Abstract
One of the primary genetic events shaping an autosomal chromosome is recombination. This is a process that occurs during meiosis, in eukaryotes, that results in the offsprings having different combinations of (homologous) genes, or chromosomal segments, of the two parents. The presence of these recombination events in the evolutionary history of each chromosome complicates the genetic landscape of a population, and understanding the manifestations of these genetic exchanges in the chromosome sequences has been a subject of intense curiosity (see [Hud83, Gri99, HSW05] and citations therein).
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References
R Bürger. The mathematical theory of selection, recombination, and mutation. New York, Wiley, 2000.
T. H. Cormen, C. E. Leiserson, and R. L. Rivest. Introduction to Algorithms. The MIT Press, Cambridge, Massachusetts, 1990.
Joanna L. Davies, Frantiek Simank, Rune Lyngs, Thomas Mailund, and Jotun Hein. On recombination-induced multiple and simultaneous coalescent events. Genetics, 177:2151–2160, December 2007.
Erling Følner. On groups with full Banach mean value. Mathematica Scandinavica, 3: 243254, December 1955.
R. C. Griffiths and P. Marjoram. An ancestral recombinations graph. Progress in Population Genetics and Human Evolution (P Donnelly and S Tavare Eds) IMA vols in Mathematics and its Applications, 87:257–270, 1997.
R. C. Griffiths. The time to the ancestor along sequences with recombination. Theoretical Population Biology, 55(2):137–144, April 1999.
Stacey B. Gabriel, Stephen F. Schaffner, Huy Nguyen, Jamie M. Moore, Jessica Roy, Brendan Blumenstiel, John Higgins, Matthew DeFelice, Amy Lochner, Maura Faggart, Shau Neen Liu-Cordero, Charles Rotimi, Adebowale Adeyemo, Richard Cooper, Ryk Ward, Eric S. Lander, Mark J. Daly, and David Altshuler. The structure of haplotype blocks in the human genome. Science, 296(5576):2225 – 2229, 2002.
Dan Gusfield, Vikas Bansal, Vineet Bafna and Yun S. Song. A decomposition theory for phylogenetic networks and incompatible characters. Journal of Computational Biology, 14(10): 1247–1272, 2007.
Jotun Hein, Mikkel H. Schierup, and Carsten Wiuf. Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford Press, 2005.
R. R. Hudson. Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology, 23(2):183–201, April 1983.
R. R. Hudson. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology. Oxford University Press, Oxford, 1990.
M.A. Jobling, M. Hurles, and C. Tyler-Smith. Human Evolutionary Genetics: Origins, Peoples and Disease. Mathematical and Computaional Biology Series. Garland Publishing, 2004.
Motoo Kimura and James F. Crow. The number of alleles that can be maintained in a finite population. Genetics, 49(4):725–738, 1964.
Motoo Kimura. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics, 61(4):893–903, 1969.
J. F. C. Kingman. On the genealogy of large populations. Journal of Applied Probability, 19A:2743, 1982.
Marta Melé, Asif Javed, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit, Genographic Consortium. Recombination-based genomics: a genetic variation analysis in human populations. under submission, 2009.
Laxmi Parida. Pattern Discovery in Bioinformatics: Theory and Algorithms. Chapman Hall Press, 2007.
Laxmi Parida. Ancestral Recombinations Graph: A Reconstructability Perspective using Random-Graphs Framework. under submission, 2009.
Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit, Genographic Consortium. Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns. Journal of Computational Biology, 15(9):1–22, 2008.
Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit, Genographic Consortium. Minimizing recombinations in consensus networks for phylogeographic studies. BMC Bioinformatics, 10(1):S72, DOI = 10.1186/1471-2105-10-S1-S72, ISSN =1471-2105, 2009.
Stephen F. Schaffner, Catherine Foo, Stacey Gabriel, David Reich, Mark J. Daly and David Altshuler. Calibrating a coalescent simulation of human genome sequence variation. Genome Res., 15:1576-1583, 2005.
Mikkel H. Schierup and Jotun Hein. Consequences of recombination on traditional phylogenetic analysis. Genetics, 156:879–891, October 2000.
Mike Steel and Jotun Hein. Reconstructing pedigrees: A combinatorial perspective. Journal of Theoretical Biology, 240(3):360–367, 2006.
Carsten Wiuf and Jotun Hein. Recombination as a point process along sequences. Theoretical Population Biology, 55:248–259, 1999.
Carsten Wiuf and Jotun Hein. The ancestry of a sample of sequences subject to recombination. Genetics, 151:1217–1228, March 1999.
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Parida, L. (2010). Graph Model of Coalescence with Recombinations. In: Heath, L., Ramakrishnan, N. (eds) Problem Solving Handbook in Computational Biology and Bioinformatics. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-09760-2_5
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DOI: https://doi.org/10.1007/978-0-387-09760-2_5
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