Integer linear programs for discovering approximate gene clusters

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4175 LNBI, Issue , 2006, Pages 298-309

  Rahmann, Sven ^a,b   Klau, Gunnar W ^c,d  

^a BIELEFELD UNIVERSITY   (Germany)

^b International NRW Graduate School in Bioinformatics and Genome Research   (Germany)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d Deutsche Forschungsgemeinschaft   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATABASE SYSTEMS; GENES; INTEGER PROGRAMMING; LINEAR PROGRAMMING; OPTIMIZATION;

GENE CLUSTERS; INTEGER LINEAR PROGRAMS; MAX-GAP CLUSTERS; OPTIMAL ALGORITHMS;

GENETIC ENGINEERING;

EID: 33750244990     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11851561_28     Document Type: Conference Paper

References (10)

1. Snel, B., Bork, P., Huynen, M. A.: The identification of functional modules from the genomic association of genes. Proc. Nat'1 Acad. Sci. USA 99 (2002) 5890-5895
2. Hoberman, R., Durand, D.: The incompatible desiderata of gene cluster properties. In Proc. 3rd RECOMB Workshop on Comparative Genomics RECOMBCG'05. Volume 3678 of LNCS, Springer Verlaf (2005) 73-87
3. Wolsey, L.A.: Integer programming. Wiley Interscience Series in Discrete Mathematics and Optimization. John Wiley & Sons (1998)
4. Heber, S., Stoye, J.: Algorithms for finding gene clusters. In Proc. 1st Workshop on Algorithms in Bioinformatics WABI'01. Volume 2149 of LNCS, Springer Verlag (2001) 252-263
5. Schmidt, T., Stoye, J.: Quadratic time algorithms for finding common intervals in two and more sequences. In Proc. 15th Symp. on Combinatorial Pattern Matching CPM'04. Volume 3109 of LNCS, Springer Verlag (2004) 347-358
6. Bergeron, A., Corteel, S., Raffinot, M.: The algorithmic of gene teams. In Proc. 2nd Workshop on Algorithms in Bioinformatics WABI'02. Volume 2452 of LNCS, Springer Verlag (2002) 464-476
7. Li, Q., Lee, B.T.K., Zhang, L.: Genome-scale analysis of positional clustering of mouse testis-specific genes. BMC Genomics 6 (2005) 7
8. Durand, D., Sankoff, D.: Tests for gene clustering. J. Comput. Biol. 10 (2003) 453-482
9. Chauve, C., Diekmann, Y., Heber, S., Mixtacki, J., Rahmann, S., Stoye, J.: On common intervals with errors. Technical Report 2006-02, Abteilung Informationstechnik, Technische Fakultät, Universität Bielefeld (2006) ISSN 0946-7831.
10. ILOG, Inc.: CPLEX. http://www.ilog.com/products/cplex (1987-2006)