Inferring the recent duplication history of a gene cluster

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

Volumn 5817 LNBI, Issue , 2009, Pages 111-125

  Song, Giltae ^a   Zhang, Louxin ^b   Vinař, Tomáš ^c   Miller, Webb ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c Physics and Informatics   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY HISTORY; EVOLUTIONARY INFORMATION; EXISTING METHOD; GENE CLUSTERS; GENOMIC REGIONS; HUMAN GENES; SEQUENCE DATA; SIMULATED DATA;

GENES;

EID: 78651248578     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04744-2_10     Document Type: Conference Paper

References (29)

1. Ohno, S.: Evolution by Gene Duplication. Springer, Berlin (1970)
2. Lynch,M., Conery, J.S.: The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155 (2000)
3. Force, A., et al.: Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545 (1999)
4. Lupski, J.R.: Genomic rearrangements and sporadic disease. Nat. Genet. 39(suppl. 7), 43-47 (2007)
5. Lander, E.S., et al.: Initial sequencing and analysis of the human genome. Nature 409(6822), 860-921 (2001)
6. Wong, K.K., et al.: A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80(1), 91-104 (2007)
7. Green, E.D.: Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2(8), 573 (2001)
8. Blanchette, M., et al.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4), 708-715 (2004)
9. Raphael, B., et al.: A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 14(11), 2336 (2004)
10. Margulies, E., et al.: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6), 760-764 (2007)
11. Hou, M.: unpublished data (2007)
12. Miller, W., et al.: 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. 17, 1797-1808 (2007)
13. Elemento, et al.: Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol. 19(3), 278 (2002)
14. Zhang, L., et al.: Greedy method for inferring tandem duplication history. Bioinformatics 19, 1497-1504 (2003)
15. Sammeth, M., Stoye, J.: Comparing tandem repeats with duplications and excisions of variable degree. TCBB 3, 395-407 (2006)
16. Bertrand, D., Lajoie, M., El-Mabrouk, N., Gascuel, O.: Evolution of tandemly repeated sequences through duplication and Inversion. In: Bourque, G., El-Mabrouk, N. (eds.) RECOMB-CG 2006. LNCS (LNBI), vol. 4205, pp. 129-140. Springer, Heidelberg (2006)
17. Ma, J., et al.: The infinite sites model of genome evolution. PNAS 105(38), 14254-14261 (2008)
18. Jiang, Z., et al.: Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat. Genet. 39(11), 1361-1368 (2007)
19. Zhang, Y., et al.: Reconstructing the evolutionary history of complex human gene clusters. In: Vingron, M.,Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 29-49. Springer, Heidelberg (2008)
20. Zhang, Y., et al.: Simultaneous history reconstruction for complex gene clusters in multiple species. In: Pacific Symposium on Biocomputing 2009, pp. 162-173 (2009)
21. Schwartz, S., et al.: Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103-107 (2003)
22. Nadeau, J.H., Taylor, B.A.: Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA 81(3), 814-818 (1984)
23. Nakayama, J., et al.: Linkage of human narcolepsy with HLA association to chromosome 4p13-q21. Genomics 65, 84-86 (2000)
24. Sollid, L., et al.: Evidence for a primary association of celiac disease to a particular HLA-DQ α/ β heterodimer. J. Exp. Med. 169, 345-350 (2000)
25. Haque, A., et al.: HLA class II protein expression in prostate cancer cells. Journal of Immunology 178, 48.22 (2007)
26. Chaudhuri, S., et al.: Genetic susceptibility to breast cancer: HLA DQB*03032 and HLA DRB1*11 may represent protective alleles. PNAS 97, 11451-11454 (2000)
27. Penning, T., et al.: Aldo-keto reductase (AKR) 1C3: Role in prostate disease and the development of specific inhibitors. Mol. Cell. Endocrinol. 248, 182-191 (2006)
28. Crofts, F., et al.: Functional significance of different human CYP1A1 genotypes. Carcinogenesis 15, 2961-2963 (1994)
29. Sato, M., et al.: Genetic polymorphism of drug-metabolizing enzymes and susceptibility to oral cancer. Carcinogenesis 20, 1927-1931 (1999)