@article {765,
	title = {Estimating and testing haplotype-trait associations in non-diploid populations.},
	journal = {J R Stat Soc Ser C Appl Stat},
	volume = {58},
	year = {2009},
	month = {2009 Dec},
	pages = {663-678},
	abstract = {Malaria is an infectious disease that is caused by a group of parasites of the genus Plasmodium. Characterizing the association between polymorphisms in the parasite genome and measured traits in an infected human host may provide insight into disease aetiology and ultimately inform new strategies for improved treatment and prevention. This, however, presents an analytic challenge since individuals are often multiply infected with a variable and unknown number of genetically diverse parasitic strains. In addition, data on the alignment of nucleotides on a single chromosome, which is commonly referred to as haplotypic phase, is not generally observed. An expectation-maximization algorithm for estimating and testing associations between haplotypes and quantitative traits has been described for diploid (human) populations. We extend this method to account for both the uncertainty in haplotypic phase and the variable and unknown number of infections in the malaria setting. Further extensions are described for the human immunodeficiency virus quasi-species setting. A simulation study is presented to characterize performance of the method. Application of this approach to data arising from a cross-sectional study of n=126 multiply infected children in Uganda reveals some interesting associations requiring further investigation.},
	issn = {0035-9254},
	doi = {10.1111/j.1467-9876.2009.00673.x},
	author = {Li, X and Thomas, B N and Rich, S M and Ecker, D and Tumwine, J K and Foulkes, A S}
}
@article {766,
	title = {Examining landscape factors influencing relative distribution of mosquito genera and frequency of virus infection.},
	journal = {Ecohealth},
	volume = {6},
	year = {2009},
	month = {2009 Jun},
	pages = {239-49},
	abstract = {Mosquito-borne infections cause some of the most debilitating human diseases, including yellow fever and malaria, yet we lack an understanding of how disease risk scales with human-driven habitat changes. We present an approach to study variation in mosquito distribution and concomitant viral infections on the landscape level. In a pilot study we analyzed mosquito distribution along a 10-km transect of a West African rainforest area, which included primary forest, secondary forest, plantations, and human settlements. Variation was observed in the abundance of Anopheles, Aedes, Culex, and Uranotaenia mosquitoes between the different habitat types. Screening of trapped mosquitoes from the different habitats led to the isolation of five uncharacterized viruses of the families Bunyaviridae, Coronaviridae, Flaviviridae, and Rhabdoviridae, as well as an unclassified virus. Polymerase chain reaction screening for these five viruses in individual mosquitoes indicated a trend toward infection with specific viruses in specific mosquito genera that differed by habitat. Based on these initial analyses, we believe that further work is indicated to investigate the impact of anthropogenic landscape changes on mosquito distribution and accompanying arbovirus infection.},
	keywords = {Africa, Western, Animals, Culicidae, Ecosystem, Humans, Insect Vectors, Polymerase Chain Reaction, Population Surveillance, RNA Viruses, Trees, Tropical Climate},
	issn = {1612-9210},
	doi = {10.1007/s10393-009-0260-y},
	author = {Junglen, S and Kurth, A and Kuehl, H and Quan, P-L and Ellerbrok, H and Pauli, G and Nitsche, A and Nunn, C and Rich, S M and Lipkin, W I and Briese, T and Leendertz, F H}
}
@article {787,
	title = {Extensive polymorphism in Cryptosporidium parvum identified by multilocus microsatellite analysis.},
	journal = {Appl Environ Microbiol},
	volume = {66},
	year = {2000},
	month = {2000 Aug},
	pages = {3344-9},
	abstract = {Restriction fragment length polymorphism and DNA sequence analysis discern two main types of Cryptosporidium parvum. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from C. parvum DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the C. parvum genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.},
	keywords = {Animals, Base Sequence, Cattle, Cryptosporidiosis, Cryptosporidium parvum, DNA, Protozoan, Humans, Karyotyping, Mice, Mice, Knockout, Microsatellite Repeats, Molecular Sequence Data, Polymerase Chain Reaction, Polymorphism, Genetic, Sequence Analysis, DNA},
	issn = {0099-2240},
	author = {Feng, X and Rich, S M and Akiyoshi, D and Tumwine, J K and Kekitiinwa, A and Nabukeera, N and Tzipori, S and Widmer, G}
}
@article {790,
	title = {Evolution of Plasmodium and the recent origin of the world populations of Plasmodium falciparum.},
	journal = {Parassitologia},
	volume = {41},
	year = {1999},
	month = {1999 Sep},
	pages = {55-68},
	abstract = {We have investigated the evolution of Plasmodium parasites by analyzing DNA sequences of several genes. We reach the following conclusions: (1) The four human parasites, P. falciparum, P. malariae, P. ovale, and P. vivax are very remotely related to each other, so that their evolutionary divergence predates the origin of the hominids; several of these parasites became associated with the human lineage by lateral transfer from other hosts. (2) P. falciparum diverged from P. reichenowi about 8 million years ago, consistently with the time of divergence of the human lineage from the apes; a parsimonious inference is that falciparum has been associated with humans since the origin of the hominids. (3) P. malariae is genetically indistinguishable from P. brasilianum, a parasite of New World monkeys; and, similarly. (4) P. vivax is genetically indistinguishable from the New World monkey parasite P. simium. We infer in each of these two cases a very recent lateral transfer between the human and monkey hosts, and explore alternative hypotheses about the direction of the transfer. We have also investigated the population structure of P. falciparum by analyzing 10 genes and conclude that the extant world populations of this parasite have evolved from a single strain within the last several thousand years. The extensive polymorphisms observed in the highly repetitive central region of the Csp gene, as well as the apparently very divergent two classes of alleles at the Msa-1 gene, are consistent with this conclusion.},
	keywords = {Amino Acid Sequence, Animals, Base Sequence, DNA, Protozoan, Evolution, Molecular, Hominidae, Humans, Merozoite Surface Protein 1, Molecular Sequence Data, Plasmodium, Plasmodium falciparum, Polymorphism, Genetic, Sequence Alignment},
	issn = {0048-2951},
	author = {Ayala, F J and Escalante, A A and Rich, S M}
}
