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87
Learning in graphical models
, 2004
"... Statistical applications in fields such as bioinformatics, information retrieval, speech processing, image processing and communications often involve largescale models in which thousands or millions of random variables are linked in complex ways. Graphical models provide a general methodology for ..."
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Cited by 612 (11 self)
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Statistical applications in fields such as bioinformatics, information retrieval, speech processing, image processing and communications often involve largescale models in which thousands or millions of random variables are linked in complex ways. Graphical models provide a general methodology for approaching these problems, and indeed many of the models developed by researchers in these applied fields are instances of the general graphical model formalism. We review some of the basic ideas underlying graphical models, including the algorithmic ideas that allow graphical models to be deployed in largescale data analysis problems. We also present examples of graphical models in bioinformatics, errorcontrol coding and language processing. Key words and phrases: Probabilistic graphical models, junction tree algorithm, sumproduct algorithm, Markov chain Monte Carlo, variational inference, bioinformatics, errorcontrol coding.
Construction of genetic linkage map in man using restriction fragment length polymorphisom
 Am. J. Hum Genet
"... We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random singlecopy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of ..."
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Cited by 101 (1 self)
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We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random singlecopy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci. " Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.
Page segmentation and classification
 CVGIP: Graphical Models and Image Processing
, 1992
"... missense mutations of disease genes ..."
Graphical Models for Genetic Analyses
 STATISTTICAL SCIENCE
, 2003
"... This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas o ..."
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Cited by 28 (0 self)
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This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas of graphical models and genetics. The potential of graphical models is explored and illustrated through a number of example applications where the genetic element is substantial or dominating.
Blocking Gibbs Sampling for Linkage Analysis in Large Pedigrees with Many Loops
 AMERICAN JOURNAL OF HUMAN GENETICS
, 1996
"... We will apply the method of blocking Gibbs sampling to a problem of great importance and complexity  linkage analysis. Blocking Gibbs combines exact local computations with Gibbs sampling in a way that complements the strengths of both. The method is able to handle problems with very high complexi ..."
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Cited by 24 (2 self)
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We will apply the method of blocking Gibbs sampling to a problem of great importance and complexity  linkage analysis. Blocking Gibbs combines exact local computations with Gibbs sampling in a way that complements the strengths of both. The method is able to handle problems with very high complexity such as linkage analysis in large pedigrees with many loops; a task that no other known method is able to handle. New developments of the method are outlined, and it is applied to a highly complex linkage problem.
Rapid Multipoint Linkage Analysis of Recessive Traits in Nuclear Families, including Homozygosity Mapping
"... this paper allows very rapid multipoint likelihood calculation in nuclear families (with or without parental consanguinity), and the accompanying software package makes multipoint mapping feasible in many experimental contexts. 18 18 Acknowledgments We thank David Botstein and Michele Gschwend for ..."
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Cited by 18 (0 self)
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this paper allows very rapid multipoint likelihood calculation in nuclear families (with or without parental consanguinity), and the accompanying software package makes multipoint mapping feasible in many experimental contexts. 18 18 Acknowledgments We thank David Botstein and Michele Gschwend for many discussions concerning homozygosity mapping and for sharing unpublished data. We thank Daniel Kastner and his colleagues for sharing the pedigree and genotype data from their FMF studies. We thank Robert Elston, Michael Boehnke, Augustine Kong, and an anonymous referee for comments on the manuscript. This work was supported in part by a grant from the National Institutes of Health (HG00098) to E.S.L. 19 19 Appendix: Description of algorithm Consider a fixed map of M ordered marker loci with known recombination fractions q i between loci i and i+1. We wish to compute the likelihood for a given pedigree. Following Lander and Green (1987), the inheritance pattern at each locus i (i=1, 2, ..., M) can be described by an nbit vector v i . Each bit describes the outcome of one of the n meioses in the pedigree: the bit is 0 if the paternally derived allele is transmitted and 1 if the maternally derived allele is transmitted. The set of all possible nbit vectors will be identified with Z 2 ( )
Probability of carrying a mutation of breastovarian cancer gene BRCA1 based on family history
 J Natl Cancer Inst
, 1997
"... BRCA1 are rare, occurring in fewer than 1 % of women in the general population, and therefore account for a small proportion of cases of breast and ovarian cancers. Nevertheless, the presence of such mutations is highly predictive of the development of these cancers. Purpose: We developed and applie ..."
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Cited by 17 (5 self)
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BRCA1 are rare, occurring in fewer than 1 % of women in the general population, and therefore account for a small proportion of cases of breast and ovarian cancers. Nevertheless, the presence of such mutations is highly predictive of the development of these cancers. Purpose: We developed and applied a mathematic model for calculating the probability that a woman with a family history of breast and/or ovarian cancer carries a mutation of BRCA1. Methods and Results: As a basis for the model, we use Mendelian genetics and apply Bayes ’ theorem to information on the family history of these diseases. Of importance are the exact relationships of all family members, including both affected and unaffected members, and ages at diagnosis of the affected members and current ages of the unaffected members. We used available estimates of BRCA1 mutation frequencies in the general
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 2005;21:90
"... Running Tile: haplotype reconstruction in general pedigrees ..."
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Cited by 15 (0 self)
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Running Tile: haplotype reconstruction in general pedigrees
Estimation of conditional multilocus gene identity among relatives
 STATISTICS IN MOLECULAR BIOLOGY AND GENETICS: SELECTED PROCEEDINGS OF A 1997 JOINT AMSIMSSIAM SUMMER CONFERENCE ON STATISTICS IN MOLECULAR BIOLOGY', VOL. 33 OF IMS LECTURE NOTEMONOGRAPH SERIES, INSTITUTE OF MATHEMATICAL STATISTICS
, 1999
"... Genetic Analysis Workshop 10 identified five key factors contributing to the resolution of the genetic factors affecting complex traits. These include analysis with multipoint methods, use of extended pedigrees, and selective sampling of pedigrees. By sampling the affected individuals in an extended ..."
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Cited by 12 (2 self)
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Genetic Analysis Workshop 10 identified five key factors contributing to the resolution of the genetic factors affecting complex traits. These include analysis with multipoint methods, use of extended pedigrees, and selective sampling of pedigrees. By sampling the affected individuals in an extended pedigree, we obtain individuals who have an increased probability of sharing genes identical by descent (IBD) at marker loci that are linked to the trait locus or loci. Given marker data on specified members of a pedigree, the conditional IBD status among relatives can be assessed, but exact computation is often impractical for multiple linked markers on complex pedigrees. The use of Markov chain Monte Carlo (MCMC) methods greatly extends the range of models and data sets for which analysis is computationally feasible. Many forms of MCMC have now been implemented in the context of genetic analysis. Here we propose a new sampler, which takes as latent variables the segregation indicators at marker loci, and jointly updates all indicators corresponding to a given meiosis. The sampler has good mixing properties. Questions of irreducibility are also addressed.
Multilocus linkage analysis by blocked Gibbs sampling
 Statistics and Computing
, 2000
"... The problem of multilocus linkage analysis is expressed as a graphical model, making explicit a previously implicit connection, and recent developments in the field are described in this context. A novel application of blocked Gibbs sampling for Bayesian networks is developed to generate inheritance ..."
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Cited by 9 (0 self)
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The problem of multilocus linkage analysis is expressed as a graphical model, making explicit a previously implicit connection, and recent developments in the field are described in this context. A novel application of blocked Gibbs sampling for Bayesian networks is developed to generate inheritance matrices from an irreducible Markov chain. This is used as the basis for reconstruction of historical meiotic states and approximate calculation of the likelihood function for the location of an unmapped genetic trait. We believe this to be the only approach that currently makes fully informative multilocus linkage analysis possible on large extended pedigrees.