@incollection{Tannier/09,
AUTHOR = {Tannier, Eric},
TITLE = {Yeast ancestral genome reconstructions: The possibilities of computational methods},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {1-12},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/m18x4t816240t048/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Yang-Sankoff/09,
AUTHOR = {Yang, Zhenyu and Sankoff, David},
TITLE = {Natural parameter values for generalized gene adjacency},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {13-23},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/6u52401808762811/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ouangraoua-Bergeron/09,
AUTHOR = {Ouangraoua, A{\"{i}}da and Bergeron, Anne},
TITLE = {Parking functions, labeled trees and DCJ sorting scenarios},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {24-35},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/n7q25h8234149rkm/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Braga-Stoye/09,
AUTHOR = {Braga, Mar{\'{i}}lia D.V. and Stoye, Jens},
TITLE = {Counting all DCJ sorting scenarios},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {36-47},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/74211721h33204x8/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chauve-Haus-Stephen-You/09,
AUTHOR = {Chauve, Cedric and Haus, Utz-Uwe and Stephen, Tamon and You, Vivija P.},
TITLE = {Minimal conflicting sets for the consecutive ones property in ancestral genome reconstruction},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {48-58},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/p551566837672277/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Blin-Stoye/09,
AUTHOR = {Blin, Guillaume and Stoye, Jens},
TITLE = {Finding nested common intervals efficiently},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {59-69},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/0225673151478043/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Xu/09,
AUTHOR = {Xu, Andrew Wei},
TITLE = {DCJ median problems on linear multichromosomal genomes: Graph representation and fast exact solutions},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {70-83},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/gh7w114066416672/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Medvedev-Stoye/09,
AUTHOR = {Medvedev, Paul and Stoye, Jens},
TITLE = {Rearrangement models and single-cut operations},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {84-97},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/107548mp23541700/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Hou-Riemer-Berman-Hardison-Miller/09,
AUTHOR = {Hou, Minmei and Riemer, Cathy and Berman, Piotr and Hardison, Ross C. and Miller, Webb},
TITLE = {Aligning two genomic sequences that contain duplications},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {98-110},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/h2m0234245017252/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Song-Zhang-Vinar-Miller/09,
AUTHOR = {Song, Giltae and Zhang, Louxin and Vina{\v{r}}, Tom{\'a}{\v{s}} and Miller, Webb},
TITLE = {Inferring the recent duplication history of a gene cluster},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {111-125},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/r122564615306311/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Angibaud-Fertin-Thevenin-Vialette/09,
AUTHOR = {Angibaud, S{\'e}bastien and Fertin, Guillaume and Th{\'e}venin, Annelyse and Vialette, St{\'e}phane},
TITLE = {Pseudo Boolean programming for partially ordered genomes},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {126-137},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/h753268096w35001/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Delgado-Lynce-Manquinho/09,
AUTHOR = {Delgado, Jo{\~a}o and Lynce, In{\^e}s and Manquinho, Vasco},
TITLE = {Computing the summed adjacency disruption number between two genomes with duplicate genes using pseudo-Boolean optimization},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {138-149},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/r8448k44qxwjh7l3/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Vinar-Brejova-Song-Siepel/09,
AUTHOR = {Vina{\v{r}}, Tom{\'a}{\v{s}} and Brejov{\'a}, Bro{\v{n}}a and Song, Giltae and Siepel, Adam},
TITLE = {Reconstructing histories of complex gene clusters on a phylogeny},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {150-163},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/h317917448401127/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Tuller-Birin-Kupiec-Ruppin/09,
AUTHOR = {Tuller, Tamir and Birin, Hadas and Kupiec, Martin and Ruppin, Eytan},
TITLE = {Co-evolutionary models for reconstructing ancestral genomic sequences: Computational issues and biological examples},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {164-180},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/jq687x4u0727w5qk/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Hsu-Zhang-Hardison-Miller/09,
AUTHOR = {Hsu, Chih-Hao and Zhang, Yu and Hardison, Ross and Miller, Webb},
TITLE = {Whole-genome analysis of gene conversion events},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {181-192},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/tq6806646512p88q/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Adam-Sankoff/09,
AUTHOR = {Adam, Zaky and Sankoff, David},
TITLE = {A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {193-204},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/k6gt030h637v4232/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Poisson-Belcaid-Bergeron/09,
AUTHOR = {Poisson, Guylaine and Belcaid, Mahdi and Bergeron, Anne},
TITLE = {Comparative genomics and extensive recombinations in phage communities},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {205-216},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/u3554165576p0751/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Richardson-Wiehe/09,
AUTHOR = {Richardson, Dale N. and Wiehe, Thomas},
TITLE = {Properties of sequence conservation in upstream regulatory and protein coding sequences among paralogs in Arabidopsis thaliana},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {217-228},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/l43k745116205866/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Liu-Clarke/09,
AUTHOR = {Liu, Xiao and Clarke, Neil D.},
TITLE = {Transcription factor binding probabilities in orthologous promoters: An alignment-free approach to the inference of functional regulatory targets},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2009 (Budapest, Hungary, September 27-29, 2009)},
SERIES = {LNCS},
VOLUME = {5817},
PAGES = {229-240},
YEAR = {2009},
EDITOR = {Ciccarelli, Francesca D. and Mikl{\'o}s, Istv{\'a}n},
URL = {http://springerlink.metapress.com/content/l07681k2n2187r65/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}