@article {771,
	title = {An expectation maximization approach to estimate malaria haplotype frequencies in multiply infected children.},
	journal = {Stat Appl Genet Mol Biol},
	volume = {6},
	year = {2007},
	month = {2007},
	pages = {Article33},
	abstract = {Characterizing genetic variability in the human pathogenic Plasmodium species, the group of parasites that cause Malaria, may have broad global health implications. Specifically, discerning the combinations of mutations that lead to viable parasites and the population level frequencies of these clonal sequences will allow for targeted vaccine development and individualized treatment choices. This presents an analytical challenge, however, since haplotypic phase (i.e. the alignment of bases on a single DNA strand) is generally unobservable in multiply infected individuals. This manuscript describes an expectation maximization (EM) approach to maximum likelihood estimation of haplotype frequencies in this missing data setting. The approach is applied to a cohort of N=341 malaria infected children in Uganda, Cameroon and Sudan to characterize regional differences. A simulation study is also presented to characterize method performance and assess sensitivity to distributional assumptions.},
	keywords = {Animals, Child, Gene Frequency, Genotype, Humans, Likelihood Functions, Malaria, Malaria Vaccines, Mutation, Plasmodium},
	issn = {1544-6115},
	doi = {10.2202/1544-6115.1321},
	author = {Li, Xiaohong and Foulkes, Andrea S and Yucel, Recai M and Rich, Stephen M}
}
@article {782,
	title = {Experimental evidence for genetic recombination in the opportunistic pathogen Cryptosporidium parvum.},
	journal = {Mol Biochem Parasitol},
	volume = {119},
	year = {2002},
	month = {2002 Jan},
	pages = {55-62},
	abstract = {Cryptosporidium parvum is an intracellular protozoan parasite causing intestinal malabsorption and diarrhea in humans. The infection is usually self-limiting, although persistent cryptosporidosis is observed in immunocompromised and malnourished individuals. As with other Apicomplexa, the life cycle of Cryptosporidium is thought to comprise a sexual phase, during which a motile microgamont fuses with a sessile macrogamont. The four sporozoites found within each oocyst (the infectious form excreted in the feces) are thought to be the product of a meiotic division taking place immediately following fertilization, but the existence of a meiotic cycle in this genus has not been tested experimentally. To substantiate the occurrence of meiotic recombination in this species, we performed a genetic cross between two distinct isolates of C. parvum co-infected in INF-gamma knockout mice. We found that mixed infections produced recombinant progeny characterized by multilocus genotypes comprising alleles inherited from each parental line. This observation represents the first demonstration of sexual recombination in this pathogen. Together with the occurrence of genetically heterogeneous infections, this finding suggests that outcrossing between genotypes may occur in nature. Experimental crosses among Cryptosporidium populations will facilitate mapping of clinically relevant genes, the delineation of Cryptosporidium species, and defining the taxonomical status of C. parvum subtypes and host-specific genotypes.},
	keywords = {Animals, Conserved Sequence, Crosses, Genetic, Cryptosporidiosis, Cryptosporidium parvum, Deer, Female, Genotype, Humans, Male, Mice, Mice, Knockout, Microsatellite Repeats, Opportunistic Infections, Polymerase Chain Reaction, Recombination, Genetic, Survival Rate},
	issn = {0166-6851},
	author = {Feng, Xiaochuan and Rich, Stephen M and Tzipori, Saul and Widmer, Giovanni}
}
