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Bayesian haplo-type inference via the dirichlet process
2004
Twenty-first international conference on Machine learning - ICML '04
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In this paper we present a Bayesian approach to this problem based on a nonparametric prior known as the Dirichlet process. ...
The problem of inferring haplotypes from genotypes of single nucleotide polymorphisms (SNPs) is essential for the understanding of genetic variation within and among populations, with important applications ...
Conclusions We have proposed a Bayesian approach to the modeling of genotypes based on a Dirichlet process prior. ...
doi:10.1145/1015330.1015423
dblp:conf/icml/XingSJ04
fatcat:llsrwbqmijebffld4gndinmgz4
A survey of current software for haplotype phase inference
2004
Human Genomics
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The alternatives to haplotype inference are to resolve haplotypes completely, either by in vitro methods or by typing close pedigrees, which is expensive and is not guaranteed in pedigrees, or to ignore ...
haplotype-level analysis in favour of genotype-level analysis, which avoids the danger of treating inferred haplotypes as real but denies the researcher, potentially, any valuable analytic insights. ...
Lin and colleagues have also proposed a separate Bayesian algorithm with a Dirichlet prior. 12 The issue of what constitutes a good prior for a Bayesian model remains unresolved. 13 While the Dirichlet ...
doi:10.1186/1479-7364-1-2-141
pmid:15601542
pmcid:PMC3525072
fatcat:s5nzzwkarnd2dgafwfopmnnm4m
Empirical vs Bayesian approach for estimating haplotypes from genotypes of unrelated individuals
2007
BMC Genetics
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Conclusion: For large sample sizes (hundreds or more), which most association studies require, the two empirical methods might be used since they infer the haplotypes as accurately as any Bayesian methods ...
A key aspect of such development is the statistical inference of individual diplotypes from unphased genotypes. ...
Peter Donnelly for suggesting X-chromosome genotypes from the HapMap Project as the basis for comparison, and thank Mike Feolo for initial discussions on the need for comparing different methods. ...
doi:10.1186/1471-2156-8-2
pmid:17261196
pmcid:PMC1803795
fatcat:gzr7ez2asbe6tp7bhx5p6pxgha
A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
2003
American Journal of Human Genetics
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In this report, we compare and contrast three previously published Bayesian methods for inferring haplotypes from genotype data in a population sample. ...
We focus here on the problem of statistically inferring haplotypes from unphased genotype data for a sample of ("unrelated") individuals from a population. ...
Thus, the use of a Dirichlet prior can be thought of as making simple but highly unrealistic assumptions about the genetic processes underlying the evolution of the study population. ...
doi:10.1086/379378
pmid:14574645
pmcid:PMC1180495
fatcat:cdpjlyr7f5f6dnuxxvkqegnhmq
Quantifying the effects of drought on abrupt growth decreases of major tree species in Switzerland
2016
Ecology and Evolution
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into the six inferred clusters for the second modal value. ...
We set the Dirichlet parameter of the allele frequency model, the trend degree to 1.0, and the admixture and spatial interaction parameters to default values. ...
doi:10.1002/ece3.2146
pmid:28725350
pmcid:PMC5513292
fatcat:sxukxb5innbptmuwu2zk5otgua
Spatial genetic structure inBeta vulgarissubsp.maritimaandBeta macrocarpareveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes
2014
Ecology and Evolution
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into the six inferred clusters for the second modal value. ...
We set the Dirichlet parameter of the allele frequency model, the trend degree to 1.0, and the admixture and spatial interaction parameters to default values. ...
doi:10.1002/ece3.1061
pmid:24963380
pmcid:PMC4063479
fatcat:zy66ae6fuzfwzbei4q2hijtivi
Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation
2005
American Journal of Human Genetics
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For the autosomal data sets, our new approach clearly outperforms the best available methods, whereas its accuracy in inferring the X chromosome haplotypes is only slightly superior. ...
Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site. ...
As noted by Stephens and Donnelly (2003) , Bayesian approaches seem to have an advantage here, since the Bayesian framework provides a natural way of assessing uncertainty, via the conditional distribution ...
doi:10.1086/428594
pmid:15700229
pmcid:PMC1196397
fatcat:4xcykjtsmje5pbf5je6yejiq3q
Global invasion history of the tropical fire ant: a stowaway on the first global trade routes
2015
Molecular Ecology
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The genetic data document a corresponding spread of S. geminata from Mexico via Manila to Taiwan and from there, throughout the Old World. ...
However, human commerce had already become global by the mid-16th century when the Spanish connected the New World with Europe and Asia via their Manila galleon and West Indies trade routes. ...
Acknowledgements We thank the following scientists and institutions for generously contributing specimens: B ...
doi:10.1111/mec.13040
pmid:25496038
fatcat:7zbw6qn22fapfph5efullzlcpy
Discovering Patterns in Biological Sequences by Optimal Segmentation
[article]
2012
arXiv
pre-print
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We show how common tasks in these problems naturally correspond to inference procedures in the learned models. ...
Our approach involves discovering the hidden variables of a Bayesian network that interact with observed sequences so as to form a set of independent mixture models. ...
Inference of missing
B., Awadalla, P., Su, X., Samudrala, R., Jojic, N., & snps and information quantity measurements for haplo-
Smith, J. (2007). ...
arXiv:1206.5256v1
fatcat:r42zsoqi2nhzhhktqjueogwlw4
Detecting Selection from Linked Sites Using an F-Model
2020
Genetics
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component along the genome. ...
We finally evidence selection in the human genome by applying our method to data from the Human Genome Diversity Project (HGDP). ...
One42 solution is to split the problem by first inferring haplotypes for 43 each sample, and then performing selection scans on the haplo-44 type structure. ...
doi:10.1534/genetics.120.303780
pmid:33067324
pmcid:PMC7768260
fatcat:lfgmtge3n5ajtcjhnlh6slsauq
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
2006
American Journal of Human Genetics
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Although it is one of the slowest methods, PHASE (v2.1) was used to infer haplotypes for the 1 million-SNP HapMap data set. ...
Here, we describe the extension of five leading algorithms for phase inference for handling father-mother-child trios. ...
P.D. was supported by the Wellcome Trust, the National Institutes of Health (NIH), The SNP Consortium, the Wolfson Foundation, the Nuffield Trust, and the Engineering and Physical Sciences Research Council ...
doi:10.1086/500808
pmid:16465620
pmcid:PMC1380287
fatcat:hvop3j4jfnakxpeub6bpnqeefm
A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
2006
American Journal of Human Genetics
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The resulting model is also fast and, as a result, is practicable for large data sets (e.g., thousands of individuals typed at hundreds of thousands of markers). ...
We illustrate the utility of the model by applying it to dense single-nucleotide-polymorphism genotype data for the tasks of imputing missing genotypes and estimating haplotypic phase. ...
Geyer, for helpful discussions, and two anonymous referees, for comments on the submitted version. This research was supported by National Institutes of Health grant 1RO1HG/LM02585-01. ...
doi:10.1086/502802
pmid:16532393
pmcid:PMC1424677
fatcat:3djp2s4xpnao7ppjnqffjurhye
Haplotype Reconstruction for Diploid Populations
2005
Human Heredity
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The inference of haplotype pairs directly from unphased genotype data is a key step in the analysis of genetic variation in relation to disease and pharmacogenetically relevant traits. ...
Based on this criterion, the 'haplotype likelihood', we develop two kinds of estimators, the maximum haplotype-likelihood (MHL) estimator and its empirical Bayesian (EB) version. ...
Hudson Lab, http://home.uchicago.edu/ rhudson1/source.html (for the simulation of coalescent-processes).
Zhang /Vingron /Hoehe Hum Hered 2005;59:144-156 ...
doi:10.1159/000085938
pmid:15925893
fatcat:jbeyspey55b7jlziaxdyh52hvm
Evaluation of a Partial Genome Screening of Two Asthma Susceptibility Regions Using Bayesian Network Based Bayesian Multilevel Analysis of Relevance
2012
PLoS ONE
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This method uses Bayesian network representation to provide detailed characterization of the relevance of factors, such as joint significance, the type of dependency, and multi-target aspects. ...
The results were evaluated with traditional frequentist methods and we applied a new statistical method, called Bayesian network based Bayesian multilevel analysis of relevance (BN-BMLA). ...
Illustration of different dependency types between variables in a Bayesian Network structure. ...
doi:10.1371/journal.pone.0033573
pmid:22432035
pmcid:PMC3303848
fatcat:eu2jq4xxrbc3bnbt6rl3djw7um
Population genomics of wild and laboratory zebrafish (Danio rerio)
2011
Molecular Ecology
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The lab strains formed two additional groups that were genetically distinct from all wild populations. ...
Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). ...
We inferred a separate a for each population (a is the Dirichlet parameter for degree of admixture). ...
doi:10.1111/j.1365-294x.2011.05272.x
pmid:21923777
pmcid:PMC3627301
fatcat:aswn6sysg5bqpatxzing4vaucm
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