mo640.bib

@UNPUBLISHED{Beginners,
  AUTHOR = {N. Castells-Brooke},
  TITLE = {Beginner's guide to molecular biology},
  NOTE = {web pages},
  HTTP = {http://www.rothamsted.ac.uk/notebook/courses/guide/}
}

@BOOK{SM97,
  AUTHOR = {J. C. Setubal and J. Meidanis},
  NOTE = {ISBN: 0-534-95262-3},
  PUBLISHER = {PWS Publishing Company},
  TITLE = {Introduction to Computational Molecular Biology},
  YEAR = {1997}
}

@UNPUBLISHED{Shamir2001,
  AUTHOR = {R. Shamir},
  TITLE = {Pairwise sequence comparison},
  YEAR = {2001},
  NOTE = {Lecture 2 from Algorithms in Molecular Biology, Tel Aviv University, Tel Aviv, Israel},
  PDF = {Shamir-2001.pdf}
}

@MASTERSTHESIS{Quit2005,
  AUTHOR = {J. A. A. Quitzau},
  TITLE = {Um consenso completamente resolvido entre \'arvores filogen\'eticas completamente resolvidas},
  SCHOOL = {Institute of Computing, University of Campinas},
  YEAR = 2005,
  PS = {Quitzau-2005.ps}
}

@ARTICLE{Pevz2004,
  AUTHOR = {P. Pevzner},
  TITLE = {Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians},
  JOURNAL = {Bioinformatics},
  YEAR = 2004,
  VOLUME = 20,
  NUMBER = 14,
  PAGES = {2159--2161},
  NOTE = {Editorial},
  PDF = {Pevzner-2004.pdf}
}

@ARTICLE{Eddy2005,
  AUTHOR = {S. R. Eddy},
  TITLE = {Antedisciplinary Science},
  JOURNAL = {PLoS Comput. Biol.},
  YEAR = 2005,
  VOLUME = 1,
  NUMBER = 1,
  PAGES = {3--4},
  NOTE = {e6},
  PDF = {Eddy-2005.pdf}
}

@ARTICLE{BP1998,
  AUTHOR = {V. Bafna and P. A. Pevzner},
  TITLE = {Sorting by Transpositions},
  JOURNAL = {{SIAM} J. Discrete Math.},
  YEAR = 1998,
  VOLUME = 11,
  NUMBER = 2,
  PAGES = {224--240},
  MONTH = {May},
  PDF = {Bafna-Pevzner-1998.pdf}
}

@ARTICLE{Chri1996,
  AUTHOR = {D. A. Christie},
  TITLE = {Sorting permutations by block-interchanges},
  JOURNAL = {Information Processing Letters},
  YEAR = 1996,
  VOLUME = 60,
  PAGES = {165--169},
  PDF = {Christie-1996.pdf}
}

@MASTERSTHESIS{Fort2005,
  AUTHOR = {V. J. Fortuna},
  TITLE = {Dist\^ancias de Transposi\c{c}\~ao entre Genomas},
  SCHOOL = {Institute of Computing, University of Campinas},
  YEAR = 2005,
  PS = {Fortuna-2005.ps}
}

@UNPUBLISHED{Mnei2004,
  AUTHOR = {S. Mneimneh},
  TITLE = {Genome rearragement, sorting signed permutations by reversals},
  NOTE = {Lectures 16 and 17 from course CSE 8354 -- Computational Biology, Southern Methodist University, Dallas, USA},
  YEAR = 2004,
  HTTP = {http://engr.smu.edu/~saad/courses/cse8354/}
}

@ARTICLE{HP1999,
  AUTHOR = {S. Hannenhalli and P. A. Pevzner},
  TITLE = {Transforming Cabbage into Turnip: Polynomial
Algorithm for Sorting Signed Permutations by Reversals},
  JOURNAL = {Journal of the {ACM}},
  YEAR = 1999,
  VOLUME = 46,
  NUMBER = 1,
  PAGES = {200--223},
  MONTH = {Jan},
  PDF = {Hannenhalli-Pevzner-1999.pdf}
}

@ARTICLE{Berg2005,
  AUTHOR = {A. Bergeron},
  TITLE = {A very elementary presentation of the {H}annenhalli-{P}evzner theory},
  JOURNAL = {Discrete Applied Mathematics},
  YEAR = 2005,
  VOLUME = 146,
  PAGES = {134--145},
  PDF = {Bergeron-2005.pdf}
}

@UNPUBLISHED{Meid2004,
  AUTHOR = {J. Meidanis},
  TITLE = {Genome Rearrangements},
  NOTE = {Talk given at Fleury Diagnostic Medicine, Sao Paulo, Brazil},
  MONTH = {Dec},
  YEAR = 2004,
  PDF = {Meidanis-2004.pdf}
}

@INCOLLECTION{MD2000,
  AUTHOR = {J. Meidanis and Z. Dias},
  TITLE = {An Alternative Algebraic Formalism for Genome Rearrangements},
  BOOKTITLE = {Comparative Genomics},
  PAGES = {213--223},
  PUBLISHER = {Kluwer Academic Publishers},
  YEAR = 2000,
  EDITOR = {David Sankoff and Joseph Nadeau},
  PS = {Meidanis-Dias-2000.ps}
}

@MASTERSTHESIS{Alme2007,
  AUTHOR = {A. A. M. Almeida},
  TITLE = {Compara\c{c}\~ao Alg\'ebrica de Genomas: O Caso da Dist\^ancia de Revers\~ao},
  SCHOOL = {Institute of Computing, University of Campinas},
  YEAR = 2007,
  PDF = {Almeida-2007.pdf}
}

@UNPUBLISHED{MM2007,
  AUTHOR = {C. V. G. Mira and J. Meidanis},
  TITLE = {Sorting by Fissions, Fusions, and Signed Reversals in {$O(n)$}},
  NOTE = {Submitted for publication},
  YEAR = 2007,
  PDF = {Mira-Meidanis-2007.pdf}
}

@INCOLLECTION{Meid1999,
  AUTHOR = {J. Meidanis},
  TITLE = {A Simple Toolkit for {DNA} Fragment Assembly},
  BOOKTITLE = {Mathematical Support for Molecular Biology},
  PAGES = {271--288},
  PUBLISHER = {American Mathematical Society},
  YEAR = 1999,
  EDITOR = {M. Farach-Colton and F. S. Roberts and M. Vingron
                  and M. Waterman},
  VOLUME = 47,
  SERIES = {{DIMACS} Series in Discrete Mathematics and
                  Theoretical Computer Science},
  PS = {Meidanis-1999.ps}
}

@ARTICLE{GJBF+2006,
  AUTHOR = {S. M. D. Goldberg and others},
  TITLE = {A {Sanger}/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes},
  JOURNAL = {Proc. Nat. Acad. Sci. - USA},
  YEAR = 2006,
  VOLUME = 103,
  NUMBER = 30,
  PAGES = {11240--11245},
  MONTH = {July},
  PDF = {Goldberg-et-al-2006.pdf}
}

@ARTICLE{Benz1959,
  AUTHOR = {S. Benzer},
  TITLE = {On the Topology of the Genetic Fine Structure},
  JOURNAL = {Proc. Nat. Acad. Sci. - USA},
  YEAR = 1959,
  VOLUME = 45,
  PAGES = {1607--1620},
  PDF = {Benzer-1959.pdf}
}

@ARTICLE{BL1976,
  AUTHOR = {K. S. Booth and G. S. Lueker},
  TITLE = {Testing for the Consecutive Ones Property, Interval Graphs, and Graph Planarity using {PQ}-Tree Algorithms},
  JOURNAL = {J. Comput. Systems Sci.},
  YEAR = 1976,
  VOLUME = 13,
  NUMBER = 3,
  PAGES = {335--379}
}

@ARTICLE{MPT1998,
  AUTHOR = {J. Meidanis and O. Porto and G. P. Telles},
  TITLE = {On the Consecutive Ones Property},
  JOURNAL = {Discrete Applied Mathematics},
  YEAR = 1998,
  VOLUME = 88,
  PAGES = {325--354},
  PDF = {Meidanis-Porto-Telles-1998.pdf}
}

@UNPUBLISHED{TM2007,
  AUTHOR = {G. P. Telles and J. Meidanis},
  TITLE = {Building {PQR} Trees in Almost Linear Time},
  NOTE = {Submitted for publication},
  YEAR = 2007,
  PS = {Telles-Meidanis-2007.ps}
}