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Combinatorial Search on Graphs Motivated by Bioinformatics Applications: A Brief Survey

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Graph-Theoretic Concepts in Computer Science (WG 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3787))

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Abstract

The goal of this paper is to present a brief survey of a collection of methods and results from the area of combinatorial search [1,8] focusing on graph reconstruction using queries of different type. The study is motivated by applications to genome sequencing.

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References

  1. Aigner, M.: Combinatorial Search. John Wiley and Sons, Chichester (1988)

    MATH  Google Scholar 

  2. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular Biology of the Cell. Garland Science (1994)

    Google Scholar 

  3. Alon, N.: Separating matrices. Private communication (May 1997)

    Google Scholar 

  4. Alon, N., Asodi, V.: Learning a hidden subgraph. In: Díaz, J., Karhumäki, J., Lepistö, A., Sannella, D. (eds.) ICALP 2004. LNCS, vol. 3142, pp. 110–121. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  5. Alon, N., Beigel, R., Kasif, S., Rudich, S., Sudakov, B.: Learning a hidden matching. In: Proceedings of the 43rd Annual IEEE Symposium on Foundations of Computer Science, FOCS 2002, Vancouver, BC, Canada, 16–19 November, pp. 197–206. IEEE Computer Society Press, Los Alamitos (2002)

    Chapter  Google Scholar 

  6. Cantor, D.G., Mills, W.H.: Determination of a subset from certain combinatorial properties. Can. J. Math. 18, 42–48 (1966)

    Article  MATH  MathSciNet  Google Scholar 

  7. Cicalese, F., Damaschke, P., Vaccaro, U.: Optimal group testing algorithms with interval queries and their application to splice site detection. In: Sunderam, V.S., van Albada, G.D., Sloot, P.M.A., Dongarra, J. (eds.) ICCS 2005. LNCS, vol. 3515, pp. 1029–1037. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  8. Du, D., Hwang, F.: Combinatorial group testing and its applications. Series on applied Mathematics, vol. 3 (1993)

    Google Scholar 

  9. Erdös, P., Rényi, A.: Asymmetric graphs. Acta Math. Acad. Sci. Hung. Acad. Sci. 14, 295–315 (1963)

    Article  MATH  Google Scholar 

  10. Grebinski, V.: On the power of additive combinatorial search model. In: Hsu, W.-L., Kao, M.-Y. (eds.) COCOON 1998. LNCS, vol. 1449, pp. 194–203. Springer, Heidelberg (1998)

    Chapter  Google Scholar 

  11. Grebinski, V., Kucherov, G.: Reconstructing a hamiltonian cycle by querying the graph: Application to DNA physical mapping. Discrete Applied Mathematics 88, 147–165 (1998)

    Article  MATH  MathSciNet  Google Scholar 

  12. Grebinski, V., Kucherov, G.: Reconstructing set partitions. In: Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1999, Baltimore, Maryland, January 17-19, pp. 915–916. ACM, SIAM, New York (1999)

    Google Scholar 

  13. Grebinski, V., Kucherov, G.: Optimal reconstruction of graphs under the additive model. Algorithmica 28, 104–124 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  14. Klau, G.W., Rahmann, S., Schliep, A., Vingron, M., Reinert, K.: Optimal robust non-unique probe selection using integer linear programming. Bioinformatics 20 (suppl. 1), i186–i193 (2004)

    Article  Google Scholar 

  15. Knill, E., Muthukrishnan, S.: Group testing problems in experimental molecular biology. Technical Report LAUR-95-1503, Los Alamos National Laboratory (March 1995)

    Google Scholar 

  16. Li, M., Vitányi, P.M.B.: Kolmogorov complexity arguments in combinatorics. J. Comb. Theory Series A 66(2), 226–236 (1994)

    Article  MATH  Google Scholar 

  17. Lindström, B.: On a combinatorial problem in number theory. Canad. Math. Bull. 8, 477–490 (1965)

    Article  MATH  MathSciNet  Google Scholar 

  18. Lindström, B.: Determination of two vectors from the sum. J. Comb. Theory 6, 402–407 (1969)

    Article  Google Scholar 

  19. Lindström, B.: On Möbius functions and a problem in combinatorial number theory. Canad. Math. Bull. 14(4), 513–516 (1971)

    Article  MATH  MathSciNet  Google Scholar 

  20. Lindström, B.: On b 2 sequences of vectors. Journal of Number Theory 4, 261–265 (1972)

    Article  MATH  MathSciNet  Google Scholar 

  21. Lindström, B.: Determining subsets by unramified experiments. In: Srivastava, J.N. (ed.) A Survey of Statistical Designs and Linear Models, pp. 407–418. North Holland, Amsterdam (1975)

    Google Scholar 

  22. Wilson, R.M.: Decomposition of complete graphs into subgraphs isomorphic to a given graph. In: Congressus Numerantium XV, pp. 647–659 (1975)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Département d’Informatique, Ecole Normale Supérieure de Cachan, 94235, France

    Mathilde Bouvel

  2. CompuGene Inc., Jamesburg, NJ, 08831, USA

    Vladimir Grebinski

  3. INRIA/LORIA, 615, rue du Jardin Botanique, B.P. 101, 54602, Villers-lès-Nancy, France

    Gregory Kucherov

Authors
  1. Mathilde Bouvel
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  2. Vladimir Grebinski
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  3. Gregory Kucherov
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Editor information

Editors and Affiliations

  1. LITA, Université Paul Verlaine-Metz, 57045, Metz Cedex 01, France

    Dieter Kratsch

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© 2005 Springer-Verlag Berlin Heidelberg

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Bouvel, M., Grebinski, V., Kucherov, G. (2005). Combinatorial Search on Graphs Motivated by Bioinformatics Applications: A Brief Survey. In: Kratsch, D. (eds) Graph-Theoretic Concepts in Computer Science. WG 2005. Lecture Notes in Computer Science, vol 3787. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11604686_2

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  • DOI: https://doi.org/10.1007/11604686_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-31000-6

  • Online ISBN: 978-3-540-31468-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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