Haplotypes histories as pathways of recombinations

Bioinformatics

Volumn 20, Issue 12, 2004, Pages 1836-1841

  El Mabrouk, Nadia ^a   Labuda, Damian ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF MONTREAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DYSTROPHIN;

ALLELE; ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; CROSSING OVER; FREQUENCY ANALYSIS; GENETIC ALGORITHM; GENETIC CODE; GENETIC RECOMBINATION; HAPLOTYPE; HISTORY; HUMAN; PLESIOMORPHY; POPULATION GENETICS; PRIORITY JOURNAL; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 4444289125     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth148     Document Type: Article

References (23)

1. Andolfatto,P. and Nordborg,M. (1998) The effect of gene conversion on intralocus associations. Genetics, 148, l397-1399.
2. Di Rienzo,A. and Wilson,A. (1991) Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc. Natl Acad. Sci., USA, 88, 1597-601.
3. Fullerton,S., Clark,A., Weiss,K., Nickerson,D., Taylor,S., Stengard,J., Salomaa,V., Vartiainen,E., Perola,M., Boerwinkle,E. and Sing,C. (2000) Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. Ann. J. Hum. Genet., 67, 881-900.
4. Gonser,R., Donnelly,P., Nicholson,G. and Di Rienzo,A. (2000) Microsatellite mutations and inferences about human demography. Genetics, 154, 1793-1807.
5. Griffiths,R. and Marjoram,P. (1996) Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol., 3, 479-502.
6. Harding,R., Fullerton,S., Griffiths,R., Bond,J., Cox,M., Schneider,J., Moulin,D. and Clegg,J., (1997) Archaic African and Asian lineages in the genetic ancestry of modern humans. Ann. J. Hum. Genet., 60, 772-789.
7. Hein,J. (1990) Reconstructing the evolution of sequences subject to recombination using parsimony. Math. Biosci., 98, 185-200.
8. Hein,J. (1993) A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol., 36, 396-405.
9. Heyer,E., Zietkiewicz,E., Rochowski,A., Yotova,V., Puymirat,J. and Labuda,D. (2001) Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. Am. J. Hum. Genet., 69, 1113-1126.
10. Hudson,R. and Kaplan,N. (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111, 147-164.
11. Jaruzelska,J., Zietkiewicz,E., Batzer,M., Cole,D., Moisan,J., Scozzari,R., Tavaré,S. and Labuda,D. (1999) Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy. Genetics, 152, 1091-1101.
12. Kaessmann,H., Heissig,F., Von Haeseler,A. and Paabo,S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet., 22, 78-81.
13. Kececioglu,J. and Gusfield,D. (1998) Reconstructing a history of recombinations from a set of sequences. Discrete Appl. Math., 88, 239-260.
14. Labuda,D., Zietkiewicz,E. and Yotova,V. (2000) Archaic lineages in the history of modern humans. Genetics, 156, 799-808.
15. Myers,S. and Griffiths,R. (2002) Bounds on the minimum number of recombination in a sample history. Genetics, 163, 375-394.
16. Przeworski,M. and Wall,J. (2001) Why is there so little intragenic linkage disequilibrium in humans? Genet. Res., 77, 143-151.
17. Rogers,A. and Harpending,H. (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol., 9, 552-569.
18. Ukkonen,E. (2002) Finding founder sequences from a set of recombinants. 2nd International Workshop, Algorithms in Bioinformatics (WABI), LNCS, Vol. 2452. Springer, pp. 277-286.
19. Wang,L., Zhang,K. and Zhang,L. (2001) Perfect phylogenetic networks with recombination. J. Comput. Biol., 8, 69-78.
20. Wiuf,C. and Hein,J. (1999a) The ancestry of a sample of sequences subject to recombination. Genetics, 151, 1217-1228.
21. Wiuf,C. and Hein,J. (1999b) Recombination as a point process along sequences. Theor. Popul. Biol., 55, 248-259.
22. Wu,S. and Gu,X. (2001) A greedy algorithm for optimal recombination. In COCOON, LNCS, 2108, Springer-Verlag, Berlin, 86-90.
23. Zietkiewicz,E., Yotova,V., Gehl,D., Wambach,T., Arrieta,I., Batzer,M., Cole,D., Hechtman,P., Kaplan,F., Modiano,D., Moisan,J., Michalski,R. and Labuda,D. (2003) Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human's diversity. Ann. J. Hum. Genet., 73, 994-1015.