
Christoph Flamm and
Daniel Merkle and
Peter F. Stadler},
title = {Maximizing Output and Recognizing Autocatalysis in Chemical Reaction
Networks is NP-Complete},
journal = {CoRR},
volume = {abs/1110.6051},
year = {2011},
url = {http://arxiv.org/abs/1110.6051},
eprinttype = {arXiv},
eprint = {1110.6051},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1110-6051.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ArnoldS10,
author = {Christian Arnold and
Peter F. Stadler},
title = {Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic
targeting on arbitrary trees},
journal = {Algorithms Mol. Biol.},
volume = {5},
pages = {25},
year = {2010},
url = {https://doi.org/10.1186/1748-7188-5-25},
doi = {10.1186/1748-7188-5-25},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/ArnoldS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangQRS10,
author = {Fenix W. D. Huang and
Jing Qin and
Christian M. Reidys and
Peter F. Stadler},
title = {Target prediction and a statistical sampling algorithm for {RNA-RNA}
interaction},
journal = {Bioinform.},
volume = {26},
number = {2},
pages = {175--181},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btp635},
doi = {10.1093/BIOINFORMATICS/BTP635},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangQRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TaferKHHS10,
author = {Hakim Tafer and
Stephanie Kehr and
Jana Hertel and
Ivo L. Hofacker and
Peter F. Stadler},
title = {\texttt{RNAsnoop}: efficient target prediction for {H/ACA} snoRNAs},
journal = {Bioinform.},
volume = {26},
number = {5},
pages = {610--616},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btp680},
doi = {10.1093/BIOINFORMATICS/BTP680},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TaferKHHS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FasoldSB10,
author = {Mario Fasold and
Peter F. Stadler and
Hans Binder},
title = {G-stack modulated probe intensities on expression arrays - sequence
corrections and signal calibration},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {207},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-207},
doi = {10.1186/1471-2105-11-207},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FasoldSB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/MarzVS10,
author = {Manja Marz and
Nathalie Vanzo and
Peter F. Stadler},
title = {Temperature-Dependent Structural Variability of RNAs: spliced Leader
RNAs and their Evolutionary History},
journal = {J. Bioinform. Comput. Biol.},
volume = {8},
number = {1},
pages = {1--17},
year = {2010},
url = {https://doi.org/10.1142/S0219720010004525},
doi = {10.1142/S0219720010004525},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/MarzVS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/SharmaHDRFSCRHR10,
author = {Cynthia M. Sharma and
Steve Hoffmann and
Fabien Darfeuille and
J{\'{e}}r{\'{e}}my Reignier and
Sven Findei{\ss} and
Alexandra Sittka and
Sandrine Chabas and
Kristin Reiche and
J{\"{o}}rg Hackerm{\"{u}}ller and
Richard Reinhardt and
Peter F. Stadler and
J{\"{o}}rg Vogel},
title = {The primary transcriptome of the major human pathogen \emph{Helicobacter
pylori}},
journal = {Nat.},
volume = {464},
number = {7286},
pages = {250--255},
year = {2010},
url = {https://doi.org/10.1038/nature08756},
doi = {10.1038/NATURE08756},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nature/SharmaHDRFSCRHR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tvcg/JanickeHHSS10,
author = {Stefan J{\"{a}}nicke and
Christian Heine and
Marc Hellmuth and
Peter F. Stadler and
Gerik Scheuermann},
title = {Visualization of Graph Products},
journal = {{IEEE} Trans. Vis. Comput. Graph.},
volume = {16},
number = {6},
pages = {1082--1089},
year = {2010},
url = {https://doi.org/10.1109/TVCG.2010.217},
doi = {10.1109/TVCG.2010.217},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tvcg/JanickeHHSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alife/UllrichFRS10,
author = {Alexander Ullrich and
Christoph Flamm and
Markus Rohrschneider and
Peter F. Stadler},
editor = {Harold Fellermann and
Mark D{\"{o}}rr and
Martin M. Hanczyc and
Lone Ladegaard Laursen and
Sarah Elizabeth Maurer and
Daniel Merkle and
Pierre{-}Alain Monnard and
Kasper St{\o}y and
Steen Rasmussen},
title = {In Silico Evolution of Early Metabolism},
booktitle = {Proceedings of the Twelfth International Conference on the Synthesis
and Simulation of Living Systems, {ALIFE} 2010, Odense, Denmark, August
19-23, 2010},
pages = {57--64},
publisher = {{MIT} Press},
year = {2010},
url = {http://mitpress2.mit.edu/books/chapters/0262290758chap12.pdf},
timestamp = {Sun, 03 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/alife/UllrichFRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/ParikesitSP10,
author = {Arli A. Parikesit and
Peter F. Stadler and
Sonja J. Prohaska},
editor = {Dietmar Schomburg and
Andreas Grote},
title = {Quantitative Comparison of Genomic-Wide Protein Domain Distributions},
booktitle = {German Conference on Bioinformatics 2010, September 20-22, 2010, Technische
Universit{\"{a}}t Carolo Wilhelmina zu Braunschweig, Germany},
series = {{LNI}},
volume = {{P-173}},
pages = {93--102},
publisher = {{GI}},
year = {2010},
url = {https://dl.gi.de/handle/20.500.12116/19676},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/ParikesitSP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isvc/RohrschneiderUKSS10,
author = {Markus Rohrschneider and
Alexander Ullrich and
Andreas Kerren and
Peter F. Stadler and
Gerik Scheuermann},
editor = {George Bebis and
Richard D. Boyle and
Bahram Parvin and
Darko Koracin and
Ronald Chung and
Riad I. Hammoud and
Muhammad Hussain and
Kar{-}Han Tan and
Roger Crawfis and
Daniel Thalmann and
David L. Kao and
Lisa Avila},
title = {Visual Network Analysis of Dynamic Metabolic Pathways},
booktitle = {Advances in Visual Computing - 6th International Symposium, {ISVC}
2010, Las Vegas, NV, USA, November 29-December 1, 2010. Proceedings,
Part {I}},
series = {Lecture Notes in Computer Science},
volume = {6453},
pages = {316--327},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-17289-2\_31},
doi = {10.1007/978-3-642-17289-2\_31},
timestamp = {Thu, 16 Mar 2023 20:00:32 +0100},
biburl = {https://dblp.org/rec/conf/isvc/RohrschneiderUKSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/BackofenCHSS10,
author = {Rolf Backofen and
Hamidreza Chitsaz and
Ivo L. Hofacker and
S{\"{u}}leyman Cenk Sahinalp and
Peter F. Stadler},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {54--56},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/intro-rna.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/BackofenCHSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/GruberFWHS10,
author = {Andreas R. Gruber and
Sven Findei{\ss} and
Stefan Washietl and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {RNAz 2.0: Improved Noncoding {RNA} Detection},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {69--79},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/gruber.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/GruberFWHS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LangenbergerBSH10,
author = {David Langenberger and
Clara Bermudez{-}Santana and
Peter F. Stadler and
Steve Hoffmann},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Identification and Classification of Small RNAs in Transcriptome Sequence
Data},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {80--87},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/langenberger.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LangenbergerBSH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/Stadler10,
author = {Peter F. Stadler},
editor = {Carlos Eduardo Ferreira and
Satoru Miyano and
Peter F. Stadler},
title = {Evolution of the Long Non-coding RNAs {MALAT1} and MEN\emph{beta}/\emph{epsilon}},
booktitle = {Advances in Bioinformatics and Computational Biology, 5th Brazilian
Symposium on Bioinformatics, {BSB} 2010, Rio de Janeiro, Brazil, August
31-September 3, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6268},
pages = {1--12},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15060-9\_1},
doi = {10.1007/978-3-642-15060-9\_1},
timestamp = {Tue, 14 May 2019 10:00:50 +0200},
biburl = {https://dblp.org/rec/conf/wob/Stadler10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/ParikesitSP10,
author = {Arli A. Parikesit and
Peter F. Stadler and
Sonja J. Prohaska},
editor = {Carlos Eduardo Ferreira and
Satoru Miyano and
Peter F. Stadler},
title = {Detection of Protein Domains in Eukaryotic Genome Sequences},
booktitle = {Advances in Bioinformatics and Computational Biology, 5th Brazilian
Symposium on Bioinformatics, {BSB} 2010, Rio de Janeiro, Brazil, August
31-September 3, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6268},
pages = {71--74},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15060-9\_9},
doi = {10.1007/978-3-642-15060-9\_9},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/ParikesitSP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wob/2010,
editor = {Carlos Eduardo Ferreira and
Satoru Miyano and
Peter F. Stadler},
title = {Advances in Bioinformatics and Computational Biology, 5th Brazilian
Symposium on Bioinformatics, {BSB} 2010, Rio de Janeiro, Brazil, August
31-September 3, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6268},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15060-9},
doi = {10.1007/978-3-642-15060-9},
isbn = {978-3-642-15059-3},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wob/2010.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/alife/BenkoCDFSS09,
author = {Gil Benk{\"{o}} and
Florian Centler and
Peter Dittrich and
Christoph Flamm and
B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
title = {A Topological Approach to Chemical Organizations},
journal = {Artif. Life},
volume = {15},
number = {1},
pages = {71--88},
year = {2009},
url = {https://doi.org/10.1162/artl.2009.15.1.15105},
doi = {10.1162/ARTL.2009.15.1.15105},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/alife/BenkoCDFSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/arsmc/OstermeierHLKS09,
author = {Philipp{-}Jens Ostermeier and
Marc Hellmuth and
Josef Leydold and
Konstantin Klemm and
Peter F. Stadler},
title = {A note on quasi-robust cycle bases},
journal = {Ars Math. Contemp.},
volume = {2},
number = {2},
pages = {231--240},
year = {2009},
url = {https://doi.org/10.26493/1855-3974.104.5b7},
doi = {10.26493/1855-3974.104.5B7},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/arsmc/OstermeierHLKS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KaczkowskiTRHSG09,
author = {Bogumil Kaczkowski and
Elfar Torarinsson and
Kristin Reiche and
Jakob Hull Havgaard and
Peter F. Stadler and
Jan Gorodkin},
title = {Structural profiles of human miRNA families from pairwise clustering},
journal = {Bioinform.},
volume = {25},
number = {3},
pages = {291--294},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btn628},
doi = {10.1093/BIOINFORMATICS/BTN628},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KaczkowskiTRHSG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RiesterSK09,
author = {Markus Riester and
Peter F. Stadler and
Konstantin Klemm},
title = {FRANz: reconstruction of wild multi-generation pedigrees},
journal = {Bioinform.},
volume = {25},
number = {16},
pages = {2134--2139},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp064},
doi = {10.1093/BIOINFORMATICS/BTP064},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RiesterSK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LangenbergerBHHKS09,
author = {David Langenberger and
Clara Bermudez{-}Santana and
Jana Hertel and
Steve Hoffmann and
Philipp Khaitovich and
Peter F. Stadler},
title = {Evidence for human microRNA-offset RNAs in small {RNA} sequencing
data},
journal = {Bioinform.},
volume = {25},
number = {18},
pages = {2298--2301},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp419},
doi = {10.1093/BIOINFORMATICS/BTP419},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LangenbergerBHHKS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangQRS09,
author = {Fenix W. D. Huang and
Jing Qin and
Christian M. Reidys and
Peter F. Stadler},
title = {Partition function and base pairing probabilities for {RNA-RNA} interaction
prediction},
journal = {Bioinform.},
volume = {25},
number = {20},
pages = {2646--2654},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp481},
doi = {10.1093/BIOINFORMATICS/BTP481},
timestamp = {Thu, 21 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuangQRS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Scheibye-AlsingHFJSMTGNCJFG09,
author = {K. Scheibye{-}Alsing and
Steve Hoffmann and
A. Frankel and
Peter Jensen and
Peter F. Stadler and
Y. Mang and
Niels Tommerup and
M. J. Gilchrist and
A.{-}B. Nyg{\aa}rd and
Susanna Cirera and
Claus B. J{\o}rgensen and
Merete Fredholm and
Jan Gorodkin},
title = {Sequence assembly},
journal = {Comput. Biol. Chem.},
volume = {33},
number = {2},
pages = {121--136},
year = {2009},
url = {https://doi.org/10.1016/j.compbiolchem.2008.11.003},
doi = {10.1016/J.COMPBIOLCHEM.2008.11.003},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/Scheibye-AlsingHFJSMTGNCJFG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/DressKSW09,
author = {Andreas W. M. Dress and
B{\"{u}}lent Karas{\"{o}}zen and
Peter F. Stadler and
Gerhard{-}Wilhelm Weber},
title = {Preface},
journal = {Discret. Appl. Math.},
volume = {157},
number = {10},
pages = {2217--2220},
year = {2009},
url = {https://doi.org/10.1016/j.dam.2009.01.021},
doi = {10.1016/J.DAM.2009.01.021},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/DressKSW09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/KlemmS09,
author = {Konstantin Klemm and
Peter F. Stadler},
title = {A note on fundamental, non-fundamental, and robust cycle bases},
journal = {Discret. Appl. Math.},
volume = {157},
number = {10},
pages = {2432--2438},
year = {2009},
url = {https://doi.org/10.1016/j.dam.2008.06.047},
doi = {10.1016/J.DAM.2008.06.047},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/KlemmS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/MosigBPS09,
author = {Axel Mosig and
T{\"{u}}rker B{\'{\i}}y{\'{\i}}koglu and
Sonja J. Prohaska and
Peter F. Stadler},
title = {Discovering cis-regulatory modules by optimizing barbecues},
journal = {Discret. Appl. Math.},
volume = {157},
number = {10},
pages = {2458--2468},
year = {2009},
url = {https://doi.org/10.1016/j.dam.2008.06.042},
doi = {10.1016/J.DAM.2008.06.042},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/MosigBPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejc/HellmuthIKS09,
author = {Marc Hellmuth and
Wilfried Imrich and
Werner Kl{\"{o}}ckl and
Peter F. Stadler},
title = {Approximate graph products},
journal = {Eur. J. Comb.},
volume = {30},
number = {5},
pages = {1119--1133},
year = {2009},
url = {https://doi.org/10.1016/j.ejc.2008.09.006},
doi = {10.1016/J.EJC.2008.09.006},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ejc/HellmuthIKS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mics/HellmuthIKS09,
author = {Marc Hellmuth and
Wilfried Imrich and
Werner Kl{\"{o}}ckl and
Peter F. Stadler},
title = {Local Algorithms for the Prime Factorization of Strong Product Graphs},
journal = {Math. Comput. Sci.},
volume = {2},
number = {4},
pages = {653--682},
year = {2009},
url = {https://doi.org/10.1007/s11786-009-0073-y},
doi = {10.1007/S11786-009-0073-Y},
timestamp = {Wed, 12 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mics/HellmuthIKS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/JuhlingMHSSP09,
author = {Frank J{\"{u}}hling and
Mario M{\"{o}}rl and
Roland K. Hartmann and
Mathias Sprinzl and
Peter F. Stadler and
Joern P{\"{u}}tz},
title = {tRNAdb 2009: compilation of tRNA sequences and tRNA genes},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {159--162},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn772},
doi = {10.1093/NAR/GKN772},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/JuhlingMHSSP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HoffmannOKSKVSH09,
author = {Steve Hoffmann and
Christian Otto and
Stefan Kurtz and
Cynthia M. Sharma and
Philipp Khaitovich and
J{\"{o}}rg Vogel and
Peter F. Stadler and
J{\"{o}}rg Hackerm{\"{u}}ller},
title = {Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions
Using Index Structures},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {9},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000502},
doi = {10.1371/JOURNAL.PCBI.1000502},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/HoffmannOKSKVSH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/ChambersMRDSC09,
author = {Karen E. Chambers and
Ryan McDaniell and
Jeremy D. Raincrow and
Maya Deshmukh and
Peter F. Stadler and
Chi{-}hua Chiu},
title = {\emph{Hox} cluster duplication in the basal teleost \emph{Hiodon alosoides}
(Osteoglossomorpha)},
journal = {Theory Biosci.},
volume = {128},
number = {2},
pages = {109--120},
year = {2009},
url = {https://doi.org/10.1007/s12064-009-0056-1},
doi = {10.1007/S12064-009-0056-1},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/ChambersMRDSC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/StadlerPFK09,
author = {Peter F. Stadler and
Sonja J. Prohaska and
Christian V. Forst and
David C. Krakauer},
title = {Defining genes: a computational framework},
journal = {Theory Biosci.},
volume = {128},
number = {3},
pages = {165--170},
year = {2009},
url = {https://doi.org/10.1007/s12064-009-0067-y},
doi = {10.1007/S12064-009-0067-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/StadlerPFK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bildmed/HeffelPSKK09,
author = {Andreas Heffel and
Sonja J. Prohaska and
Peter F. Stadler and
Gerhard Kauer and
Jens{-}Peer Kuska},
editor = {Hans{-}Peter Meinzer and
Thomas Martin Deserno and
Heinz Handels and
Thomas Tolxdorff},
title = {Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns},
booktitle = {Bildverarbeitung f{\"{u}}r die Medizin 2009: Algorithmen - Systeme
- Anwendungen, Proceedings des Workshops vom 22. bis 25. M{\"{a}}rz
2009 in Heidelberg},
series = {Informatik Aktuell},
pages = {415--419},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-540-93860-6\_84},
doi = {10.1007/978-3-540-93860-6\_84},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bildmed/HeffelPSKK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/MenzelGS09,
author = {Peter Menzel and
Jan Gorodkin and
Peter F. Stadler},
editor = {Ivo Grosse and
Steffen Neumann and
Stefan Posch and
Falk Schreiber and
Peter F. Stadler},
title = {Maximum Likelihood Estimation of Weight Matrices for Targeted Homology
Search},
booktitle = {German Conference on Bioinformatics 2009, 28th to 30th September 2009,
Martin Luther University Halle-Wittenberg, Germany},
series = {{LNI}},
volume = {{P-157}},
pages = {211--220},
publisher = {{GI}},
year = {2009},
url = {https://dl.gi.de/handle/20.500.12116/20305},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/MenzelGS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/gcb/2009,
editor = {Ivo Grosse and
Steffen Neumann and
Stefan Posch and
Falk Schreiber and
Peter F. Stadler},
title = {German Conference on Bioinformatics 2009, 28th to 30th September 2009,
Martin Luther University Halle-Wittenberg, Germany},
series = {{LNI}},
volume = {{P-157}},
publisher = {{GI}},
year = {2009},
url = {https://dl.gi.de/handle/20.500.12116/21225},
isbn = {978-3-88579-251-2},
timestamp = {Wed, 13 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gcb/2009.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DressFFGKPS08,
author = {Andreas W. M. Dress and
Christoph Flamm and
Guido Fritzsch and
Stefan Gr{\"{u}}newald and
Matthias Kruspe and
Sonja J. Prohaska and
Peter F. Stadler},
title = {Noisy: Identification of problematic columns in multiple sequence
alignments},
journal = {Algorithms Mol. Biol.},
volume = {3},
year = {2008},
url = {https://doi.org/10.1186/1748-7188-3-7},
doi = {10.1186/1748-7188-3-7},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/DressFFGKPS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HertelHS08,
author = {Jana Hertel and
Ivo L. Hofacker and
Peter F. Stadler},
title = {SnoReport: computational identification of snoRNAs with unknown targets},
journal = {Bioinform.},
volume = {24},
number = {2},
pages = {158--164},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btm464},
doi = {10.1093/BIOINFORMATICS/BTM464},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HertelHS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BernhartHWGS08,
author = {Stephan H. Bernhart and
Ivo L. Hofacker and
Sebastian Will and
Andreas R. Gruber and
Peter F. Stadler},
title = {RNAalifold: improved consensus structure prediction for {RNA} alignments},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-474},
doi = {10.1186/1471-2105-9-474},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BernhartHWGS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LehmannSP08,
author = {J{\"{o}}rg Lehmann and
Peter F. Stadler and
Sonja J. Prohaska},
title = {SynBlast: Assisting the analysis of conserved synteny information},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-351},
doi = {10.1186/1471-2105-9-351},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LehmannSP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/RoseJHRLS08,
author = {Dominic Rose and
Julian J{\"{o}}ris and
J{\"{o}}rg Hackerm{\"{u}}ller and
Kristin Reiche and
Qiang Li and
Peter F. Stadler},
title = {Duplicated {RNA} genes in teleost Fish genomes},
journal = {J. Bioinform. Comput. Biol.},
volume = {6},
number = {6},
pages = {1157--1175},
year = {2008},
url = {https://doi.org/10.1142/S0219720008003886},
doi = {10.1142/S0219720008003886},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/RoseJHRLS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/ProhaskaS08,
author = {Sonja J. Prohaska and
Peter F. Stadler},
title = {"Genes"},
journal = {Theory Biosci.},
volume = {127},
number = {3},
pages = {215--221},
year = {2008},
url = {https://doi.org/10.1007/s12064-008-0025-0},
doi = {10.1007/S12064-008-0025-0},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/ProhaskaS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bird/MucksteinTBHVSH08,
author = {Ulrike M{\"{u}}ckstein and
Hakim Tafer and
Stephan H. Bernhart and
Maribel Hernandez{-}Rosales and
J{\"{o}}rg Vogel and
Peter F. Stadler and
Ivo L. Hofacker},
editor = {Mourad Elloumi and
Josef K{\"{u}}ng and
Michal Linial and
Robert F. Murphy and
Kristan Schneider and
Cristian Toma},
title = {Translational Control by {RNA-RNA} Interaction: Improved Computation
of {RNA-RNA} Binding Thermodynamics},
booktitle = {Bioinformatics Research and Development, Second International Conference,
{BIRD} 2008, Vienna, Austria, July 7-9, 2008, Proceedings},
series = {Communications in Computer and Information Science},
volume = {13},
pages = {114--127},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-70600-7\_9},
doi = {10.1007/978-3-540-70600-7\_9},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bird/MucksteinTBHVSH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/RiesterSK08,
author = {Markus Riester and
Peter F. Stadler and
Konstantin Klemm},
editor = {Andreas Beyer and
Michael Schroeder},
title = {FRANz: Fast Reconstruction of Wild Pedigrees},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2008,
September 9-12, 2008, Dresden, Germany},
series = {{LNI}},
volume = {{P-136}},
pages = {168--177},
publisher = {{GI}},
year = {2008},
url = {https://dl.gi.de/handle/20.500.12116/21213},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/RiesterSK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icip/HeffelSPKK08,
author = {Andreas Heffel and
Peter F. Stadler and
Sonja J. Prohaska and
Gerhard Kauer and
Jens{-}Peer Kuska},
title = {Process flow for classification and clustering of fruit fly gene expression
patterns},
booktitle = {Proceedings of the International Conference on Image Processing, {ICIP}
2008, October 12-15, 2008, San Diego, California, {USA}},
pages = {721--724},
publisher = {{IEEE}},
year = {2008},
url = {https://doi.org/10.1109/ICIP.2008.4711856},
doi = {10.1109/ICIP.2008.4711856},
timestamp = {Wed, 16 Oct 2019 14:14:52 +0200},
biburl = {https://dblp.org/rec/conf/icip/HeffelSPKK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/08/0002SFHS08,
author = {Christian Heine and
Gerik Scheuermann and
Christoph Flamm and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Lars Linsen and
Hans Hagen and
Bernd Hamann},
title = {Visualization of Barrier Tree Sequences Revisited},
booktitle = {Visualization in Medicine and Life Sciences},
series = {Mathematics and Visualization},
pages = {275--290},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-72630-2\_16},
doi = {10.1007/978-3-540-72630-2\_16},
timestamp = {Wed, 08 Feb 2023 10:32:17 +0100},
biburl = {https://dblp.org/rec/books/sp/08/0002SFHS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ReicheS07,
author = {Kristin Reiche and
Peter F. Stadler},
title = {RNAstrand: reading direction of structured RNAs in multiple sequence
alignments},
journal = {Algorithms Mol. Biol.},
volume = {2},
year = {2007},
url = {https://doi.org/10.1186/1748-7188-2-6},
doi = {10.1186/1748-7188-2-6},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/ReicheS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BerntMRFPBSSM07,
author = {Matthias Bernt and
Daniel Merkle and
Kai Ramsch and
Guido Fritzsch and
Marleen Perseke and
Detlef Bernhard and
Martin Schlegel and
Peter F. Stadler and
Martin Middendorf},
title = {CREx: inferring genomic rearrangements based on common intervals},
journal = {Bioinform.},
volume = {23},
number = {21},
pages = {2957--2958},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm468},
doi = {10.1093/BIOINFORMATICS/BTM468},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BerntMRFPBSSM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KruspeS07,
author = {Matthias Kruspe and
Peter F. Stadler},
title = {Progressive multiple sequence alignments from triplets},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-254},
doi = {10.1186/1471-2105-8-254},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KruspeS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpb/MarzMSS07,
author = {Manja Marz and
Axel Mosig and
B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
title = {{U7} snRNAs: {A} Computational Survey},
journal = {Genom. Proteom. Bioinform.},
volume = {5},
number = {3-4},
pages = {187--195},
year = {2007},
url = {https://doi.org/10.1016/S1672-0229(08)60006-6},
doi = {10.1016/S1672-0229(08)60006-6},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/gpb/MarzMSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WillRHSB07,
author = {Sebastian Will and
Kristin Reiche and
Ivo L. Hofacker and
Peter F. Stadler and
Rolf Backofen},
title = {Inferring Noncoding {RNA} Families and Classes by Means of Genome-Scale
Structure-Based Clustering},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {4},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030065},
doi = {10.1371/JOURNAL.PCBI.0030065},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WillRHSB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/BreidbachJS07,
author = {Olaf Breidbach and
J{\"{u}}rgen Jost and
Peter F. Stadler},
title = {Towards theoretical formalisms},
journal = {Theory Biosci.},
volume = {126},
number = {1},
pages = {1--2},
year = {2007},
url = {https://doi.org/10.1007/s12064-007-0002-z},
doi = {10.1007/S12064-007-0002-Z},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/BreidbachJS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/MosigMSS07,
author = {Axel Mosig and
Guofeng Meng and
B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
title = {Evolution of the vertebrate {Y} {RNA} cluster},
journal = {Theory Biosci.},
volume = {126},
number = {1},
pages = {9--14},
year = {2007},
url = {https://doi.org/10.1007/s12064-007-0003-y},
doi = {10.1007/S12064-007-0003-Y},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/MosigMSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/PersekeHWFSIBS07,
author = {Marleen Perseke and
Thomas Hankeln and
Bettina Weich and
Guido Fritzsch and
Peter F. Stadler and
Olle Israelsson and
Detlef Bernhard and
Martin Schlegel},
title = {The mitochondrial {DNA} of \emph{Xenoturbella bocki}: genomic architecture
and phylogenetic analysis},
journal = {Theory Biosci.},
volume = {126},
number = {1},
pages = {35--42},
year = {2007},
url = {https://doi.org/10.1007/s12064-007-0007-7},
doi = {10.1007/S12064-007-0007-7},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/PersekeHWFSIBS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/foga/FlammHSS07,
author = {Christoph Flamm and
Ivo L. Hofacker and
B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
editor = {Christopher R. Stephens and
Marc Toussaint and
L. Darrell Whitley and
Peter F. Stadler},
title = {Saddles and Barrier in Landscapes of Generalized Search Operators},
booktitle = {Foundations of Genetic Algorithms, 9th International Workshop, {FOGA}
2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4436},
pages = {194--212},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-73482-6\_11},
doi = {10.1007/978-3-540-73482-6\_11},
timestamp = {Tue, 14 May 2019 10:00:41 +0200},
biburl = {https://dblp.org/rec/conf/foga/FlammHSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/MosigMS07,
author = {Axel Mosig and
Peter Menzel and
Peter F. Stadler},
editor = {Claudia Falter and
Alexander Schliep and
Joachim Selbig and
Martin Vingron and
Dirk Walther},
title = {Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto
Scores},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2007,
September 26-28, 2007, Potsdam, Germany},
series = {{LNI}},
volume = {{P-115}},
pages = {68--77},
publisher = {{GI}},
year = {2007},
url = {https://dl.gi.de/handle/20.500.12116/22375},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/MosigMS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MosigCS07,
author = {Axel Mosig and
Julian J.{-}L. Chen and
Peter F. Stadler},
editor = {Raffaele Giancarlo and
Sridhar Hannenhalli},
title = {Homology Search with Fragmented Nucleic Acid Sequence Patterns},
booktitle = {Algorithms in Bioinformatics, 7th International Workshop, {WABI} 2007,
Philadelphia, PA, USA, September 8-9, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4645},
pages = {335--345},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74126-8\_31},
doi = {10.1007/978-3-540-74126-8\_31},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MosigCS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/foga/2007,
editor = {Christopher R. Stephens and
Marc Toussaint and
L. Darrell Whitley and
Peter F. Stadler},
title = {Foundations of Genetic Algorithms, 9th International Workshop, {FOGA}
2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4436},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-73482-6},
doi = {10.1007/978-3-540-73482-6},
isbn = {978-3-540-73479-6},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/foga/2007.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BernhartTMFSH06,
author = {Stephan H. Bernhart and
Hakim Tafer and
Ulrike M{\"{u}}ckstein and
Christoph Flamm and
Peter F. Stadler and
Ivo L. Hofacker},
title = {Partition function and base pairing probabilities of {RNA} heterodimers},
journal = {Algorithms Mol. Biol.},
volume = {1},
year = {2006},
url = {https://doi.org/10.1186/1748-7188-1-3},
doi = {10.1186/1748-7188-1-3},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/BernhartTMFSH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MorgensternPPS06,
author = {Burkhard Morgenstern and
Sonja J. Prohaska and
Dirk P{\"{o}}hler and
Peter F. Stadler},
title = {Multiple sequence alignment with user-defined anchor points},
journal = {Algorithms Mol. Biol.},
volume = {1},
year = {2006},
url = {https://doi.org/10.1186/1748-7188-1-6},
doi = {10.1186/1748-7188-1-6},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/MorgensternPPS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MorgensternS06,
author = {Burkhard Morgenstern and
Peter F. Stadler},
title = {New journal: Algorithms for Molecular Biology},
journal = {Algorithms Mol. Biol.},
volume = {1},
year = {2006},
url = {https://doi.org/10.1186/1748-7188-1-1},
doi = {10.1186/1748-7188-1-1},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/MorgensternS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BernhartHS06,
author = {Stephan H. Bernhart and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Local {RNA} base pairing probabilities in large sequences},
journal = {Bioinform.},
volume = {22},
number = {5},
pages = {614--615},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btk014},
doi = {10.1093/BIOINFORMATICS/BTK014},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BernhartHS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HofackerS06,
author = {Ivo L. Hofacker and
Peter F. Stadler},
title = {Memory efficient folding algorithms for circular {RNA} secondary structures},
journal = {Bioinform.},
volume = {22},
number = {10},
pages = {1172--1176},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl023},
doi = {10.1093/BIOINFORMATICS/BTL023},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HofackerS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MucksteinTHBSH06,
author = {Ulrike M{\"{u}}ckstein and
Hakim Tafer and
J{\"{o}}rg Hackerm{\"{u}}ller and
Stephan H. Bernhart and
Peter F. Stadler and
Ivo L. Hofacker},
title = {Thermodynamics of {RNA-RNA} binding},
journal = {Bioinform.},
volume = {22},
number = {10},
pages = {1177--1182},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl024},
doi = {10.1093/BIOINFORMATICS/BTL024},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MucksteinTHBSH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ForstFHS06,
author = {Christian V. Forst and
Christoph Flamm and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Algebraic comparison of metabolic networks, phylogenetic inference,
and metabolic innovation},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {67},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-67},
doi = {10.1186/1471-2105-7-67},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ForstFHS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dmgt/ImrichS06,
author = {Wilfried Imrich and
Peter F. Stadler},
title = {A prime factor theorem for a generalized direct product},
journal = {Discuss. Math. Graph Theory},
volume = {26},
number = {1},
pages = {135--140},
year = {2006},
url = {https://doi.org/10.7151/dmgt.1307},
doi = {10.7151/DMGT.1307},
timestamp = {Mon, 08 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dmgt/ImrichS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpb/MosigSS06,
author = {Axel Mosig and
Katrin Sameith and
Peter F. Stadler},
title = {Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic
Sequences},
journal = {Genom. Proteom. Bioinform.},
volume = {4},
number = {1},
pages = {56--60},
year = {2006},
url = {https://doi.org/10.1016/S1672-0229(06)60017-X},
doi = {10.1016/S1672-0229(06)60017-X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/gpb/MosigSS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HsuHHLTTSWH06,
author = {Paul Wei{-}Che Hsu and
Hsien{-}Da Huang and
Sheng{-}Da Hsu and
Li{-}Zen Lin and
Ann{-}Ping Tsou and
Ching{-}Ping Tseng and
Peter F. Stadler and
Stefan Washietl and
Ivo L. Hofacker},
title = {miRNAMap: genomic maps of microRNA genes and their target genes in
mammalian genomes},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {135--139},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj135},
doi = {10.1093/NAR/GKJ135},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HsuHHLTTSWH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tvcg/HeineSFHS06,
author = {Christian Heine and
Gerik Scheuermann and
Christoph Flamm and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Visualization of Barrier Tree Sequences},
journal = {{IEEE} Trans. Vis. Comput. Graph.},
volume = {12},
number = {5},
pages = {781--788},
year = {2006},
url = {https://doi.org/10.1109/TVCG.2006.196},
doi = {10.1109/TVCG.2006.196},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tvcg/HeineSFHS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/MosigHS06,
author = {Axel Mosig and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Daniel H. Huson and
Oliver Kohlbacher and
Andrei N. Lupas and
Kay Nieselt and
Andreas Zell},
title = {Comparative Analysis of Cyclic Sequences: Viroids and other Small
Circular RNAs},
booktitle = {German Conference on Bioinformatics {GCB} 2006, 19.09. 2006 - 22.09.
2006 in T{\"{u}}bingen, Germany},
series = {{LNI}},
volume = {{P-83}},
pages = {93--102},
publisher = {{GI}},
year = {2006},
url = {https://dl.gi.de/handle/20.500.12116/24202},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/MosigHS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/HertelS06,
author = {Jana Hertel and
Peter F. Stadler},
title = {Hairpins in a Haystack: recognizing microRNA precursors in comparative
genomics data},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {197--202},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl257},
doi = {10.1093/BIOINFORMATICS/BTL257},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/HertelS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iv/PotzschSSWF06,
author = {Sebastian Potzsch and
Gerik Scheuermann and
Peter F. Stadler and
Michael T. Wolfinger and
Christoph Flamm},
title = {Visualization of Lattice-Based Protein Folding Simulations},
booktitle = {10th International Conference on Information Visualisation, {IV} 2006,
5-7 July 2006, London, {UK}},
pages = {89--94},
publisher = {{IEEE} Computer Society},
year = {2006},
url = {https://doi.org/10.1109/IV.2006.127},
doi = {10.1109/IV.2006.127},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iv/PotzschSSWF06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/AttoliniS05,
author = {Camille Stephan{-}Otto Attolini and
Peter F. Stadler},
title = {Neutral Networks of Interacting {RNA} Secondary Structures},
journal = {Adv. Complex Syst.},
volume = {8},
number = {2-3},
pages = {275--283},
year = {2005},
url = {https://doi.org/10.1142/S0219525905000427},
doi = {10.1142/S0219525905000427},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/AttoliniS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MorgensternWPSSSSW05,
author = {Burkhard Morgenstern and
Nadine Werner and
Sonja J. Prohaska and
Rasmus Steinkamp and
Isabelle Schneider and
Amarendran Ramaswami Subramanian and
Peter F. Stadler and
Jan Weyer{-}Menkhoff},
title = {Multiple sequence alignment with user-defined constraints at {GOBICS}},
journal = {Bioinform.},
volume = {21},
number = {7},
pages = {1271--1273},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti142},
doi = {10.1093/BIOINFORMATICS/BTI142},
timestamp = {Wed, 20 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MorgensternWPSSSSW05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/StocsitsHFS05,
author = {Roman R. Stocsits and
Ivo L. Hofacker and
Claudia Fried and
Peter F. Stadler},
title = {Multiple sequence alignments of partially coding nucleic acid sequences},
journal = {{BMC} Bioinform.},
volume = {6},
pages = {160},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-160},
doi = {10.1186/1471-2105-6-160},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/StocsitsHFS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/networks/GleissLS05,
author = {Petra M. Gleiss and
Josef Leydold and
Peter F. Stadler},
title = {Minimum path bases and relevant paths},
journal = {Networks},
volume = {46},
number = {3},
pages = {119--123},
year = {2005},
url = {https://doi.org/10.1002/net.20080},
doi = {10.1002/NET.20080},
timestamp = {Fri, 30 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/networks/GleissLS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pnas/WashietlHS05,
author = {Stefan Washietl and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Fast and reliable prediction of noncoding RNAs},
journal = {Proc. Natl. Acad. Sci. {USA}},
volume = {102},
number = {7},
pages = {2454--2459},
year = {2005},
url = {https://doi.org/10.1073/pnas.0409169102},
doi = {10.1073/PNAS.0409169102},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pnas/WashietlHS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/GraovacS05,
author = {Ante Graovac and
Peter F. Stadler},
title = {{MATH/CHEM/COMP} 2004 Contributions},
journal = {Theory Biosci.},
volume = {123},
number = {4},
pages = {263--264},
year = {2005},
url = {https://doi.org/10.1016/j.thbio.2005.02.003},
doi = {10.1016/J.THBIO.2005.02.003},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/GraovacS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/BompfunewererFFFHLMMMPSSTWW05,
author = {Athanasius F. Bompf{\"{u}}newerer and
Christoph Flamm and
Claudia Fried and
Guido Fritzsch and
Ivo L. Hofacker and
J{\"{o}}rg Lehmann and
Kristin Missal and
Axel Mosig and
Bettina M{\"{u}}ller and
Sonja J. Prohaska and
B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler and
Andrea Tanzer and
Stefan Washietl and
Christina Witwer},
title = {Evolutionary patterns of non-coding RNAs},
journal = {Theory Biosci.},
volume = {123},
number = {4},
pages = {301--369},
year = {2005},
url = {https://doi.org/10.1016/j.thbio.2005.01.002},
doi = {10.1016/J.THBIO.2005.01.002},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/BompfunewererFFFHLMMMPSSTWW05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/ShpakSWH05,
author = {Max Shpak and
Peter F. Stadler and
G{\"{u}}nter P. Wagner and
Joachim Hermisson},
title = {Erratum to "Aggregation of variables and system decomposability:
Applications to fitness landscape analysis},
journal = {Theory Biosci.},
volume = {124},
number = {1},
pages = {87--88},
year = {2005},
url = {https://doi.org/10.1016/j.thbio.2005.05.001},
doi = {10.1016/J.THBIO.2005.05.001},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/ShpakSWH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecal/AttoliniSF05,
author = {Camille Stephan{-}Otto Attolini and
Peter F. Stadler and
Christoph Flamm},
editor = {Mathieu S. Capcarr{\`{e}}re and
Alex Alves Freitas and
Peter J. Bentley and
Colin G. Johnson and
Jon Timmis},
title = {CelloS: {A} Multi-level Approach to Evolutionary Dynamics},
booktitle = {Advances in Artificial Life, 8th European Conference, {ECAL} 2005,
Canterbury, UK, September 5-9, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3630},
pages = {500--509},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11553090\_51},
doi = {10.1007/11553090\_51},
timestamp = {Tue, 14 May 2019 10:00:42 +0200},
biburl = {https://dblp.org/rec/conf/ecal/AttoliniSF05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecal/BenkoFS05,
author = {Gil Benk{\"{o}} and
Christoph Flamm and
Peter F. Stadler},
editor = {Mathieu S. Capcarr{\`{e}}re and
Alex Alves Freitas and
Peter J. Bentley and
Colin G. Johnson and
Jon Timmis},
title = {Explicit Collision Simulation of Chemical Reactions in a Graph Based
Artificial Chemistry},
booktitle = {Advances in Artificial Life, 8th European Conference, {ECAL} 2005,
Canterbury, UK, September 5-9, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3630},
pages = {725--733},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11553090\_73},
doi = {10.1007/11553090\_73},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ecal/BenkoFS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/MissalRS05,
author = {Kristin Missal and
Dominic Rose and
Peter F. Stadler},
title = {Non-coding RNAs in \emph{Ciona intestinalis}},
booktitle = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational
Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas
de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain,
September 28 - October 1, 2005},
pages = {78},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1113},
doi = {10.1093/BIOINFORMATICS/BTI1113},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/MissalRS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/MucksteinTHBSH05,
author = {Ulrike M{\"{u}}ckstein and
Hakim Tafer and
J{\"{o}}rg Hackerm{\"{u}}ller and
Stephan H. Bernhart and
Peter F. Stadler and
Ivo L. Hofacker},
editor = {Andrew E. Torda and
Stefan Kurtz and
Matthias Rarey},
title = {Thermodynamics of {RNA-RNA} Binding},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2005),
Hamburg, Germany, October 5-7, 2005},
series = {{LNI}},
volume = {{P-71}},
pages = {3--13},
publisher = {{GI}},
year = {2005},
url = {https://dl.gi.de/handle/20.500.12116/24932},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/MucksteinTHBSH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/HofackerS05,
author = {Ivo L. Hofacker and
Peter F. Stadler},
editor = {Andrew E. Torda and
Stefan Kurtz and
Matthias Rarey},
title = {Memory Efficient Folding Algorithms for Circular {RNA} Secondary Structures},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2005),
Hamburg, Germany, October 5-7, 2005},
series = {{LNI}},
volume = {{P-71}},
pages = {15--25},
publisher = {{GI}},
year = {2005},
url = {https://dl.gi.de/handle/20.500.12116/24936},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/HofackerS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HofackerPS04,
author = {Ivo L. Hofacker and
Barbara Priwitzer and
Peter F. Stadler},
title = {Prediction of locally stable {RNA} secondary structures for genome-wide
surveys},
journal = {Bioinform.},
volume = {20},
number = {2},
pages = {186--190},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg388},
doi = {10.1093/BIOINFORMATICS/BTG388},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HofackerPS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HofackerSS04,
author = {Ivo L. Hofacker and
Peter F. Stadler and
Roman R. Stocsits},
title = {Conserved {RNA} secondary structures in viral genomes: a survey},
journal = {Bioinform.},
volume = {20},
number = {10},
pages = {1495--1499},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth108},
doi = {10.1093/BIOINFORMATICS/BTH108},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HofackerSS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HofackerBS04,
author = {Ivo L. Hofacker and
Stephan H. Bernhart and
Peter F. Stadler},
title = {Alignment of {RNA} base pairing probability matrices},
journal = {Bioinform.},
volume = {20},
number = {14},
pages = {2222--2227},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth229},
doi = {10.1093/BIOINFORMATICS/BTH229},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HofackerBS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BergerFGLS04,
author = {Franziska Berger and
Christoph Flamm and
Petra M. Gleiss and
Josef Leydold and
Peter F. Stadler},
title = {Counterexamples in Chemical Ring Perception},
journal = {J. Chem. Inf. Model.},
volume = {44},
number = {2},
pages = {323--331},
year = {2004},
url = {https://doi.org/10.1021/ci030405d},
doi = {10.1021/CI030405D},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/BergerFGLS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FriedHPSS04,
author = {Claudia Fried and
Wim Hordijk and
Sonja J. Prohaska and
Claus R. Stadler and
Peter F. Stadler},
title = {The Footprint Sorting Problem},
journal = {J. Chem. Inf. Model.},
volume = {44},
number = {2},
pages = {332--338},
year = {2004},
url = {https://doi.org/10.1021/ci030411\%2B},
doi = {10.1021/CI030411\%2B},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FriedHPSS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/WitwerHS04,
author = {Christina Witwer and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Prediction of Consensus {RNA} Secondary Structures Including Pseudoknots},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {1},
number = {2},
pages = {66--77},
year = {2004},
url = {https://doi.org/10.1109/TCBB.2004.22},
doi = {10.1109/TCBB.2004.22},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/WitwerHS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/BreidbachJSW04,
author = {Olaf Breidbach and
J{\"{u}}rgen Jost and
Peter F. Stadler and
Michael S. Weingarten},
title = {Editorial},
journal = {Theory Biosci.},
volume = {123},
number = {1},
pages = {1--2},
year = {2004},
url = {https://doi.org/10.1016/j.thbio.2004.03.002},
doi = {10.1016/J.THBIO.2004.03.002},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/BreidbachJSW04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/ShpakSWH04,
author = {Max Shpak and
Peter F. Stadler and
G{\"{u}}nter P. Wagner and
Joachim Hermisson},
title = {Aggregation of variables and system decomposition: Applications to
fitness landscape analysis},
journal = {Theory Biosci.},
volume = {123},
number = {1},
pages = {33--68},
year = {2004},
url = {https://doi.org/10.1016/j.thbio.2004.02.001},
doi = {10.1016/J.THBIO.2004.02.001},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/ShpakSWH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/ProhaskaS04,
author = {Sonja J. Prohaska and
Peter F. Stadler},
title = {The duplication of the \emph{Hox} gene clusters in teleost fishes},
journal = {Theory Biosci.},
volume = {123},
number = {1},
pages = {89--110},
year = {2004},
url = {https://doi.org/10.1016/j.thbio.2004.03.004},
doi = {10.1016/J.THBIO.2004.03.004},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/ProhaskaS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tib/ShpakSWA04,
author = {Max Shpak and
Peter F. Stadler and
G{\"{u}}nter P. Wagner and
Lee Altenberg},
title = {Simon-Ando decomposability and fitness landscapes},
journal = {Theory Biosci.},
volume = {123},
number = {2},
pages = {139--180},
year = {2004},
url = {https://doi.org/10.1016/j.thbio.2004.04.001},
doi = {10.1016/J.THBIO.2004.04.001},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tib/ShpakSWA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/MorgensternPWWSSS04,
author = {Burkhard Morgenstern and
Sonja J. Prohaska and
Nadine Werner and
Jan Weyer{-}Menkhoff and
Isabelle Schneider and
Amarendran Ramaswami Subramanian and
Peter F. Stadler},
editor = {Robert Giegerich and
Jens Stoye},
title = {Multiple sequence alignment with user-defined constraints},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2004),
Bielefeld, Germany, October 4-6, 2004},
series = {{LNI}},
volume = {{P-53}},
pages = {25--36},
publisher = {{GI}},
year = {2004},
url = {https://dl.gi.de/handle/20.500.12116/28673},
timestamp = {Wed, 20 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/MorgensternPWWSSS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/ThurnerHS04,
author = {C. Thurner and
Ivo L. Hofacker and
Peter F. Stadler},
editor = {Robert Giegerich and
Jens Stoye},
title = {Conserved {RNA} Pseudoknots},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2004),
Bielefeld, Germany, October 4-6, 2004},
series = {{LNI}},
volume = {{P-53}},
pages = {207--216},
publisher = {{GI}},
year = {2004},
url = {https://dl.gi.de/handle/20.500.12116/28668},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/ThurnerHS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/HofackerS04,
author = {Ivo L. Hofacker and
Peter F. Stadler},
editor = {Marian Bubak and
G. Dick van Albada and
Peter M. A. Sloot and
Jack J. Dongarra},
title = {The Partition Function Variant of Sankoff's Algorithm},
booktitle = {Computational Science - {ICCS} 2004, 4th International Conference,
Krak{\'{o}}w, Poland, June 6-9, 2004, Proceedings, Part {IV}},
series = {Lecture Notes in Computer Science},
volume = {3039},
pages = {728--735},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-25944-2\_94},
doi = {10.1007/978-3-540-25944-2\_94},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iccS/HofackerS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/StadlerS03,
author = {B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
title = {Molecular Replicator Dynamics},
journal = {Adv. Complex Syst.},
volume = {6},
number = {1},
pages = {47--78},
year = {2003},
url = {https://doi.org/10.1142/S0219525903000724},
doi = {10.1142/S0219525903000724},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/StadlerS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dmgt/GleissLS03,
author = {Petra M. Gleiss and
Josef Leydold and
Peter F. Stadler},
title = {Circuit bases of strongly connected digraphs},
journal = {Discuss. Math. Graph Theory},
volume = {23},
number = {2},
pages = {241--260},
year = {2003},
url = {https://doi.org/10.7151/dmgt.1200},
doi = {10.7151/DMGT.1200},
timestamp = {Mon, 08 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dmgt/GleissLS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpem/StadlerF03,
author = {Peter F. Stadler and
Christoph Flamm},
title = {Barrier Trees on Poset-Valued Landscapes},
journal = {Genet. Program. Evolvable Mach.},
volume = {4},
number = {1},
pages = {7--20},
year = {2003},
url = {https://doi.org/10.1023/A:1021821009420},
doi = {10.1023/A:1021821009420},
timestamp = {Tue, 01 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/gpem/StadlerF03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BenkoFS03,
author = {Gil Benk{\"{o}} and
Christoph Flamm and
Peter F. Stadler},
title = {A Graph-Based Toy Model of Chemistry},
journal = {J. Chem. Inf. Comput. Sci.},
volume = {43},
number = {4},
pages = {1085--1093},
year = {2003},
url = {https://doi.org/10.1021/ci0200570},
doi = {10.1021/CI0200570},
timestamp = {Thu, 14 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BenkoFS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jgt/Stadler03,
author = {Peter F. Stadler},
title = {Minimum cycle bases of Halin graphs},
journal = {J. Graph Theory},
volume = {43},
number = {2},
pages = {150--155},
year = {2003},
url = {https://doi.org/10.1002/jgt.10111},
doi = {10.1002/JGT.10111},
timestamp = {Fri, 02 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jgt/Stadler03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecal/BenkoFS03,
author = {Gil Benk{\"{o}} and
Christoph Flamm and
Peter F. Stadler},
editor = {Wolfgang Banzhaf and
Thomas Christaller and
Peter Dittrich and
Jan T. Kim and
Jens Ziegler},
title = {Generic Properties of Chemical Networks: Artificial Chemistry Based
on Graph Rewriting},
booktitle = {Advances in Artificial Life, 7th European Conference, {ECAL} 2003,
Dortmund, Germany, September 14-17, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2801},
pages = {10--19},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-39432-7\_2},
doi = {10.1007/978-3-540-39432-7\_2},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ecal/BenkoFS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/AbfalterFS03,
author = {Ingrid G. Abfalter and
Christoph Flamm and
Peter F. Stadler},
title = {Design of multi-stable nucleid acid sequences},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2003,
October 12-14, 2003, Neuherberg/Garching near Munich, Germany},
pages = {1--7},
year = {2003},
timestamp = {Tue, 15 Mar 2005 13:11:15 +0100},
biburl = {https://dblp.org/rec/conf/gcb/AbfalterFS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/HofackerSS03,
author = {Ivo L. Hofacker and
Peter F. Stadler and
Roman R. Stocsits},
title = {Conserved {RNA} secondary structures in viral genomes: {A} survey},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2003,
October 12-14, 2003, Neuherberg/Garching near Munich, Germany},
pages = {57--62},
year = {2003},
timestamp = {Tue, 15 Mar 2005 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gcb/HofackerSS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ajc/ImrichS02,
author = {Wilfried Imrich and
Peter F. Stadler},
title = {Minimum cycle bases of product graphs},
journal = {Australas. {J} Comb.},
volume = {26},
pages = {233--244},
year = {2002},
url = {http://ajc.maths.uq.edu.au/pdf/26/ajc\_v26\_p233.pdf},
timestamp = {Wed, 11 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ajc/ImrichS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/amc/BastertRST02,
author = {Oliver Bastert and
Daniel N. Rockmore and
Peter F. Stadler and
Gottfried Tinhofer},
title = {Landscapes on spaces of trees},
journal = {Appl. Math. Comput.},
volume = {131},
number = {2-3},
pages = {439--459},
year = {2002},
url = {https://doi.org/10.1016/S0096-3003(01)00164-3},
doi = {10.1016/S0096-3003(01)00164-3},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/amc/BastertRST02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/StadlerS02,
author = {B{\"{a}}rbel M. R. Stadler and
Peter F. Stadler},
title = {Generalized Topological Spaces in Evolutionary Theory and Combinatorial
Chemistry},
journal = {J. Chem. Inf. Comput. Sci.},
volume = {42},
number = {3},
pages = {577--585},
year = {2002},
url = {https://doi.org/10.1021/ci0100898},
doi = {10.1021/CI0100898},
timestamp = {Thu, 14 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/StadlerS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamrev/ReidysS02,
author = {Christian M. Reidys and
Peter F. Stadler},
title = {Combinatorial Landscapes},
journal = {{SIAM} Rev.},
volume = {44},
number = {1},
pages = {3--54},
year = {2002},
url = {https://doi.org/10.1137/S0036144501395952},
doi = {10.1137/S0036144501395952},
timestamp = {Tue, 29 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamrev/ReidysS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/MucksteinHS02,
author = {Ulrike M{\"{u}}ckstein and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Stochastic pairwise alignments},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2002), October 6-9, 2002, Saarbr{\"{u}}cken, Germany},
pages = {153--160},
year = {2002},
timestamp = {Thu, 23 Jun 2016 15:53:27 +0200},
biburl = {https://dblp.org/rec/conf/eccb/MucksteinHS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/GleissSWF01,
author = {Petra M. Gleiss and
Peter F. Stadler and
Andreas Wagner and
David A. Fell},
title = {Relevant cycles in Chemical reaction Networks},
journal = {Adv. Complex Syst.},
volume = {4},
number = {2-3},
pages = {207--226},
year = {2001},
url = {https://doi.org/10.1142/S0219525901000140},
doi = {10.1142/S0219525901000140},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/GleissSWF01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/StadlerML01,
author = {Peter F. Stadler and
Anita Mehta and
Jean{-}Marc Luck},
title = {Glassy States in a shaken Sandbox},
journal = {Adv. Complex Syst.},
volume = {4},
number = {4},
pages = {429--440},
year = {2001},
url = {https://doi.org/10.1142/S0219525901000346},
doi = {10.1142/S0219525901000346},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/StadlerML01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/amc/ReidysS01,
author = {Christian M. Reidys and
Peter F. Stadler},
title = {Neutrality in fitness landscapes},
journal = {Appl. Math. Comput.},
volume = {117},
number = {2-3},
pages = {321--350},
year = {2001},
url = {https://doi.org/10.1016/S0096-3003(99)00166-6},
doi = {10.1016/S0096-3003(99)00166-6},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/amc/ReidysS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/alife/CupalKS00,
author = {Jan Cupal and
Stephan Kopp and
Peter F. Stadler},
title = {{RNA} Shape Space Topology},
journal = {Artif. Life},
volume = {6},
number = {1},
pages = {3--23},
year = {2000},
url = {https://doi.org/10.1162/106454600568294},
doi = {10.1162/106454600568294},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/alife/CupalKS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/combinatorics/GleissLS00,
author = {Petra M. Gleiss and
Josef Leydold and
Peter F. Stadler},
title = {Interchangeability of Relevant Cycles in Graphs},
journal = {Electron. J. Comb.},
volume = {7},
year = {2000},
url = {https://doi.org/10.37236/1494},
doi = {10.37236/1494},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/combinatorics/GleissLS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/FeketeHS00,
author = {Martin Fekete and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Prediction of {RNA} Base Pairing Probabilities on Massively Parallel
Computers},
journal = {J. Comput. Biol.},
volume = {7},
number = {1-2},
pages = {171--182},
year = {2000},
url = {https://doi.org/10.1089/10665270050081441},
doi = {10.1089/10665270050081441},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/FeketeHS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/FlammHS99,
author = {Christoph Flamm and
Ivo L. Hofacker and
Peter F. Stadler},
title = {{RNA} \emph{In Silico} The Computational Biology of {RNA} Secondary
Structures},
journal = {Adv. Complex Syst.},
volume = {2},
number = {1},
pages = {65--100},
year = {1999},
url = {https://doi.org/10.1142/S0219525999000059},
doi = {10.1142/S0219525999000059},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/FlammHS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/BonabeauS99,
author = {Eric Bonabeau and
Peter F. Stadler},
title = {Call for proposals},
journal = {Adv. Complex Syst.},
volume = {2},
number = {3},
pages = {195--196},
year = {1999},
url = {https://doi.org/10.1142/S0219525999000230},
doi = {10.1142/S0219525999000230},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/BonabeauS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/HofackerS99,
author = {Ivo L. Hofacker and
Peter F. Stadler},
title = {Automatic Detection of Conserved Base Pairing Patterns in {RNA} Virus
Genomes},
journal = {Comput. Chem.},
volume = {23},
number = {3-4},
pages = {401--414},
year = {1999},
url = {https://doi.org/10.1016/S0097-8485(99)00013-3},
doi = {10.1016/S0097-8485(99)00013-3},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/HofackerS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/StocsitsHS99,
author = {Roman R. Stocsits and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Conserved secondary structures in hepatitis {B} virus {DNA}},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1999,
October 4-6, 1999, Hannover, Germany},
pages = {73--79},
year = {1999},
timestamp = {Fri, 02 Aug 2019 15:48:16 +0200},
biburl = {https://dblp.org/rec/conf/gcb/StocsitsHS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/WeberndorferHS99,
author = {G. Weberndorfer and
Ivo L. Hofacker and
Peter F. Stadler},
title = {An efficient potential for protein sequence design},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1999,
October 4-6, 1999, Hannover, Germany},
pages = {107--112},
year = {1999},
timestamp = {Fri, 02 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/WeberndorferHS99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/HordijkS98,
author = {Wim Hordijk and
Peter F. Stadler},
title = {Amplitude Spectra of Fitness Landscapes},
journal = {Adv. Complex Syst.},
volume = {1},
number = {1},
pages = {39--66},
year = {1998},
url = {https://doi.org/10.1142/S0219525998000041},
doi = {10.1142/S0219525998000041},
timestamp = {Thu, 08 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/advcs/HordijkS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/combinatorics/LeydoldS98,
author = {Josef Leydold and
Peter F. Stadler},
title = {Minimal Cycle Bases of Outerplanar Graphs},
journal = {Electron. J. Comb.},
volume = {5},
year = {1998},
url = {https://doi.org/10.37236/1354},
doi = {10.37236/1354},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/combinatorics/LeydoldS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/HofackerSS98,
author = {Ivo L. Hofacker and
Peter Schuster and
Peter F. Stadler},
title = {Combinatorics of {RNA} Secondary Structures},
journal = {Discret. Appl. Math.},
volume = {88},
number = {1-3},
pages = {207--237},
year = {1998},
url = {https://doi.org/10.1016/S0166-218X(98)00073-0},
doi = {10.1016/S0166-218X(98)00073-0},
timestamp = {Thu, 20 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dam/HofackerSS98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ec/StadlerW97,
author = {Peter F. Stadler and
G{\"{u}}nter P. Wagner},
title = {Algebraic Theory of Recombination Spaces},
journal = {Evol. Comput.},
volume = {5},
number = {3},
pages = {241--275},
year = {1997},
url = {https://doi.org/10.1162/evco.1997.5.3.241},
doi = {10.1162/EVCO.1997.5.3.241},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ec/StadlerW97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/CupalFRS97,
author = {Jan Cupal and
Christoph Flamm and
Alexander Renner and
Peter F. Stadler},
editor = {Terry Gaasterland and
Peter D. Karp and
Kevin Karplus and
Christos A. Ouzounis and
Chris Sander and
Alfonso Valencia},
title = {Density of States, Metastable States, and Saddle Points: Exploring
the Energy Landscape of an {RNA} Molecule},
booktitle = {Proceedings of the 5th International Conference on Intelligent Systems
for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
pages = {88--91},
publisher = {{AAAI}},
year = {1997},
url = {http://www.aaai.org/Library/ISMB/1997/ismb97-013.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/CupalFRS97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ReidysS96,
author = {Christian M. Reidys and
Peter F. Stadler},
title = {Bio-molecular Shapes and Algebraic Structures},
journal = {Comput. Chem.},
volume = {20},
number = {1},
pages = {85--94},
year = {1996},
url = {https://doi.org/10.1016/S0097-8485(96)80010-6},
doi = {10.1016/S0097-8485(96)80010-6},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/ReidysS96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/complexity/HappelS96,
author = {Robert Happel and
Peter F. Stadler},
title = {Canonical approximation of fitness landscapes},
journal = {Complex.},
volume = {2},
number = {1},
pages = {53--58},
year = {1996},
url = {https://doi.org/10.1002/(SICI)1099-0526(199609/10)2:1\&\#60;53::AID-CPLX11\&\#62;3.0.CO;2-W},
doi = {10.1002/(SICI)1099-0526(199609/10)2:1\&\#60;53::AID-CPLX11\&\#62;3.0.CO;2-W},
timestamp = {Thu, 24 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/complexity/HappelS96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HuynenPVS96,
author = {Martijn A. Huynen and
Alan S. Perelson and
W. A. Vieira and
Peter F. Stadler},
title = {Base Pairing Probabilities in a Complete {HIV-1} {RNA}},
journal = {J. Comput. Biol.},
volume = {3},
number = {2},
pages = {253--274},
year = {1996},
url = {https://doi.org/10.1089/cmb.1996.3.253},
doi = {10.1089/CMB.1996.3.253},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/HuynenPVS96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/CupalHS96,
author = {Jan Cupal and
Ivo L. Hofacker and
Peter F. Stadler},
title = {Dynamic Programming Algorithm for the Density of States of {RNA} Secondary
Structures},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1996,
Leipzig, Germany, September 30 - October 2, 1996},
pages = {184--186},
year = {1996},
timestamp = {Sat, 07 Sep 2019 11:59:23 +0200},
biburl = {https://dblp.org/rec/conf/gcb/CupalHS96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/HofackerHSS96,
author = {Ivo L. Hofacker and
Martijn A. Huynen and
Peter F. Stadler and
Paul E. Stolorz},
editor = {Evangelos Simoudis and
Jiawei Han and
Usama M. Fayyad},
title = {Knowledge Discovery in {RNA} Sequence Families of {HIV} Using Scalable
Computers},
booktitle = {Proceedings of the Second International Conference on Knowledge Discovery
and Data Mining (KDD-96), Portland, Oregon, {USA}},
pages = {20--25},
publisher = {{AAAI} Press},
year = {1996},
url = {http://www.aaai.org/Library/KDD/1996/kdd96-004.php},
timestamp = {Mon, 05 Jun 2017 13:20:21 +0200},
biburl = {https://dblp.org/rec/conf/kdd/HofackerHSS96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dm/Stadler95,
author = {Peter F. Stadler},
title = {Random walks and orthogonal functions associated with highly symmetric
graphs},
journal = {Discret. Math.},
volume = {145},
number = {1-3},
pages = {229--237},
year = {1995},
url = {https://doi.org/10.1016/0012-365X(94)00038-K},
doi = {10.1016/0012-365X(94)00038-K},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dm/Stadler95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/SchusterS94,
author = {Peter Schuster and
Peter F. Stadler},
title = {Landscapes: Complex Optimization Problems and Biopolymer Structures},
journal = {Comput. Chem.},
volume = {18},
number = {3},
pages = {295--324},
year = {1994},
url = {https://doi.org/10.1016/0097-8485(94)85025-9},
doi = {10.1016/0097-8485(94)85025-9},
timestamp = {Thu, 20 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/SchusterS94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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