@incollection{Speer-Spieth-Zell/05,
AUTHOR = {Speer, Nora and Spieth, Christian and Zell, Andreas},
TITLE = {Spectral clustering gene ontology terms to group genes by function},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {1-12},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_1},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Zilberstein-Ziv-Ukelson/05,
AUTHOR = {Zilberstein, Chaya Ben-Zaken and Ziv-Ukelson, Michal},
TITLE = {Dynamic de-novo prediction of microRNAs associated with cell conditions: A search pruned by expression},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {13-26},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_2},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Brehhelin/05,
AUTHOR = {Br{\'eh}h{\'e}lin, Laurent},
TITLE = {Clustering gene expression series with prior knowledge},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {27-38},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_3},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Madeira-Oliveira/05,
AUTHOR = {Madeira, Sara C. and Oliveira, Arlindo L.},
TITLE = {A linear time biclustering algorithm for time series gene expression data},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {39-52},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_4},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Tuller-Oron-Makavy-Chamovitz-Chor/05,
AUTHOR = {Tuller, Tamir and Oron, Efrat and Makavy, Erez and Chamovitz, Daniel A. and Chor, Benny},
TITLE = {Time-window analysis of developmental gene expression data with multiple genetic backgrounds},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {53-64},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_5},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Wu-You-Lin/05,
AUTHOR = {Wu, Gang and You, Jia-Huai and Lin, Guohui},
TITLE = {A lookahead branch-and-bound algorithm for the maximum quartet consistency problem},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {65-76},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_6},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Christiansen-Mailund-Pedersen-Randers/05,
AUTHOR = {Christiansen, Chris and Mailund, Thomas and Pedersen, Christian N.S. and Randers, Martin},
TITLE = {Computing the quartet distance between trees of arbitrary degree},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {77-88},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_7},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Moran-Rao-Snir/05,
AUTHOR = {Moran, Shlomo and Rao, Satish and Snir, Sagi},
TITLE = {Using semi-definite programming to enhance supertree resolvability},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {89-103},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_8},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Peng-Ting/05,
AUTHOR = {Peng, Z.S. and Ting, H.F.},
TITLE = {An efficient reduction from constrained to unconstrained maximum agreement subtree},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {104-115},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_9},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Ganapathy-Goodson-Jansen-Ramachandran-Warnow/05,
AUTHOR = {Ganapathy, Ganeshkumar and Goodson, Barbara and Jansen, Robert and Ramachandran, Vijaya and Warnow, Tandy},
TITLE = {Pattern identification in biogeography},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {116-127},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_10},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Cilibrasi-van_Iersel-Kelk-Tromp/05,
AUTHOR = {Cilibrasi, Rudi and van Iersel, Leo and Kelk, Steven and Tromp, John},
TITLE = {On the complexity of several haplotyping problems},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {128-139},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_11},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Rastas-Koivisto-Mannila-Ukkonen/05,
AUTHOR = {Rastas, Pasi and Koivisto, Mikko and Mannila, Heikki and Ukkonen, Esko},
TITLE = {A hidden Markov technique for haplotype reconstruction},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {140-151},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_12},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Song-Wu-Gusfield/05a,
AUTHOR = {Song, Yun S. and Wu, Yufeng and Gusfield, Dan},
TITLE = {Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {152-164},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_13},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Wernicke/05,
AUTHOR = {Wernicke, Sebastian},
TITLE = {A faster algorithm for detecting network motifs},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {165-177},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_14},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Lacroix-Fernandes-Sagot/05,
AUTHOR = {Lacroix, Vincent and Fernandes, Cristina G. and Sagot, Marie-France},
TITLE = {Reaction motifs in metabolic networks},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {178-191},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_15},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Tucker-Moulton/05,
AUTHOR = {Tucker, Warwick and Moulton, Vincent},
TITLE = {Reconstructing metabolic networks using interval analysis},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {192-203},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_16},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Elias-Hartman/05,
AUTHOR = {Elias, Isaac and Hartman, Tzvika},
TITLE = {A 1.375-approximation algorithm for sorting by transpositions},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {204-215},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_17},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Labarre/05,
AUTHOR = {Labarre, Anthony},
TITLE = {A new tight upper bound on the transposition distance},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {216-227},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_18},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Berard-Bergeron-Chauve-Paul/05,
AUTHOR = {B{\'e}rard, S{\`e}verine and Bergeron, Anne and Chauve, Cedric and Paul, Christophe},
TITLE = {Perfect sorting by reversals is not always difficult},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {228-238},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_19},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Lyngso-SSong-Hein/05,
AUTHOR = {Lyngs{\o}, B. Rune and S.Song, Yun and Hein, Jotun},
TITLE = {Minimum recombination histories by branch and bound},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {239-250},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_20},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Kucherov-Noe-Roytberg/05,
AUTHOR = {Kucherov, Gregory and No{\'e}, Laurent and Roytberg, Mikhail},
TITLE = {A unifying framework for seed sensitivity and its application to subset seeds},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {251-263},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_21},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Leung-Chin/05a,
AUTHOR = {Leung, Henry C.M. and Chin, Francis Y.L.},
TITLE = {Generalized planted $(l,d)$-motif problem with negative set},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {264-275},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_22},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Sammeth-Weniger-Harmsen-Stoye/05,
AUTHOR = {Sammeth, Michael and Weniger, Thomas and Harmsen, Dag and Stoye, Jens},
TITLE = {Alignment of tandem repeats with excision, duplication, substitution and indels (EDSI)},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {276-290},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_23},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Dalevi-Dubhashi/05,
AUTHOR = {Dalevi, Daniel and Dubhashi, Devdatt},
TITLE = {The Peres-Shields order estimator for fixed and variable length Markov models with applications to DNA sequence similarity},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {291-302},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_24},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Bauer-Klau-Reinert/05,
AUTHOR = {Bauer, Markus and Klau, Gunnar W. and Reinert, Knut},
TITLE = {Multiple structural RNA alignment with Lagrangian relaxation},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {303-314},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_25},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Agarwal-Bilu-Kolodny/05,
AUTHOR = {Agarwal, Pankaj K. and Bilu, Yonatan and Kolodny, Rachel},
TITLE = {Faster algorithms for optimal multiple sequence alignment based on pairwise comparisons},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {315-327},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_26},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Vashist-Kulikowski-Muchnik/05,
AUTHOR = {Vashist, Akshay and Kulikowski, Casimir and Muchnik, Ilya},
TITLE = {Ortholog clustering on a multipartite graph},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {328-340},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_27},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Rastegari-Condon/05,
AUTHOR = {Rastegari, Baharak and Condon, Anne},
TITLE = {Linear time algorithm for parsing RNA secondary structure},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {341-352},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_28},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Boyer-Hunt-Nelesen/05,
AUTHOR = {Boyer, Robert S. and Hunt, Warren A., Jr. and Nelesen, Serita},
TITLE = {A compressed format for collections of phylogenetic trees and improved consensus performance},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {353-364},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_29},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Veber-Yanev-Andonov-Poirriez/05,
AUTHOR = {Veber, P. and Yanev, N. and Andonov, R. and Poirriez, V.},
TITLE = {Optimal protein threading by cost-splitting},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {365-375},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_30},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Song-Liu-Huang-Malmberg-Xu-Cai/05,
AUTHOR = {Song, Yinglei and Liu, Chunmei and Huang, Xiuzhen and Malmberg, Russell L. and Xu, Ying and Cai, Liming},
TITLE = {Efficient parameterized algorithm for biopolymer structure-sequence alignment},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {376-388},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_31},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Leaver-Fay-Kuhlman-Snoeyink/05,
AUTHOR = {Leaver-Fay, Andrew and Kuhlman, Brian and Snoeyink, Jack},
TITLE = {Rotamer-pair energy calculations using a trie data structure},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {389-400},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_32},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Eyal-Halperin/05,
AUTHOR = {Eyal, Eran and Halperin, Dan},
TITLE = {Improved maintenance of molecular surfaces using dynamic graph connectivity},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {401-413},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_33},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Kister/05,
AUTHOR = {Kister, Alexander},
TITLE = {The main structural regularities of the sandwich proteins},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {414-422},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_34},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Lasker-Dror-Nussinov-Wolfson/05,
AUTHOR = {Lasker, Keren and Dror, Oranit and Nussinov, Ruth and Wolfson, Haim},
TITLE = {Discovery of protein substructures in EM maps},
BOOKTITLE = {Proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI'2005 (Mallorca, Spain, October 3-6, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3692},
PAGES = {423-434},
YEAR = {2005},
EDITOR = {Casadio, Rita and Myers, Gene},
KEYWORDS = {structural bioinformatics, intermediate resolution cryo EM maps, 3D alignment of secondary structures, macromolecular assemblies},
URL = {http://springerlink.metapress.com/openurl.asp?genre=article&id=doi:10.1007/11557067_35},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg-New York},
}
@incollection{Bachrach-Chen-Harrelson-Mihaescu-Rao-Shah/05,
AUTHOR = {Bachrach, Abraham and Chen, Kevin and Harrelson, Chris and Mihaescu, Radu and Rao, Satish and Shah, Apurva},
TITLE = {Lower bounds for maximum parsimony with gene order data},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {1-10},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/761n756g03752l46/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Blin-Chauve-Fertin/05,
AUTHOR = {Blin, Guillaume and Chauve, Cedric and Fertin, Guillaume},
TITLE = {Genes order and phylogenetic reconstruction: Application to $\gamma$-proteobacteria},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {11-20},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/pp438r5x4618p67x/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bourque-Yacef-El-Mabrouk/05,
AUTHOR = {Bourque, Guillaume and Yacef, Yasmine and El-Mabrouk, Nadia},
TITLE = {Maximizing synteny blocks to identify ancestral homologs},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {21-34},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/y8661607q582q6l8/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Carmel-Rogozin-Wolf-Koonin/05,
AUTHOR = {Carmel, Liran and Rogozin, Igor B. and Wolf, Yuri I. and Koonin, Eugene V.},
TITLE = {An expectation-maximization algorithm for analysis of evolution of exon-intron structure of eukaryotic genes},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {35-46},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/pk3x44w64n44238k/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
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@incollection{Csuros/05,
AUTHOR = {Cs{\H{u}}r{\"o}s, Mikl{\'o}s},
TITLE = {Likely scenarios of intron evolution},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {47-60},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/y40n6g145675p047/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
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@incollection{Dessimoz-Cannarozzi-Gil-Margadant-Roth-Schneider-Gonnet/05,
AUTHOR = {Dessimoz, Christophe and Cannarozzi, Gina and Gil, Manuel and Margadant, Daniel and Roth, Alexander and Schneider, Adrian and Gonnet, Gaston H.},
TITLE = {OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: Introduction and first achievements},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {61-72},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/733r061h22l3w115/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Hoberman-Durand/05,
AUTHOR = {Hoberman, Rose and Durand, Dannie},
TITLE = {The incompatible desiderata of gene cluster properties},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {73-87},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/p421673602948347/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Dalpasso-Lancia-Rizzi/05,
AUTHOR = {Dalpasso, Marcello and Lancia, Giuseppe and Rizzi, Romeo},
TITLE = {The string barcoding problem is $NP$-hard},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {88-96},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/74l7134858626h30/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Marcus/05,
AUTHOR = {Marcus, Jeffrey M.},
TITLE = {A partial solution to the C-value paradox},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {97-105},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/f32881wj77611634/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Raghupathy-Durand/05,
AUTHOR = {Raghupathy, Narayanan and Durand, Dannie},
TITLE = {Individual gene cluster statistics in noisy maps},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {106-120},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/p00p252193096182/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sankoff-Haque/05,
AUTHOR = {Sankoff, David and Haque, Lani},
TITLE = {Power boosts for cluster tests},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {121-130},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/y07n782402122456/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sankoff-Zheng-Lenert/05,
AUTHOR = {Sankoff, David and Zheng, Chungfang and Lenert, Aleksander},
TITLE = {Reversals of fortune},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {131-141},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/7185136l44082354/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Seoighe-Scheffler/05,
AUTHOR = {Seoighe, Cathal and Scheffler, Konrad},
TITLE = {Very low power to detect asymmetric divergence of duplicated genes},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {142-152},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
URL = {http://springerlink.metapress.com/content/p43tulkmx0h0k0m6/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Swenson-Pattengale-Moret/05,
AUTHOR = {Swenson, Krister M. and Pattengale, Nicholas D. and Moret, B.M.E.},
TITLE = {A framework for orthology assignment from gene rearrangement data},
BOOKTITLE = {Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, RCG'2005 (Dublin, Ireland, September 18-20, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3678},
PAGES = {153-166},
YEAR = {2005},
EDITOR = {McLysaght, Aoife and Huson, Daniel H.},
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@incollection{Scott-Ideker-Karp-Sharan/05,
AUTHOR = {Scott, Jacob and Ideker, Trey and Karp, Richard M. and Sharan, Roded},
TITLE = {Efficient algorithms for detecting signaling pathways in protein interaction networks},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {1-13},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/xxkuv92jbvlevrka/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Jaimovich-Elidan-Margalit-Friedman/05,
AUTHOR = {Jaimovich, Ariel and Elidan, Gal and Margalit, Hanah and Friedman, Nir},
TITLE = {Towards an integrated protein-protein interaction network},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {14-30},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/ta0rj2wacjt3xtta/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gat-Viks-Tanay-Raijman-Shamir/05,
AUTHOR = {Gat-Viks, Irit and Tanay, Amos and Raijman, Daniela and Shamir, Ron},
TITLE = {The factor graph network model for biological systems},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {31-47},
YEAR = {2005},
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URL = {http://springerlink.metapress.com/content/xtfp53f6gw5dwj4c/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Koyuturk-Grama-Szpankowski/05,
AUTHOR = {Koyut{\"u}rk, Mehmet and Grama, Ananth and Szpankowski, Wojciech},
TITLE = {Pairwise local alignment of protein interaction networks guided by models of evolution},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {48-65},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/r518bde106elf7kg/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Frey-Morris-Robinson-Hughes/05,
AUTHOR = {Frey, Brendan J. and Morris, Quaid D. and Robinson, Mark and Hughes, Timothy R.},
TITLE = {Finding novel transcripts in high-resolution genome-wide microarray data using the GenRate model},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {66-82},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/ybrkfbdbemmwqh7d/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lipson-Aumann-Ben-Dor-Linial-Yakhini/05,
AUTHOR = {Lipson, Doron and Aumann, Yonatan and Ben-Dor, Amir and Linial, Nathan and Yakhini, Zohar},
TITLE = {Efficient calculation of interval scores for DNA copy number data analysis},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {83-100},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/x4bcw04rdv229hbm/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Papatsenko-Levine/05,
AUTHOR = {Papatsenko, Dmitri and Levine, Mike},
TITLE = {A regulatory network controlling Drosophila development},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {101-101},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/ketx9dt3p875j114/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lindquist-Fraenkel-Outeiro-Gitler-Su-Cashikar-Jagadish/05,
AUTHOR = {Lindquist, Susan and Fraenkel, Ernest and Outeiro, Tiago and Gitler, Aaron and Su, Julie and Cashikar, Anil and Jagadish, Smitha},
TITLE = {Yeast cells as a discovery platform for neurodegenerative disease},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {102-102},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/x3e6exy1r4887xrg/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wu-Chang-Chen-Chang-Wu-Huang-Sung-Hsu/05,
AUTHOR = {Wu, Kuen-Pin and Chang, Jia-Ming and Chen, Jun-Bo and Chang, Chi-Fon and Wu, Wen-Jin and Huang, Tai-Huang and Sung, Ting-Yi and Hsu, Wen-Lian},
TITLE = {RIBRA-An error-tolerant algorithm for the NMR backbone assignment problem},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {103-117},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/r67vb4cmuu2x2234/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bern-Chen-Wong/05,
AUTHOR = {Bern, Marshall and Chen, Jindong and Wong, Hao Chi},
TITLE = {Avoiding local optima in single particle reconstruction},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {118-132},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/mx9y0etn213u8fv7/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zilberstein-Ziv-Ukelson-Pinter-Yakhini/05,
AUTHOR = {Zilberstein, Chaya Ben-Zaken and Ziv-Ukelson, Michal and Pinter, Ron Y. and Yakhini, Zohar},
TITLE = {A high-throughput approach for associating microRNAs with their activity conditions},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {133-151},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/q4h9g7nmagmfxq9j/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Alkan-Karakoc-Nadeau-Sahinalp-Zhang/05,
AUTHOR = {Alkan, Can and Karako{\c{c}}, Emre and Nadeau, Joseph H. and {\c{S}}ahinalp, S. Cenk and Zhang, Kaizhong},
TITLE = {RNA-RNA interaction prediction and antisense RNA target search},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {152-171},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/hcx5yhaajy76aer9/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bafna-Tang-Zhang/05,
AUTHOR = {Bafna, Vineet and Tang, Haixu and Zhang, Shaojie},
TITLE = {Consensus folding of unaligned RNA sequences revisited},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {172-187},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/kme4pgbw79ew07p2/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{DeLisi/05,
AUTHOR = {DeLisi, Charles},
TITLE = {Discovery and annotation of genetic modules},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {188-188},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/vw9u3p2y1m90kynw/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Rasmussen-Stoye-Myers/05,
AUTHOR = {Rasmussen, Kim R. and Stoye, Jens and Myers, Eugene W.},
TITLE = {Efficient $q$-gram filters for finding all $\epsilon$-matches over a given length},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {189-203},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/mp92cf1hl33pp0tj/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sze-Lu-Yang/05,
AUTHOR = {Sze, Sing-Hoi and Lu, Yue and Yang, Qingwu},
TITLE = {A polynomial time solvable formulation of multiple sequence alignment},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {204-216},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/x4ekamju6rmucl5d/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gusfield-Bansal/05,
AUTHOR = {Gusfield, Dan and Bansal, Vikas},
TITLE = {A fundamental decomposition theory for phylogenetic networks and incompatible characters},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {217-232},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/gr1p0qen7av2lfe7/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Huson-Klopper-Lockhart-Steel/05,
AUTHOR = {Huson, Daniel H. and Kl{\"o}pper, Tobias and Lockhart, Pete J. and Steel, Mike A.},
TITLE = {Reconstruction of reticulate networks from gene trees},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {233-249},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/vjjd4jc9lap7anea/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Durand-Halldorsson-Vernot/05,
AUTHOR = {Durand, Dannie and Halld{\'o}rsson, Bjarni V. and Vernot, Benjamin},
TITLE = {A hybrid micro-macroevolutionary approach to gene tree reconstruction},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {250-264},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/l1bfhfj7xvk7qw1c/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Huynh-Jansson-Nguyen-Sung/05,
AUTHOR = {Huynh, Trinh N.D. and Jansson, Jesper and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Constructing a smallest refining galled phylogenetic network},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {265-280},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/m1xq0hr8wfj5500h/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Baumeister/05,
AUTHOR = {Baumeister, Wolfgang},
TITLE = {Mapping molecular landscapes inside cells},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {281-282},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/m6yvk9nd56y2ywwa/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Burstein-Ulitsky-Tuller-Chor/05,
AUTHOR = {Burstein, David and Ulitsky, Igor and Tuller, Tamir and Chor, Benny},
TITLE = {Information theoretic approaches to whole genome phylogenies},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {283-295},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/ju4wejgc1u2flmc4/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Chor-Tuller/05a,
AUTHOR = {Chor, Benny and Tuller, Tamir},
TITLE = {Maximum likelihood of evolutionary trees is hard},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {296-310},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/ncml6g9vbx3fxdtt/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Przytycka-Davis-Song-Durand/05,
AUTHOR = {Przytycka, Teresa and Davis, George and Song, Nan and Durand, Dannie},
TITLE = {Graph theoretical insights into evolution of multidomain proteins},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {311-325},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/uxy3mxth02h8dab4/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Frank-Tanner-Pevzner/05,
AUTHOR = {Frank, Ari and Tanner, Stephen and Pevzner, Pavel},
TITLE = {Peptide sequence tags for fast database search in mass-spectrometry},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {326-341},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/ugbmw0txktx75kl2/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wan-Chen/05,
AUTHOR = {Wan, Yunhu and Chen, Ting},
TITLE = {A hidden Markov model based scoring function for mass spectrometry database search},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {342-356},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/wd7a66vqkmnp18m1/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bern-Goldberg/05,
AUTHOR = {Bern, Marshall and Goldberg, David},
TITLE = {EigenMS: De novo analysis of peptide tandem mass spectra by spectral graph partitioning},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {357-372},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/rvm2duk1k8fry4rg/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lander/05,
AUTHOR = {Lander, Eric},
TITLE = {Biology as information},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {373-373},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/qcvetc5qwpt6rnfl/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gross-Brent/05,
AUTHOR = {Gross, Samuel S. and Brent, Michael R.},
TITLE = {Using multiple alignments to improve gene prediction},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {374-388},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/pxa9cgv4jw29gxx6/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sonnenburg-Ratsch-Schafer/05,
AUTHOR = {Sonnenburg, S. and R{\"a}tsch, G. and Sch{\"a}fer, C.},
TITLE = {Learning interpretable SVMs for biological sequence classification},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {389-407},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/qb6bf6a2xg6cepx8/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Liu-Carbonell-Weigele-Gopalakrishnan/05,
AUTHOR = {Liu, Yan and Carbonell, Jaime and Weigele, Peter and Gopalakrishnan, Vanathi},
TITLE = {Segmentation conditional random fields (SCRFs): A new approach for protein fold recognition},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {408-422},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/k0q2lun5eth1d1mf/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Xu/05,
AUTHOR = {Xu, Jinbo},
TITLE = {Rapid protein side-chain packing via tree decomposition},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {423-439},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/j56wabagv41b5ece/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Shatsky-Shulman-Peleg-Nussinov-Wolfson/05,
AUTHOR = {Shatsky, Maxim and Shulman-Peleg, Alexandra and Nussinov, Ruth and Wolfson, Haim J.},
TITLE = {Recognition of binding patterns common to a set of protein structures},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {440-455},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/nln7a7j4b63le3pk/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Yanover-Hertz/05,
AUTHOR = {Yanover, Chen and Hertz, Tomer},
TITLE = {Predicting protein-peptide binding affinity by learning peptide-peptide distance functions},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {456-471},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/lanjv7v7m0gwqbtk/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{King-Haase-Pettingell-Simkovsky-Weigele/05,
AUTHOR = {King, Jonathan and Haase-Pettingell, Cammie and Simkovsky, Ryan and Weigele, Peter},
TITLE = {Amino acid sequence control of the folding of the parallel $\beta$-helix, the simplest $\beta$-sheet fold},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {472-473},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/vg00b2mhuyvgmybb/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chia-Bundschuh/05,
AUTHOR = {Chia, Nicholas and Bundschuh, Ralf},
TITLE = {A practical approach to significance assessment in alignment with gaps},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {474-488},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/lna795ye2t81hcva/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Valouev-Li-Liu-Schwartz-Yang-Zhang-Waterman/05,
AUTHOR = {Valouev, Anton and Li, Lei and Liu, Yu-Chi and Schwartz, David C. and Yang, Yi and Zhang, Yu and Waterman, Michael S.},
TITLE = {Alignment of optical maps},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {489-504},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/u9cqtut4nwnl3qm4/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Collins/05,
AUTHOR = {Collins, James J.},
TITLE = {Engineering gene regulatory networks: A reductionist approach to systems biology},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {505-505},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/p41mt8kyb8h23t2f/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Yeang-Jaakkola/05,
AUTHOR = {Yeang, Chen-Hsiang and Jaakkola, Tommi},
TITLE = {Modeling the combinatorial functions of multiple transcription factors},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {506-521},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/hthjc8rl6l38g73j/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kaplan-Friedman-Margalit/05,
AUTHOR = {Kaplan, Tommy and Friedman, Nir and Margalit, Hanah},
TITLE = {Predicting transcription factor binding sites using structural knowledge},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {522-537},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/htfc9h5h4tbxnjp0/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Middendorf-Kundaje-Shah-Freund-Wiggins-Leslie/05,
AUTHOR = {Middendorf, Manuel and Kundaje, Anshul and Shah, Mihir and Freund, Yoav and Wiggins, Chris H. and Leslie, Christina},
TITLE = {Motif discovery through predictive modeling of gene regulation},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {538-552},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/m8xe90vqrl91g4qt/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Halperin-Hazan/05,
AUTHOR = {Halperin, Eran and Hazan, Elad},
TITLE = {HAPLOFREQ --- Estimating haplotype frequencies efficiently},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {553-568},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/t3dw769gyf86d4v1/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bafna-Bansal/05,
AUTHOR = {Bafna, Vineet and Bansal, Vikas},
TITLE = {Improved recombination lower bounds for haplotype data},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {569-584},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/wc9m8ec6gl2c2vwj/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ding-Filkov-Gusfield/05,
AUTHOR = {Ding, Zhihong and Filkov, Vladimir and Gusfield, Dan},
TITLE = {A linear-time algorithm for the Perfect Phylogeny Haplotyping (PPH) problem},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {585-600},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/m2fvjmt509r9y5ae/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Altshuler/05,
AUTHOR = {Altshuler, David},
TITLE = {Human genome sequence variation and the inherited basis of common disease},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {601-602},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/u6fcv01708m5k1hf/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sankoff-Mazowita/05a,
AUTHOR = {Sankoff, David and Mazowita, Matthew},
TITLE = {Stability of rearrangement measures in the comparison of genome sequences},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {603-614},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
URL = {http://springerlink.metapress.com/content/kulamrjfclqj70ee/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bergeron-Mixtacki-Stoye/05,
AUTHOR = {Bergeron, Anne and Mixtacki, Julia and Stoye, Jens},
TITLE = {On sorting by translocations},
BOOKTITLE = {Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2005 (Cambridge, MA, USA, May 14-18, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {3500},
PAGES = {615-629},
YEAR = {2005},
EDITOR = {Miyano, Satoru and Mesirov, Jill and Kasif, Simon and Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
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PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Berard-Bergeron-Chauve/05,
AUTHOR = {B{\'e}rard, S{\`e}verine and Bergeron, Anne and Chauve, Cedric},
TITLE = {Conservation of combinatorial structures in evolution scenarios},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {1-14},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/b2uq792rhua5vydk/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Buhler-Nordgren/05,
AUTHOR = {Buhler, Jeremy and Nordgren, Rachel},
TITLE = {Toward a phylogenetically aware algorithm for fast DNA similarity search},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {15-29},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/pdxf5nrle13wtk2k/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Choi-Choi-Cho-Kim/05,
AUTHOR = {Choi, Jeong-Hyeon and Choi, Kwangmin and Cho, Hwan-Gue and Kim, Sun},
TITLE = {Multiple genome alignment by clustering pairwise matches},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {30-41},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
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PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gorecki-Tiuryn/05,
AUTHOR = {G{\'o}recki, Pawe{\l} and Tiuryn, Jerzy},
TITLE = {On the structure of reconciliations},
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SERIES = {LNCS/LNBI},
VOLUME = {3388},
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YEAR = {2005},
EDITOR = {Lagergren, Jens},
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PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
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@incollection{Hoberman-Sankoff-Durand/05,
AUTHOR = {Hoberman, Rose and Sankoff, David and Durand, Dannie},
TITLE = {The statistical significance of max-gap clusters},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {55-71},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/vqqn6c6ecn9t0nm0/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Mau-Darling-Perna/05,
AUTHOR = {Mau, Bob and Darling, Aaron E. and Perna, Nicole T.},
TITLE = {Identifying evolutionarily conserved segments among multiple divergent and rearranged genomes},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {72-84},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/3784199deqrd8159/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Miklos-Hein/05,
AUTHOR = {Mikl{\'o}s, Istv{\'a}n and Hein, Jotun},
TITLE = {Genome rearrangement in mitochondria and its computational biology},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {85-96},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/nrea7kxwtghnvygg/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sankoff-Lefebvre-Tillier-Maler-El-Mabrouk/05,
AUTHOR = {Sankoff, David and Lefebvre, Jean-Fran{\c{c}}ois and Tillier, Elisabeth and Maler, Adrian and El-Mabrouk, Nadia},
TITLE = {The distribution of inversion lengths in bacteria},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {97-108},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/lh6tbd6e3qf08v1w/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sankoff-Mazowita/05,
AUTHOR = {Sankoff, David and Mazowita, Matthew},
TITLE = {Estimators of translocations and inversions in comparative maps},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {109-122},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/x9ub71ht8gffw2qf/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Taneri-Novoradovsky-Snyder-Gaasterland/05,
AUTHOR = {Taneri, Bahar and Novoradovsky, Alexey and Snyder, Ben and Gaasterland, Terry},
TITLE = {Databases for comparative analysis of human-mouse orthologous alternative splicing},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Comparative Genomics, RCG'2004 (Bertinoro, Italy, October 16-19, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3388},
PAGES = {123-131},
YEAR = {2005},
EDITOR = {Lagergren, Jens},
URL = {http://springerlink.metapress.com/content/du4baj7xa13ry7k8/fulltext.pdf" title="Download PDF (376.4 KB)"><span>Download PDF (376.4 KB)</span></a></li> 	</ul></li><li class="primitive primitiveResource Backmatter"><p class="title">Back matter</p><ul class="resources fulltextResources" data-ftxUrl="/content/978-3-540-24455-4/#section=580782"> 		<li><a class="sprite pdf-resource-spritehttp://springerlink.metapress.com/content/978-3-540-24455-4/back-matter.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
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@incollection{Middendorf-Kundaje-Wiggins-Freund-Leslie/05,
AUTHOR = {Middendorf, Manuel and Kundaje, Anshul and Wiggins, Chris and Freund, Yoav and Leslie, Christina},
TITLE = {Predicting genetic regulatory response using classification: Yeast stress response},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {1-13},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/tf38jftm48jvg406/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Manke-Dieterich-Vingron/05,
AUTHOR = {Manke, Thomas and Dieterich, Christoph and Vingron, Martin},
TITLE = {Detecting functional modules of transcription factor binding sites in the human genome},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {14-21},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/fktx3y833jm8n086/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Krivan/05,
AUTHOR = {Krivan, William},
TITLE = {Fishing for proteins in the Pacific Northwest},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {22-29},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/68j17ga2p6jur1h7/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
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@incollection{Siddharthan-van_Nimwegen-Siggia/05,
AUTHOR = {Siddharthan, Rahul and van Nimwegen, Erik and Siggia, Eric D.},
TITLE = {PhyloGibbs: A Gibbs sampler incorporating phylogenetic information},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {30-41},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/qt738qy8e1e2x5ar/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kel-Tikunov-Voss-Borlak-Wingender/05,
AUTHOR = {Kel, Alexander and Tikunov, Yury and Voss, Nico and Borlak, J{\"u}rgen and Wingender, Edgar},
TITLE = {Application of kernel method to reveal subtypes of TF binding motifs --- Causal analysis of gene expression data},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {42-51},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/4avm513607nxpela/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Noto-Craven/05,
AUTHOR = {Noto, Keith and Craven, Mark},
TITLE = {Learning regulatory network models that represent regulator states and roles},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {52-64},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/ha1k4jnvu075fdwy/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zilberstein-Eskin-Yakhini/05,
AUTHOR = {Zilberstein, Chaya Ben-Zaken and Eskin, Eleazar and Yakhini, Zohar},
TITLE = {Using expression data to discover RNA and DNA regulatory sequence motifs},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {65-78},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/muprh6nn0hknfq8c/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Polouliakh-Konno-Horton-Nakai/05,
AUTHOR = {Polouliakh, Natalia and Konno, Michiko and Horton, Paul and Nakai, Kenta},
TITLE = {Parameter landscape analysis for common motif discovery programs},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {79-87},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/634aurd0vwettf6e/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Filkov-Shah/05,
AUTHOR = {Filkov, Vladimir and Shah, Nameeta},
TITLE = {Inferring cis-region hierarchies from patterns in time-course gene expression data},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {88-97},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
URL = {http://springerlink.metapress.com/content/0paj6njf2nbblr80/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gat-Viks-Tanay-Shamir/05,
AUTHOR = {Gat-Viks, Irit and Tanay, Amos and Shamir, Ron},
TITLE = {Modeling and analysis of heterogeneous regulation in biological networks},
BOOKTITLE = {Proceedings of the RECOMB 2004 International Workshop on Regulatory Genomics, RRG'2004 (San Diego, CA, USA, March 26-27, 2004)},
SERIES = {LNCS/LNBI},
VOLUME = {3318},
PAGES = {98-113},
YEAR = {2005},
EDITOR = {Eskin, Eleazar and Workman, Chris},
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PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}