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@article{bompfunewerer_variations_2008,
title = {Variations on {RNA} folding and alignment: lessons from Benasque},
volume = {56},
issn = {0303-6812},
doi = {10.1007/s00285-007-0107-5},
shorttitle = {Variations on {RNA} folding and alignment},
issue = {1-2},
pages = {129-144},
journaltitle = {Journal of mathematical biology},
author = {Bompfünewerer, Athanasius F and Backofen, Rolf and Bernhart, Stephan H and Hertel, Jana and Hofacker, Ivo L and Stadler, Peter F and Will, Sebastian},
date = {2008},
note = {{PMID:} 17611759},
keywords = {base-pairing-probabilities, canonization, dynamic-programming, single-rna, thermodynamic-model},
file = {Variations on RNA folding and alignment (Stadler u.a., 2008).pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\Q8K9MDT8\Variations on RNA folding and alignment (Stadler u.a., 2008).pdf:application/pdf}
}
@inproceedings{giegerich_implementing_2002,
title = {Implementing Algebraic Dynamic Programming in the Functional and the Imperative Programming Paradigm},
isbn = {978-3-540-43857-1},
pages = {1-20},
booktitle = {Proceedings of the 6th International Conference on Mathematics of Program Construction},
booktitle = {Proceedings of the 6th International Conference on Mathematics of Program Construction},
publisher = {Springer},
author = {Giegerich, Robert and Steffen, Peter},
date = {2002},
keywords = {adp},
file = {adp_implementing.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\EAJM9K43\adp_implementing.pdf:application/pdf}
}
@report{hutton_monadic_1996,
title = {Monadic parser combinators},
url = {http://eprints.nottingham.ac.uk/237/},
author = {Hutton, G. and Meijer, E.},
urldate = {2012-07-19},
date = {1996},
keywords = {parser-combinators, parsing},
file = {monparsing.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\A8DE65TC\monparsing.pdf:application/pdf}
}
@article{fekete_prediction_2000,
title = {Prediction of {RNA} Base Pairing Probabilities on Massively Parallel Computers},
volume = {7},
issn = {1066-5277, 1557-8666},
doi = {10.1089/10665270050081441},
issue = {1-2},
pages = {171-182},
journaltitle = {Journal of Computational Biology},
author = {Fekete, Martin and Hofacker, Ivo L. and Stadler, Peter F.},
date = {2000},
keywords = {base-pairing-probabilities, dynamic-programming, parallelization, single-rna, thermodynamic-model},
file = {10665270050081441:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\P2TP7EC9\10665270050081441.pdf:application/pdf}
}
@article{kato_rna_2006,
title = {{RNA} Pseudoknotted Structure Prediction Using Stochastic Multiple Context-Free Grammar},
volume = {2},
issn = {1349-7456},
doi = {10.2197/ipsjdc.2.655},
pages = {655-664},
journaltitle = {{IPSJ} Digital Courier},
author = {Kato, Yuki and Seki, Hiroyuki and Kasami, Tadao},
date = {2006},
keywords = {dynamic-programming, mcfg, parsing, probabilistic-model, single-rna, smcfg},
file = {_pdf.unlocked.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\57TWKU6C\_pdf.unlocked.pdf:application/pdf}
}
@unpublished{gotzmann_multiple_2007,
location = {Saarland University},
title = {Multiple kontextfreie Grammatiken},
url = {http://www.ps.uni-saarland.de/courses/seminar-ws06/slides/04_daniel_goetzmann.pdf},
type = {Seminar},
howpublished = {Seminar},
author = {Götzmann, Daniel},
urldate = {2012-06-13},
date = {2007},
keywords = {introduction, mcfg},
file = {04_daniel_goetzmann.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\EG8R77S8\04_daniel_goetzmann.pdf:application/pdf}
}
@article{kanazawa_parsing_2011,
title = {Parsing and generation as Datalog query evaluation},
url = {http://research.nii.ac.jp/~kanazawa/publications/pagadqe.pdf},
journaltitle = {To appear},
author = {Kanazawa, {MAKOTO}},
urldate = {2013-05-03},
date = {2011},
keywords = {mcfg, parsing, pmcfg},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\RP6TTB3T\pagadqe.pdf:application/pdf}
}
@article{chomsky_three_1956,
title = {Three models for the description of language},
volume = {2},
issn = {0096-1000},
doi = {10.1109/TIT.1956.1056813},
issue = {3},
pages = {113-124},
journaltitle = {{IRE} Transactions on Information Theory},
author = {Chomsky, Noam},
date = {1956},
file = {three_models_for_the_description_of_language.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\VWRCQPEH\three_models_for_the_description_of_language.pdf:application/pdf}
}
@inproceedings{eisner_program_2007,
title = {Program transformations for optimization of parsing algorithms and other weighted logic programs},
pages = {45-85},
booktitle = {Proceedings of {FG} 2006: The 11th Conference on Formal Grammar},
booktitle = {Proceedings of {FG} 2006: The 11th Conference on Formal Grammar},
publisher = {{CSLI} Publications},
author = {Eisner, Jason and Blatz, John},
date = {2007},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\PTJ3NQXP\eisner.pdf:application/pdf}
}
@article{huang_advanced_2008,
title = {Advanced dynamic programming in semiring and hypergraph frameworks},
url = {http://www.ircs.upenn.edu/~lhuang3/coling.pdf},
journaltitle = {{COLING}, Manchester, {UK}},
author = {Huang, L.},
urldate = {2012-11-01},
date = {2008},
keywords = {dynamic-programming, semi-ring},
file = {coling.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\J3H6K86K\coling.pdf:application/pdf}
}
@report{boullier_proposal_1998,
location = {Le Chesnay, {FR}},
title = {Proposal for a Natural Language Processing Syntactic Backbone},
url = {http://hal.inria.fr/docs/00/07/33/47/PDF/RR-3342.pdf},
number = {3342},
institution = {{INRIA}},
type = {Technical Report},
author = {Boullier, Pierre},
urldate = {2013-04-19},
date = {1998},
keywords = {rcg},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\H89H9MZR\RR-3342.pdf:application/pdf}
}
@article{reidys_addendum:_2012,
title = {Addendum: topology and prediction of {RNA} pseudoknots},
volume = {28},
doi = {10.1093/bioinformatics/btr643},
shorttitle = {Addendum},
issue = {2},
pages = {300},
journaltitle = {Bioinformatics},
author = {Reidys, C. M. and Huang, F. W. D. and Andersen, J. E. and Penner, R. C. and Stadler, P. F. and Nebel, M. E.},
date = {2012},
keywords = {mcfg, pseudoknots, single-rna},
file = {11-030_addendum.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\84H2TRH7\11-030_addendum.pdf:application/pdf}
}
@inproceedings{lefebvre_grammar-based_1996,
title = {A grammar-based unification of several alignment and folding algorithms},
isbn = {1-57735-002-2},
booktitle = {Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology},
booktitle = {Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology},
publisher = {{AAAI} Press},
author = {Lefebvre, Fabrice},
date = {1996},
keywords = {attribute-grammars, pseudoknots},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\I6TJBPT7\jerome.pdf:application/pdf;download;jsessionid=2932C5D5DBDAA2B8445A1987BCD597CD.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\GGCN246Z\download;jsessionid=2932C5D5DBDAA2B8445A1987BCD597CD.pdf:application/pdf}
}
@inproceedings{giegerich_challenges_2006,
location = {New York, {NY}, {USA}},
title = {Challenges in the compilation of a domain specific language for dynamic programming},
isbn = {1-59593-108-2},
doi = {10.1145/1141277.1141653},
pages = {1603-1609},
booktitle = {Proceedings of the 2006 {ACM} symposium on Applied computing},
booktitle = {Proceedings of the 2006 {ACM} symposium on Applied computing},
series = {{SAC} '06},
publisher = {{ACM}},
author = {Giegerich, Robert and Steffen, Peter},
date = {2006},
keywords = {adp, adpc, dynamic-programming, external-dsl},
file = {ADP as eDSL in Haskell - Challenges (Haskell, ADPC) 2006.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\UIQPD4P7\ADP as eDSL in Haskell - Challenges (Haskell, ADPC) 2006.pdf:application/pdf}
}
@article{leijen_parsec:_2001,
title = {Parsec: Direct style monadic parser combinators for the real world},
url = {http://igitur-archive.library.uu.nl/math/2002-0308-102935/UUindex.html},
shorttitle = {Parsec},
author = {Leijen, D. and Meijer, E.},
date = {2001},
keywords = {parser-combinators, parsing},
file = {parsec-paper.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\8ITCVTU2\parsec-paper.pdf:application/pdf}
}
@article{poolsap_prediction_2009,
title = {Prediction of {RNA} secondary structure with pseudoknots using integer programming},
volume = {10},
doi = {10.1186/1471-2105-10-S1-S38},
issue = {Suppl 1},
pages = {S38},
journaltitle = {{BMC} bioinformatics},
author = {Poolsap, U. and Kato, Y. and Akutsu, T.},
date = {2009},
keywords = {integer-programming, single-rna, thermodynamic-model},
file = {1471-2105-10-S1-S38.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\C8A4B6NG\1471-2105-10-S1-S38.pdf:application/pdf}
}
@unpublished{giegerich_modeling_2013,
title = {Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems},
author = {Giegerich, Robert and Touzet, Hélène},
date = {2013},
note = {Submitted for publication},
keywords = {adp},
file = {icores.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\2ZDD67EQ\icores.pdf:application/pdf}
}
@inproceedings{gimpel_cube_2009,
title = {Cube summing, approximate inference with non-local features, and dynamic programming without semirings},
url = {http://dl.acm.org/citation.cfm?id=1609102},
pages = {318–326},
booktitle = {Proceedings of the 12th Conference of the European Chapter of the Association for Computational Linguistics},
booktitle = {Proceedings of the 12th Conference of the European Chapter of the Association for Computational Linguistics},
author = {Gimpel, K. and Smith, N. A.},
urldate = {2012-11-01},
date = {2009},
keywords = {dynamic-programming, semi-ring},
file = {p318-gimpel.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\TIUXEMAZ\p318-gimpel.pdf:application/pdf}
}
@article{knuth_semantics_1968,
title = {Semantics of context-free languages},
volume = {2},
issn = {0025-5661},
doi = {10.1007/BF01692511},
issue = {2},
pages = {127-145},
journaltitle = {Mathematical systems theory},
author = {Knuth, Donald E.},
date = {1968},
keywords = {attribute-grammars},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\8I8DKAMI\Knuth67AG.pdf:application/pdf}
}
@inproceedings{vijay-shanker_characterizing_1987,
location = {Stroudsburg, {PA}, {USA}},
title = {Characterizing structural descriptions produced by various grammatical formalisms},
url = {http://dx.doi.org/10.3115/981175.981190},
doi = {10.3115/981175.981190},
pages = {104–111},
booktitle = {Proceedings of the 25th annual meeting on Association for Computational Linguistics},
booktitle = {Proceedings of the 25th annual meeting on Association for Computational Linguistics},
series = {{ACL} '87},
publisher = {Association for Computational Linguistics},
author = {Vijay-Shanker, K. and Weir, David J. and Joshi, Aravind K.},
urldate = {2013-05-03},
date = {1987},
file = {ACM Full Text PDF:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\2R4IZGA9\Vijay-Shanker et al. - 1987 - Characterizing structural descriptions produced by.pdf:application/pdf}
}
@inproceedings{sakakibara_recent_1994,
title = {Recent methods for {RNA} modeling using stochastic context-free grammars},
isbn = {978-3-540-58094-2},
doi = {10.1007/3-540-58094-8_25},
pages = {289-306},
booktitle = {Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching},
booktitle = {Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching},
publisher = {Springer},
author = {Sakakibara, Yasubumi and Brown, Michael and Hughey, Richard and Mian, Saira and Sjölander, Kimmen and Underwood, Rebecca C. and Haussler, David},
date = {1994},
keywords = {parsing, probabilistic-model, {RNA}, scfg},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\FQ7Q7SD9\recent_methods_for_rna_modeling_using_stochastic_context_free_grammars.pdf:application/pdf}
}
@book{mcnaught_compendium_1997,
location = {Oxford},
edition = {2nd ed. (the {"Gold} Book")},
title = {Compendium of Chemical Terminology},
isbn = {0-9678550-9-8},
publisher = {Blackwell Scientific Publications},
author = {{McNaught}, A. D. and Wilkinson, A.},
urldate = {2012-08-19},
date = {1997},
note = {Online corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates by A. Jenkins}
}
@article{huang_partition_2009,
title = {Partition function and base pairing probabilities for {RNA–RNA} interaction prediction},
volume = {25},
issue = {20},
pages = {2646-2654},
journaltitle = {Bioinformatics},
author = {Huang, F. W. D. and Qin, J. and Reidys, C. M. and Stadler, P. F.},
date = {2009},
keywords = {dynamic-programming, partition-function, rna-rna},
file = {2646.full.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\X6HFN3CT\2646.full.pdf:application/pdf}
}
@article{joshi_note_2003,
title = {A note on the strong and weak generative powers of formal systems},
volume = {293},
issn = {0304-3975},
doi = {10.1016/S0304-3975(01)00347-4},
issue = {2},
pages = {243–259},
journaltitle = {Theor. Comput. Sci.},
author = {Joshi, Aravind K.},
date = {2003},
keywords = {crossing dependencies, Lambek grammars, lexicalized tree-adjoining grammars, multi-component grammars, strong generative capacity, tree insertion grammars},
file = {download;jsessionid=CA1CA30DEAF85644A61D8054FECA343B.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\S7J83THH\download;jsessionid=CA1CA30DEAF85644A61D8054FECA343B.pdf:application/pdf}
}
@article{schrijvers_monadic_2009,
title = {Monadic constraint programming},
volume = {19},
issn = {0956-7968},
doi = {10.1017/S0956796809990086},
issue = {6},
pages = {663-697},
journaltitle = {Journal of Functional Programming},
author = {Schrijvers, Tom and Stuckey, Peter and Wadler, Philip},
date = {2009},
keywords = {constraint-programming},
file = {monadic_cp_draft.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\J8WBB82S\monadic_cp_draft.pdf:application/pdf}
}
@article{huang_target_2009,
title = {Target prediction and a statistical sampling algorithm for {RNA-RNA} interaction},
volume = {26},
issn = {1367-4803, 1460-2059},
doi = {10.1093/bioinformatics/btp635},
issue = {2},
pages = {175-181},
journaltitle = {Bioinformatics},
author = {Huang, F. W. D. and Qin, J. and Reidys, C. M. and Stadler, P. F.},
date = {2009},
keywords = {partition-function, probabilistic-model, rna-rna, stochastic-backtracking, thermodynamic-model},
file = {175.full.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\DB95FK8N\175.full.pdf:application/pdf}
}
@article{eddy_how_2004,
title = {How do {RNA} folding algorithms work?},
volume = {22},
issn = {1087-0156},
doi = {10.1038/nbt1104-1457},
issue = {11},
pages = {1457-1458},
journaltitle = {Nature Biotechnology},
author = {Eddy, Sean R.},
date = {2004},
keywords = {dynamic-programming, introduction, pseudoknots, single-rna},
file = {Eddy-ATG5-reprint.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\KBD9JKMS\Eddy-ATG5-reprint.pdf:application/pdf}
}
@inproceedings{brown_small_2000,
title = {Small subunit ribosomal {RNA} modeling using stochastic context-free grammars},
isbn = {1-57735-115-0},
pages = {57-66},
booktitle = {Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology},
booktitle = {Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology},
publisher = {{AAAI} Press},
author = {Brown, Michael {P.S.}},
date = {2000},
keywords = {scfg},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\CA3WCNZG\ISMB00-006.pdf:application/pdf}
}
@article{cai_stochastic_2003,
title = {Stochastic modeling of {RNA} pseudoknotted structures: a grammatical approach},
volume = {19},
shorttitle = {Stochastic modeling of {RNA} pseudoknotted structures},
issue = {suppl. 1},
pages = {i66-i73},
journaltitle = {Bioinformatics},
author = {Cai, L. and Malmberg, R. L. and Wu, Y.},
date = {2003},
keywords = {dynamic-programming, pcgs, pseudoknots, single-rna},
file = {i66.full.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\35CC464U\i66.full.pdf:application/pdf}
}
@book{hopcroft_introduction_2001,
edition = {2nd edition},
title = {Introduction to Automata Theory, Languages, and Computation},
isbn = {0-201-44124-1},
publisher = {Addison-Wesley},
author = {Hopcroft, John E. and Motwani, Rajeev and Ullman, Jeffrey D.},
date = {2001}
}
@thesis{steffen_compiling_2006,
title = {Compiling a Domain Specific Language for Dynamic Programming},
url = {http://pub.uni-bielefeld.de/publication/2304348},
pagetotal = {145},
school = {Bielefeld University},
type = {{Ph.D.}},
author = {Steffen, Peter},
date = {2006},
keywords = {adp, adpc, dynamic-programming, external-dsl, introduction},
file = {download:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\MCCWT8WI\download.pdf:application/pdf}
}
@unpublished{sahinalp_rna-rna_2005,
location = {Simon Fraser University},
title = {{RNA-RNA} Interaction Prediction and Antisense {RNA} Target Search},
url = {http://www.cri.haifa.ac.il/events/2005/string/presentations/Sahinalp.pdf},
author = {Sahinalp, S. C.},
urldate = {2012-06-13},
date = {2005},
keywords = {introduction, rna-rna, thermodynamic-model},
file = {Sahinalp.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\7NQCAHQC\Sahinalp.pdf:application/pdf}
}
@inproceedings{giegerich_algebraic_2002,
location = {London},
title = {Algebraic Dynamic Programming},
isbn = {3-540-44144-1},
pages = {349-364},
booktitle = {Proceedings of the 9th International Conference on Algebraic Methodology and Software Technology},
booktitle = {Proceedings of the 9th International Conference on Algebraic Methodology and Software Technology},
series = {{AMAST} '02},
publisher = {Springer-Verlag},
author = {Giegerich, Robert and Meyer, Carsten},
date = {2002},
keywords = {adp, dynamic-programming, introduction},
file = {ADP (Haskell) 2002.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\86MTTPS7\ADP (Haskell) 2002.pdf:application/pdf}
}
@article{uemura_tree_1999,
title = {Tree adjoining grammars for {RNA} structure prediction},
volume = {210},
issn = {0304-3975},
doi = {10.1016/S0304-3975(98)00090-5},
issue = {2},
pages = {277–303},
journaltitle = {Theoretical Computer Science},
author = {Uemura, Yasuo and Hasegawa, Aki and Kobayashi, Satoshi and Yokomori, Takashi},
date = {1999},
keywords = {pseudoknots},
file = {1-s2.0-S0304397598000905-main.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\Q63JZGVF\1-s2.0-S0304397598000905-main.pdf:application/pdf}
}
@article{searls_linguistic_1997,
title = {Linguistic approaches to biological sequences},
volume = {13},
doi = {10.1093/bioinformatics/13.4.333},
issue = {4},
pages = {333-344},
journaltitle = {Computer applications in the biosciences},
author = {Searls, David B.},
date = {1997},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\XI5I2HDZ\333.full.pdf:application/pdf}
}
@inproceedings{giegerich_towards_2002,
title = {Towards A Discipline of Dynamic Programming},
isbn = {3-88579-348-2},
pages = {3-44},
booktitle = {Informatik bewegt: Informatik 2002 - 32. Jahrestagung der Gesellschaft f\ür Informatik e.v. {(GI)}},
booktitle = {Informatik bewegt: Informatik 2002 - 32. Jahrestagung der Gesellschaft f\ür Informatik e.v. {(GI)}},
publisher = {{GI}},
author = {Giegerich, Robert},
date = {2002},
keywords = {adp, adpc, dynamic-programming, introduction, parsing, yield-grammar},
file = {ADP tutorial-style (Haskell, ADPC-alpha) 2002.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\3RR85XC7\ADP tutorial-style (Haskell, ADPC-alpha) 2002.pdf:application/pdf}
}
@thesis{theis_algorithmic_2010,
title = {Algorithmic ideas for efficient prediction of {RNA} secondary structures including Kissing Hairpin Motifs using Algebraic Dynamic Programming and Haskell},
url = {http://bibiserv.techfak.uni-bielefeld.de/pkiss/mastersthesisCTheis.pdf},
school = {Universität Bielefeld},
type = {Master Thesis},
author = {Theis, Corinna},
urldate = {2012-09-08},
date = {2010},
keywords = {adp, pseudoknots},
file = {mastersthesisCTheis.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\ENTBITUZ\mastersthesisCTheis.pdf:application/pdf}
}
@inbook{joshi_tree_1985,
title = {Tree adjoining grammars: How much context-sensitivity is required to provide reasonable structural descriptions?},
isbn = {9-780-521-262-033},
pages = {206-250},
booktitle = {Natural language parsing},
series = {Studies in Natural Language Processing},
publisher = {Cambridge University Press},
author = {Joshi, Aravind K.},
editor = {Dowty, David R. and Karttunen, Lauri and Zwicky, Arnold M.},
date = {1985},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\GD39QXBF\joshi85.pdf:application/pdf}
}
@article{akutsu_dynamic_2000,
title = {Dynamic programming algorithms for {RNA} secondary structure prediction with pseudoknots},
volume = {104},
doi = {10.1016/S0166-218X(00)00186-4},
issue = {1},
pages = {45–62},
journaltitle = {Discrete Applied Mathematics},
author = {Akutsu, Tatsuya},
date = {2000},
file = {nereida.deioc.ull.es%2F~rumen%2Fdnarna.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\6UTTZDT8\nereida.deioc.ull.es2F~rumen2Fdnarna.pdf:application/pdf}
}
@inproceedings{filardo_flexible_2012,
title = {A Flexible Solver for Finite Arithmetic Circuits},
isbn = {978-3-939897-43-9},
pages = {425-438},
booktitle = {Technical Communications of the 28th International Conference on Logic Programming},
booktitle = {Technical Communications of the 28th International Conference on Logic Programming},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
author = {Filardo, Nathaniel Wesley and Eisner, Jason},
date = {2012},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\V8R7EGK8\filardo+eisner.iclp12.pdf:application/pdf}
}
@article{blizard_multiset_1988,
title = {Multiset theory},
volume = {30},
issn = {0029-4527},
doi = {10.1305/ndjfl/1093634995},
issue = {1},
pages = {36–66},
journaltitle = {Notre Dame Journal of formal logic},
author = {Blizard, Wayne D.},
date = {1988},
keywords = {multisets},
file = {Disseminate:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\N6ZD9ZZS\Disseminate.pdf:application/pdf}
}
@thesis{kotowski_constructive_2011,
title = {Constructive reasoning for semantic wikis},
url = {http://edoc.ub.uni-muenchen.de/13591/},
school = {Ludwig-Maximilians-Universität München},
type = {{Ph.D.}},
author = {Kotowski, Jakub},
urldate = {2013-02-25},
date = {2011},
file = {DISS_Jakub.Kotowski.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\RKVMT8VC\DISS_Jakub.Kotowski.pdf:application/pdf}
}
@article{younger_recognition_1967,
title = {Recognition and parsing of context-free languages in time n3},
volume = {10},
issn = {0019-9958},
doi = {10.1016/S0019-9958(67)80007-X},
issue = {2},
pages = {189-208},
journaltitle = {Information and Control},
author = {Younger, Daniel H.},
date = {1967},
file = {ScienceDirect Full Text PDF:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\D2AJXMFK\Younger - 1967 - Recognition and parsing of context-free languages .pdf:application/pdf;ScienceDirect Snapshot:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\SQ95NIAG\S001999586780007X.html:text/html}
}
@article{lyngso_rna_2000,
title = {{RNA} pseudoknot prediction in energy-based models},
volume = {7},
issn = {1066-5277},
doi = {10.1089/106652700750050862},
issue = {3-4},
pages = {409-427},
journaltitle = {Journal of computational biology},
author = {Lyngsø, Rune B. and Pedersen, Christian N. S.},
date = {2000},
file = {106652700750050862:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\7P9GJUC9\106652700750050862.pdf:application/pdf}
}
@article{goodman_semiring_1999,
title = {Semiring parsing},
volume = {25},
issn = {0891-2017},
issue = {4},
pages = {573-605},
journaltitle = {Computational Linguistics},
author = {Goodman, Joshua},
date = {1999},
keywords = {parsing, semi-ring},
file = {J99-4004.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\3EE8P8ZV\J99-4004.pdf:application/pdf}
}
@misc{hartenfeller_ausarbeitung_2005,
title = {Ausarbeitung - {RNA} folding, Pseudoknots},
author = {Hartenfeller, Markus},
date = {2005},
keywords = {introduction, pseudoknots, single-rna},
file = {Ausarbeitung - RNA, Pseudoknots.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\I8VBKA7G\Ausarbeitung - RNA, Pseudoknots.pdf:application/pdf}
}
@inproceedings{bertsch_complexity_2001,
location = {Beijing, China},
title = {On the Complexity of Some Extensions of {RCG} Parsing},
isbn = {7-302-04925-4},
booktitle = {Proceedings of the Seventh International Workshop on Parsing Technologies},
booktitle = {Proceedings of the Seventh International Workshop on Parsing Technologies},
publisher = {Tsinghua University Press},
author = {Bertsch, Eberhard and Nederhof, Mark-Jan},
date = {2001},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\UFSJRXEI\2001d.pdf:application/pdf}
}
@article{unger_global_1968,
title = {A global parser for context-free phrase structure grammars},
volume = {11},
issn = {0001-0782},
doi = {10.1145/362991.363001},
issue = {4},
pages = {240-247},
journaltitle = {Communications of the {ACM}},
author = {Unger, Stephen H.},
date = {1968},
keywords = {parser}
}
@unpublished{clote_rna:_2007,
location = {University of Singapore},
title = {{RNA:} partition function},
url = {http://www.ims.nus.edu.sg/Programs/biomolecular07/files/clote_tut2_slide4.pdf},
type = {Lecture slides},
howpublished = {Lecture slides},
author = {Clote, P.},
date = {2007},
keywords = {introduction, partition-function, pseudoknots, single-rna, thermodynamic-model},
file = {Partition function (class slides).pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\ISMHT282\Partition function (class slides).pdf:application/pdf}
}
@report{huerta_nih_2000,
title = {{NIH} working definition of bioinformatics and computational biology},
url = {http://www.bisti.nih.gov/docs/CompuBioDef.pdf},
institution = {{US} National Institute of Health},
author = {Huerta, Michael and Downing, Gregory and Haseltine, Florence and Seto, Belinda and Liu, Yuan},
urldate = {2013-05-27},
date = {2000},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\3EE5XVBK\CompuBioDef.pdf:application/pdf}
}
@article{giegerich_systematic_2000,
title = {A systematic approach to dynamic programming in bioinformatics},
volume = {16},
issn = {1367-4803},
doi = {10.1093/bioinformatics/16.8.665},
issue = {8},
pages = {665-677},
journaltitle = {Bioinformatics {(Oxford}, England)},
author = {Giegerich, R},
date = {2000},
keywords = {adp, dynamic-programming, introduction},
file = {ADP Intro (Haskell) 2002.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\MVZNAQCD\ADP Intro (Haskell) 2002.pdf:application/pdf}
}
@report{coppey_dynaprog_2012,
location = {Lausanne, {CH}},
title = {{DynaProg} For Scala -- A Scala {DSL} for Dynamic Programming on {CPU} and {GPU}},
url = {https://raw.github.com/manojo/lamp-dp-mt/master/docs/report/report.pdf},
institution = {École polytechnique fédérale de Lausanne},
type = {Master project report},
author = {Coppey, Thierry},
urldate = {2013-04-18},
date = {2012},
file = {report.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\N7RCP29H\report.pdf:application/pdf}
}
@inproceedings{theis_prediction_2010,
title = {Prediction of {RNA} secondary structure including kissing hairpin motifs},
isbn = {3-642-15293-7},
doi = {10.1007/978-3-642-15294-8_5},
pages = {52-64},
booktitle = {Proceedings of the 10th international conference on Algorithms in bioinformatics},
booktitle = {Proceedings of the 10th international conference on Algorithms in bioinformatics},
publisher = {Springer},
author = {Theis, Corinna and Janssen, Stefan and Giegerich, Robert},
date = {2010},
keywords = {adp, pseudoknots},
file = {pkiss_paper.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\TJW6HIVT\pkiss_paper.pdf:application/pdf}
}
@article{brainerd_tree_1969,
title = {Tree generating regular systems},
volume = {14},
issn = {0019-9958},
doi = {10.1016/S0019-9958(69)90065-5},
issue = {2},
pages = {217-231},
journaltitle = {Information and Control},
author = {Brainerd, Walter S.},
date = {1969},
file = {ScienceDirect Full Text PDF:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\7UR8EZFV\Brainerd - 1969 - Tree generating regular systems.pdf:application/pdf;ScienceDirect Snapshot:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\NCZIKUUQ\S0019995869900655.html:text/html}
}
@inproceedings{honer_zu_siederdissen_sneaking_2012,
title = {Sneaking around {concatMap:} efficient combinators for dynamic programming},
isbn = {978-1-4503-1054-3},
doi = {10.1145/2364527.2364559},
pages = {215-226},
booktitle = {Proceedings of the 17th {ACM} {SIGPLAN} international conference on Functional programming},
booktitle = {Proceedings of the 17th {ACM} {SIGPLAN} international conference on Functional programming},
series = {{ICFP} '12},
publisher = {{ACM}},
library = {Copenhagen, Denmark},
author = {Höner zu Siederdissen, Christian},
date = {2012},
keywords = {adp, functional programming, program fusion},
file = {HOE-2012 Sneaking Around concatMap.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\8S92WQDD\HOE-2012 Sneaking Around concatMap.pdf:application/pdf}
}
@unpublished{zarba_many-sorted_????,
title = {Many-Sorted Logic},
url = {http://web.archive.org/web/20070929131504/http://react.cs.uni-sb.de/~zarba/snow/ch01.pdf},
author = {Zarba, Calogero G.},
urldate = {2013-02-16},
file = {ch01.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\MN4B8D8I\ch01.pdf:application/pdf}
}
@unpublished{van_eijck_deductive_2004,
title = {Deductive parsing in Haskell},
url = {https://faui20a.informatik.uni-erlangen.de/teaching/SS2008/Haskell/Earley.pdf},
author = {van Eijck, J.},
urldate = {2012-07-05},
date = {2004},
keywords = {parsing},
file = {download.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\U68X9ISB\download.pdf:application/pdf}
}
@book{kastens_modellierung:_2008,
edition = {2., überarbeitete und erweiterte Auflage},
title = {Modellierung: Grundlagen und formale Methoden},
isbn = {3-446-415-378},
shorttitle = {Modellierung},
pagetotal = {293},
publisher = {Carl Hanser Verlag},
author = {Kastens, Uwe and Büning, Hans Kleine},
date = {2008}
}
@inproceedings{pereira_parsing_1983,
title = {Parsing as deduction},
doi = {10.3115/981311.981338},
pages = {137-144},
booktitle = {Proceedings of the 21st annual meeting on Association for Computational Linguistics},
booktitle = {Proceedings of the 21st annual meeting on Association for Computational Linguistics},
publisher = {Association for Computational Linguistics},
author = {Pereira, Fernando C. N. and Warren, David H. D.},
date = {1983},
keywords = {parsing},
file = {ACM Full Text PDF:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\UKXS6B74\Pereira und Warren - 1983 - Parsing as deduction.pdf:application/pdf}
}
@article{blizard_dedekind_1993,
title = {Dedekind multisets and function shells},
volume = {110},
url = {http://www.sciencedirect.com/science/article/pii/030439759390351S},
issue = {1},
pages = {79–98},
journaltitle = {Theoretical Computer Science},
author = {Blizard, Wayne D.},
urldate = {2013-02-23},
date = {1993},
keywords = {multisets},
file = {1-s2.0-030439759390351S-main.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\ASK44EBQ\1-s2.0-030439759390351S-main.pdf:application/pdf}
}
@inproceedings{eisner_compiling_2005,
title = {Compiling Comp Ling: Practical weighted dynamic programming and the Dyna language},
doi = {10.3115/1220575.1220611},
pages = {281-290},
booktitle = {Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing},
booktitle = {Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing},
publisher = {Association for Computational Linguistics},
author = {Eisner, Jason and Goldlust, Eric and Smith, Noah A.},
date = {2005},
keywords = {dynamic-programming, parsing},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\HR4Z9C4G\eisner+goldlust+smith.hltemnlp05.pdf:application/pdf}
}
@article{reeder_design_2004,
title = {Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics},
volume = {5},
issn = {1471-2105},
doi = {10.1186/1471-2105-5-104},
issue = {1},
journaltitle = {{BMC} Bioinformatics},
author = {Reeder, Jens and Giegerich, Robert},
date = {2004},
keywords = {adp, canonization, dynamic-programming, pseudoknots, single-rna, thermodynamic-model},
file = {1471-2105-5-104.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\GH5RMEEB\1471-2105-5-104.pdf:application/pdf}
}
@unpublished{mneimneh_rna-rna_????,
location = {The City University of New York},
title = {{RNA-RNA} Interaction Algorithms},
url = {http://www.cs.hunter.cuny.edu/~saad/rnai_talk.pdf},
author = {Mneimneh, Saad},
urldate = {2012-06-14},
keywords = {dynamic-programming, introduction, rna-rna, single-rna},
file = {rnai_talk.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\QCCVA2A4\rnai_talk.pdf:application/pdf}
}
@inproceedings{teitelbaum_context-free_1973,
title = {Context-free error analysis by evaluation of algebraic power series},
doi = {10.1145/800125.804050},
pages = {196-199},
booktitle = {Proceedings of the fifth annual {ACM} symposium on Theory of computing},
booktitle = {Proceedings of the fifth annual {ACM} symposium on Theory of computing},
publisher = {{ACM}},
author = {Teitelbaum, Ray},
date = {1973},
keywords = {semi-ring, weighted-grammars},
file = {p196-teitelbaum.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\GKX6NKZF\p196-teitelbaum.pdf:application/pdf}
}
@article{rivas_language_2000,
title = {The language of {RNA:} a formal grammar that includes pseudoknots},
volume = {16},
issn = {1367-4803},
doi = {10.1093/bioinformatics/16.4.334},
shorttitle = {The language of {RNA}},
issue = {4},
pages = {334-340},
journaltitle = {Bioinformatics},
author = {Rivas, Elena and Eddy, Sean R.},
date = {2000},
keywords = {pseudoknots},
file = {334.full.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\Z62TMDGF\334.full.pdf:application/pdf}
}
@thesis{goodman_parsing_1998,
location = {Cambridge, Massachusetts},
title = {Parsing inside-out},
url = {http://research.microsoft.com/en-us/um/people/joshuago/thesis.ps},
school = {Harvard University},
author = {Goodman, Joshua},
urldate = {2012-10-15},
date = {1998},
keywords = {parsing, semi-ring},
file = {thesis.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\HTFEKQRS\thesis.pdf:application/pdf}
}
@article{giegerich_discipline_2004,
title = {A discipline of dynamic programming over sequence data},
volume = {51},
issn = {0167-6423},
doi = {10.1016/j.scico.2003.12.005},
issue = {3},
pages = {215-263},
journaltitle = {Science of Computer Programming},
author = {Giegerich, Robert and Meyer, Carsten and Steffen, Peter},
date = {2004},
keywords = {adp, adpc, dynamic-programming, introduction, parsing, yield-grammar},
file = {GIE-MEY-STE-2004.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\VG4DPGDU\GIE-MEY-STE-2004.pdf:}
}
@inbook{eisner_dyna:_2011,
title = {Dyna: extending datalog for modern {AI}},
isbn = {978-3-642-24205-2},
pages = {181-220},
booktitle = {Datalog Reloaded},
publisher = {Springer},
author = {Eisner, Jason and Filardo, Nathaniel Wesley},
date = {2011},
keywords = {dynamic-programming, parsing},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\SSX86BAI\eisner+filardo.datalog11-long.pdf:application/pdf}
}
@online{overton_constraint_2008,
title = {Constraint Programming in Haskell},
url = {http://overtond.blogspot.de/2008/07/pre.html},
titleaddon = {David's Blog},
author = {Overton, David},
urldate = {2013-04-05},
date = {2008},
file = {David's Blog: Constraint Programming in Haskell:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\9539E6U9\pre.html:text/html}
}
@article{richard_buchi_regular_1964,
title = {Regular canonical systems},
volume = {6},
url = {http://www.springerlink.com/index/xl01867q87464j00.pdf},
issue = {3},
pages = {91–111},
journaltitle = {Archive for Mathematical Logic},
author = {Richard Büchi, J.},
urldate = {2012-11-10},
date = {1964},
file = {fulltext.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\GF46I79P\fulltext.pdf:application/pdf}
}
@article{rivas_dynamic_1999,
title = {A dynamic programming algorithm for {RNA} structure prediction including pseudoknots},
volume = {285},
issn = {0022-2836},
doi = {10.1006/jmbi.1998.2436},
issue = {5},
pages = {2053–2068},
journaltitle = {Journal of molecular biology},
author = {Rivas, Elena and Eddy, Sean R.},
date = {1999},
file = {RivasEddy99-reprint.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\5EGBR9Z5\RivasEddy99-reprint.pdf:application/pdf}
}
@article{ogden_helpful_1968,
title = {A helpful result for proving inherent ambiguity},
volume = {2},
issn = {0025-5661},
doi = {10.1007/BF01694004},
issue = {3},
pages = {191-194},
journaltitle = {Mathematical systems theory},
author = {Ogden, William},
date = {1968},
keywords = {Computational Mathematics and Numerical Analysis, Theory of Computation}
}
@article{lorenz_viennarna_2011,
title = {{ViennaRNA} Package 2.0},
volume = {6},
issn = {1748-7188},
doi = {10.1186/1748-7188-6-26},
issue = {1},
pages = {26},
journaltitle = {Algorithms for Molecular Biology},
author = {Lorenz, Ronny and Bernhart, Stephan H and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F and Hofacker, Ivo L},
date = {2011},
keywords = {dynamic-programming, parallelization, rna-rna, single-rna, thermodynamic-model},
file = {ViennaRNA.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\R5BVVGIV\ViennaRNA.pdf:application/pdf}
}
@article{rivas_range_2011,
title = {A range of complex probabilistic models for {RNA} secondary structure prediction that includes the nearest-neighbor model and more},
volume = {18},
issn = {1355-8382},
doi = {10.1261/rna.030049.111},
issue = {2},
pages = {193-212},
journaltitle = {{RNA}},
author = {Rivas, Elena and Lang, Raymond and Eddy, Sean R.},
date = {2011},
keywords = {dynamic-programming, external-dsl, probabilistic-model, single-rna, tornado},
file = {193.full.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\M43352W6\193.full.pdf:application/pdf}
}
@article{steffen_versatile_2005,
title = {Versatile and declarative dynamic programming using pair algebras},
volume = {6},
issue = {1},
pages = {224},
journaltitle = {{BMC} bioinformatics},
author = {Steffen, Peter and Giegerich, Robert},
date = {2005},
keywords = {adp},
file = {1471-2105-6-224.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\W94SRJBD\1471-2105-6-224.pdf:application/pdf}
}
@article{ignacio_how_1999,
title = {How {RNA} folds},
volume = {293},
doi = {10.1006/jmbi.1999.3001},
pages = {271-281},
journaltitle = {Journal of Molecular Biology},
author = {Ignacio, Tinoco and Bustamante, Carlos},
date = {1999},
file = {rnafolds.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\Q34CKRUK\rnafolds.pdf:application/pdf}
}
@inproceedings{ljunglof_polynomial_2005,
title = {A Polynomial Time Extension of Parallel Multiple Context-Free Grammar},
rights = {©2005 Springer-Verlag Berlin Heidelberg},
isbn = {978-3-540-25783-7},
doi = {10.1007/11422532_12},
pages = {177-188},
booktitle = {Proceedings of the 5th international conference on Logical Aspects of Computational Linguistics},
booktitle = {Proceedings of the 5th international conference on Logical Aspects of Computational Linguistics},
publisher = {Springer},
author = {Ljunglöf, Peter},
date = {2005},
keywords = {mcfg, pmcfg},
file = {:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\JISD9UUV\10789.pdf:application/pdf;Snapshot:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\QBQA9IWQ\10.html:text/html}
}
@article{seki_generative_2008,
title = {On the Generative Power of Multiple Context-Free Grammars and Macro Grammars},
volume = {E91-D},
issn = {0916-8532},
doi = {10.1093/ietisy/e91-d.2.209},
issue = {2},
pages = {209-221},
journaltitle = {{IEICE} - Transactions on Information and Systems},
author = {Seki, Hiroyuki and Kato, Yuki},
date = {2008},
keywords = {context-free tree grammar, generative power, linearity, macro grammar, multiple context-free grammar},
file = {2006007.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\NAMSTP8R\2006007.pdf:application/pdf}
}
@article{mathews_expanded_1999,
title = {Expanded sequence dependence of thermodynamic parameters improves prediction of {RNA} secondary structure},
volume = {288},
doi = {10.1006/jmbi.1999.2700},
issue = {5},
pages = {911-940},
journaltitle = {Journal of molecular biology},
author = {Mathews, David H. and Sabina, Jeffrey and Zuker, Michael and Turner, Douglas H.},
date = {1999},
file = {1-s2.0-S0022283699927006-main.pdf:D:\Profile\maik\AppData\Roaming\Mozilla\Firefox\Profiles\pt1yuguv.default\zotero\storage\FTUGSFUF\1-s2.0-S0022283699927006-main.pdf:application/pdf}
}
@inproceedings{sauthoff_bellmans_2011,