MO640 - Textos

Criada: 2005-03-09
Modificada: 2005-03-18

A lista abaixo enumera os textos que serão usados na disciplina. Todos eles exceto os trechos do livro de Setubal e Meidanis (1997) estão disponíveis no Xerox do Instituto de Artes. A maioria deles têm versão eletrônica disponível nesta página.

  1. Meidanis 2003a - MEIDANIS, J. Current Challenges in Bioinformatics. Invited talk at SPIRE 2003, Manaus, Brasil.
  2. Meidanis 2003b - MEIDANIS, J. Current Challenges in Bioinformatics. In: M. A. Nascimento, E. S. Moura, A. L. Oliveira (Eds.): SPIRE 2003 - Proceedings of the Workshop on String Processing and Information Retrieval. Lecture Notes in Computer Sciences, Vol. 2857, pp. 16-27, 2003. Springer-Verlag.
  3. Pevzner 2004 - PEVZNER, P. A. Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics, Vol. 20, no. 14, pp. 2159-2161 (2004). Editorial.
  4. Setubal e Meidanis 1997 - SETUBAL, J. C.; MEIDANIS, J. Introduction to Computational Molecular Biology. PWS Publishing Company, 1997. ISBN: 0-534-95262-3.
  5. Ewens e Grant 2001 - EWENS, W. J.; GRANT, G. R. Statistcial Methods in Bioinformatics: An Introduction. Springer-Verlag, 2001. ISBN: 0-387-95229-2.
  6. Meidanis 2004 - MEIDANIS, J. Genome Rearrangements. Talk given in 2004 at Fleury Diagnostic Medicine, Sao Paulo, Brazil.
  7. McLysaght et al. 2003 - MCLYSAGHT, A.; BALDI, P. F.; GAUT, B. S. Extensive gene gain associated with adaptive evolution of poxviruses. Proceedings of the National Academy of Sciences of the USA, Vol. 100, no. 26, pp. 15655-15660 (2003).
  8. Dias e Meidanis 2002a - DIAS, Z.; MEIDANIS, J. The Genome Rearrangement Distance by Fusion, Fission, and Transposition with Arbitrary Weights. Relatório Técnico IC-02-001, IC-Unicamp, 2002.
  9. Hannenhalli et al. 1999 - HANNENHALLI, S.; PEVZNER, P. A. Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals. Journal of the ACM, Vol. 46, no. 1, pp. 1-27 (1999).
  10. Kaplan et al. 1997 - KAPLAN, H.; SHAMIR, R.; TARJAN, R. E. Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. SODA 1997 - Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms, pp. 344-351, 1997. Society for Industrial and Applied Mathematics.
  11. Bergeron 2005 - BERGERON, A. A very elementary presentation of the Hannenhalli-Pevzner theory. Discrete Applied Mathematics, Vol. 146, pp. 134-145 (2005).
  12. Bafna e Pevzner 1998 - BAFNA, V; PEVZNER, P. A. Sorting by transpositions. SIAM J. Discrete Mathematics, Vol. 11, No. 2, pp. 224-240 (1998).
  13. Meidanis et al. 1997 - MEIDANIS, J.; WALTER, M. E. M. T.; DIAS, Z. Transposition Distance Between a Permutation and Its Reverse. WSP 1997 - Proceedings of the Fourth South American Workshop on String Processing. November, 12-13, pp. 70-79 (1997).
  14. DM 2002b - MEIDANIS, J.; DIAS, Z. Sorting by Prefix Transpositions. SPIRE 2002 - Proceedings of the Workshop on String Processing and Information Retrieval. Lecture Notes in Computer Sciences, vol. 2476, 2002. Springer-Verlag.
  15. Fortuna 2005 - FORTUNA, V. J. Distâncias de Transposição entre Genomas. Tese de Mestrado, IC-Unicamp, seção 3.3. Defesa marcada: 28 de março de 2005, 14:00 horas.
  16. Christie 1996 - CHRISTIE, D. A. Sorting permutations by block-interchange. Information Processing Letters, Vol. 60, pp. 165-169 (1996).
  17. Walter et al. 1999 - WALTER, M. E. M. T.; DIAS, Z.; MEIDANIS, J. A Lower Bound on the Reversal and Transposition Diameter. Revised version of paper in: Proceedings of SPIRE 1998 - String Processing and Information Retrieval: A South American Symposium. September, 9-11, 1998, pp. 96-102. Santa Cruz de la Sierra, Bolivia. A compact version appeared in: Journal of Computational Biology, Vol.9, No.5, pp. 743-745 (2002).
  18. Meidanis e Dias 2001 - MEIDANIS, J.; DIAS, Z. Genome Rearrangement Distance by Fusion, Fission, and Transposition is Easy. Relatório Técnico IC-01-07, IC-Unicamp, 2001.
  19. Benzer 1959 - BENZER, D. A. On the topology of genetic fine structure. Proceedings of the National Academy of Science, USA, Vol. 45, pp. 1607-1620 (1959).
  20. Booth e Leuker 1976 - BOOTH, K. S.; LEUKER, G. S. Testing for the Consecutive Ones Property, Interval Graphs, and Graph Planarity Using PQ-Tree Algorithms. J. of Computer and Systems Sciences, 13, 335-379 (1976).
  21. MPT 1998 - MEIDANIS, J.; PORTO, O.; TELLES, G. P. On the consecutive ones property. Discrete Applied Mathematics, 88, 325-354 (1998).
  22. Meidanis e Telles 2004 - TELLES, G. P.; MEIDANIS, J. Building PQR Trees in Almost-Linear Time. Submetido a publicação, 2004.
  23. Jacy Monteiro 1974 - JACY MONTEIRO, L. H. Elementos de Álgebra, Livros Técnicos e Científicos Editora, Rio de Janeiro, 1974.
  24. Dias 2002 - DIAS, Z. An Alternative Algebraic Formalism for Genome Rearrangements. In: Dias, Z., Rearranjo de Genomas: Uma Coletânea de Artigos, Tese de Doutorado, IC-Unicamp, cap. 6. Defendida em 2002.
  25. MWD 2002 - MEIDANIS, J.; WALTER, M. E. M. T.; DIAS, Z. A Lower Bound on the Reversal and Transposition Diameter. J. of Computational Biology, Vol. 9, No. 5, pp. 743-745, 2002.
  26. DFM 2004 - DIAS, Z.; FORTUNA, V.; MEIDANIS, J. Sorting by Prefix Transpositions. Submetido a publicação, 2004.
  27. Fortuna e Meidanis 2004 - FORTUNA, V.; MEIDANIS, J. Sorting the Reverse Permutation by Prefix Transpositions. Relatório Técnico IC-04-04, IC-Unicamp, 2004.
  28. Bergeron - BERGERON, A. A Very Elementary Presentation of the Hannenhalli-Pevzner Theory. Aceito para publicação, Discrete Applied Mathematics, 2003.
  29. Quitzau 2004b - QUITZAU, J. A. A. Grafos, Cortes, Subgrupos e Árvores Filogenéticas. Tese de Mestrado, IC-Unicamp, cap. 3. Defesa prevista: 2004.

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