Lipari School on BioInformatics and Computational Biology
Jacob T. Schwartz International School for Scientific ResearchFilippo Utro, Computational Genomics, T. J. Watson Research Center, Yorktown Heights, NY USA
Ancestral Recombination Graph: Theory and Applications
In this tutorial we present the basic concepts of Ancestral Recombination Graph (ARG), which describes the
history of mutations and recombinations giving rise to chromosomes.
The ARG plays a key role in population studies since it is used both for modeling population evolution and
in the reconstruction of the evolution history from the haplotypes of extant samples.
We then present some computational methods to the ARG construction and its application in population
studies. Finally, we focus on one of the most fundamental questions in combinatorial structure: "Is it
possible to identify a substructure that really matters to the extant units?"
References
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Griffiths, R.C., and Marjoram, P., 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.
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Parida, L., Ancestral Recombinations Graph: A Reconstructability Perspective using Random-Graphs Framework, Journal of Computational Biology, vol 17, No 10, pp 1345--1370, 2010
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Parida, L., Palamara, P.F., and Javed, A., A Minimal Descriptor of an Ancestral Recombinations Graph, BMC Bioinformatics, APBC, Inchon, Korea, 2011
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Javed, A., Pybus, M., Melè, M., Utro, F., Bertranpetit, J., Calafell, F., and Parida, L., IRiS: Construction of ARG network at genomic scales, Bioinformatics, 2011
- Javed, A., Melè, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M., Balanovsky, O., Balanovska, E., Jin, L., Yang, Y., Arunkumar G., Pitchappan, R.M., Bertranpetit, J., Calafell, F., Parida, L., and The Genographic Consortium, Recombination networks as genetic markers: a human variation study of the Old World, Human Genetics, 2011