ref.bib

%
% $Id: ref.bib,v 1.1 2011-02-26 22:41:54 laci Exp $
%
% Project      : RNA motif searching in genomic sequences
% Description  : the reference library
%
% Author       : Ladislav Rampasek <rampasek@gmail.com>
% Institution  : Comenius University in Bratislava
%

@conference{schaefer1978,
  title={{The complexity of satisfiability problems}},
  author={Schaefer, T.J.},
  booktitle={Proceedings of the tenth annual ACM symposium on Theory of computing},
  pages={216--226},
  year={1978},
  organization={ACM}
}

@article{rivas2000,
  title={{The language of RNA: a formal grammar that includes pseudoknots}},
  author={Rivas, E. and Eddy, S.R.},
  journal={Bioinformatics},
  volume={16},
  number={4},
  pages={334},
  issn={1367-4803},
  year={2000},
  publisher={Oxford University Press}
}

@article{lyngso2004,
  title={{Complexity of pseudoknot prediction in simple models}},
  author={Lyngs{\o}, R.B.},
  journal={Automata, Languages and Programming},
  pages={171--211},
  year={2004},
  publisher={Springer}
}

@article{lathrop1994,
  title={{The protein threading problem with sequence amino acid interaction preferences is NP-complete}},
  author={Lathrop, R.H.},
  journal={Protein Engineering Design and Selection},
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  number={9},
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  publisher={Oxford University Press}
}

@book{garey1979,
  title={{Computers and intractability. A guide to the theory of NP-completeness.}},
  author={Garey, M.R. and Johnson, D.S.},
  year={1979},
  publisher={WH Freeman and Company, San Francisco, California}
}

@article{webb2009,
author = "C. H.  Webb and N. J.  Riccitelli and D. J.  Ruminski and A.  Luptak",
title = "{Widespread occurrence of self-cleaving ribozymes}",
journal = "Science",
volume = "326",
number = "5955",
pages = "953",
year = "2009",
pmid = "19965505",
}

@Article{george2009,
AUTHOR = {George, A. D. and Tenenbaum, S. A.},
TITLE = {{Informatic resources for identifying and annotating structural RNA motifs.}},
JOURNAL = {Mol Biotechnol},
VOLUME = {41},
YEAR = {2009},
NUMBER = {2},
PAGES = {180-93},
ISSN = {1073-6085},
}

@Article{gautheret1990,
author = {Gautheret, D. and Major, F. and Cedergren, R.},
TITLE = {{Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA.}},
JOURNAL = {Comput Appl Biosci},
VOLUME = {6},
YEAR = {1990},
NUMBER = {4},
PAGES = {325-31},
ISSN = {0266-7061}
}

@article{macke2001,
author = {Macke, T. J. and Ecker, D. J. and Gutell, R. R. and Gautheret, D. and Case, D. A. and Sampath, R.},
title = {{RNAMotif, an RNA secondary structure definition and search algorithm}},
journal = {Nucl. Acids Res.},
volume = {29},
number = {22},
pages = {4724-4735},
year = {2001}
}

@article{chang2006,
author = {Chang, Tzu-Hao and Huang, Hsien-Da and Chuang, Tzu-Neng and Shien, Dray-Ming and Horng, Jorng-Tzong},
title = {{RNAMST: efficient and flexible approach for identifying RNA structural homologs}},
journal = {Nucl. Acids Res.},
volume = {34},
pages = {W423-428},
year = {2006}
}

@book{durbin1998,
  title={{Biological sequence analysis: Probabilistic models of proteins and nucleic acids}},
  author={Durbin, R. and Eddy, S.R. and Krogh, A. and Mitchison, G.},
  year={1998},
  isbn = {0521629713},
  publisher={Cambridge University Press}
}

@unpublished{eddy1996,
  title={{RNABob: a program to search for RNA secondary structure motifs in sequence databases}},
  author={S.R. Eddy},
  year = {1996},
	note = {unpublished}
}

@article{billoud1996,
  title={{Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database}},
  author={Billoud, B. and Kontic, M. and Viari, A.},
  journal={Nucleic Acids Research},
  volume={24},
  number={8},
  pages={1395},
  year={1996},
  publisher={Oxford Univ Press}
}

@article{grillo2003,
  title={{PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences}},
  author={Grillo, G. and Licciulli, F. and Liuni, S. and Sbisa, E. and Pesole, G.},
  journal={Nucleic Acids Research},
  volume={31},
  number={13},
  pages={3608},
  year={2003},
  publisher={Oxford Univ Press}
}

@article{schattner2005,
  title={{The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs}},
  author={Schattner, P. and Brooks, A.N. and Lowe, T.M.},
  journal={Nucleic acids research},
  volume={33},
  number={Web Server Issue},
  pages={W686},
  year={2005},
  publisher={Oxford Univ Press}
}

@article{bengert2004,
  title={{Riboswitch finder--a tool for identification of riboswitch RNAs}},
  author={Bengert, P. and Dandekar, T.},
  journal={Nucleic acids research},
  volume={32},
  number={Web Server Issue},
  pages={W154},
  year={2004},
  publisher={Oxford Univ Press}
}

@book{gusfield1997,
  title={{Algorithms on strings, trees, and sequences: computer science and computational biology}},
  author={Gusfield, D.},
  year={1997},
  publisher={Cambridge University Press}
}

@conference{baeza1992,
  title={{Fast and practical approximate string matching}},
  author={Baeza-Yates, R. and Perleberg, C.},
  booktitle={Combinatorial Pattern Matching},
  pages={185--192},
  year={1992},
  organization={Springer}
}

@article{arlazarov1970,
  title={{On economic construction of the transitive closure of a directed graph}},
  author={Arlazarov, V. L. and Dinic, E. A. and Kronrod, M. A. and Faradzev, I. A.},
  journal={Dokl. Acad. Nauk SSSR},
  volume={194},
  pages={487-488},
  year={1970}
}

@misc{luptak2010,
  author={A. Lupták},
  howpublished={personal communication},
  year={2010}
}

@misc{unigene,
  author={{UniGene}},
  title={{National Center for Biotechnology Information database}},
  howpublished={"\url{ftp://ftp.ncbi.nih.gov/repository/UniGene/Drosophila_melanogaster/}"},
}

@misc{intro2001,
  author={Brazma, A. and Parkinson, H. and Schlitt, T. and Shojatalab, M.},
  title={{A quick introduction to elements of biology - cells, molecules, genes, functional genomics, microarrays}},
  howpublished={"\url{http://www.ebi.ac.uk/microarray/biology_intro.html}", European Bioinformatics Institute},
  year={2001}
}

@article{sperschneider2010dotknot,
  title={{DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model}},
  author={Sperschneider, Jana and Datta, Amitava},
  journal={Nucleic acids research},
  volume={38},
  number={7},
  pages={e103--e103},
  year={2010},
  publisher={Oxford Univ Press}
}

@article{sperschneider2011heuristic,
  title={{Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins}},
  author={Sperschneider, Jana and Datta, Amitava and Wise, Michael J},
  journal={RNA},
  volume={17},
  number={1},
  pages={27--38},
  year={2011},
  publisher={Cold Spring Harbor Lab}
}

@article{lorenz2011viennarna,
  title={{ViennaRNA Package 2.0}},
  author={Lorenz, Ronny and Bernhart, Stephan HF and Zu Siederdissen, Christian Hoener and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F and Hofacker, Ivo L and others},
  journal={Algorithms for Molecular Biology},
  volume={6},
  number={1},
  pages={26},
  year={2011}
}

@article{edgar2010search,
  title={{Search and clustering orders of magnitude faster than BLAST}},
  author={Edgar, Robert C},
  journal={Bioinformatics},
  volume={26},
  number={19},
  pages={2460--2461},
  year={2010},
  publisher={Oxford Univ Press}
}