The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform
Dan Geiger - One of the best experts on this subject based on the ideXlab platform.
-
Optimizing exact Genetic Linkage computations.
Journal of Computational Biology, 2020Co-Authors: Maáyan Fishelson, Dan GeigerAbstract:: Genetic Linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the probability of data, which is needed for learning Linkage parameters, using exact computation procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper, we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of SUPERLINK, which is a fast Genetic Linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm and hence enlarge the class of problems that can be handled effectively by exact computations.
-
Genetic Linkage Analysis in the Presence of Germline Mosaicism
Statistical Applications in Genetics and Molecular Biology, 2011Co-Authors: Omer Weissbrod, Dan GeigerAbstract:Germline mosaicism is a Genetic condition in which some germ cells of an individual contain a mutation. This condition violates the assumptions underlying classic Genetic analysis and may lead to failure of such analysis. In this work we extend the statistical model used for Genetic Linkage analysis in order to incorporate germline mosaicism. We develop a likelihood ratio test for detecting whether a Genetic trait has been introduced into a pedigree by germline mosaicism. We analyze the statistical properties of this test and evaluate its performance via computer simulations. We demonstrate that Genetic Linkage analysis has high power to identify Linkage in the presence of germline mosaicism when our extended model is used. We further use this extended model to provide solid statistical evidence that the MDN syndrome studied by Genzer-Nir et al. has been introduced by germline mosaicism.
-
RECOMB - Optimizing exact Genetic Linkage computations
Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03, 2003Co-Authors: Maáyan Fishelson, Dan GeigerAbstract:Genetic Linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the likelihood of data, which is needed for learning Linkage parameters, using exact inference procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of superlink , which is currently the fastest Genetic Linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm, and hence enlarge the class of problems that can be handled effectively by exact computations.
-
exact Genetic Linkage computations for general pedigrees
Intelligent Systems in Molecular Biology, 2002Co-Authors: Maáyan Fishelson, Dan GeigerAbstract:Motivation: Genetic Linkage analysis is a useful statistical tool for mapping disease genes and for associating functionality of genes with their location on the chromosome. There is a need for a program that computes multipoint likelihood on general pedigrees with many markers that also deals with two-locus disease models. Results: In this paper we present algorithms for performing exact multipoint likelihood calculations on general pedigrees with a large number of highly polymorphic markers, taking into account a variety of disease models. We have implemented these algorithms in a new computer program called SUPERLINK which outperforms leading Linkage software with regards to functionality, speed, memory requirements and extensibility. Availability: SUPERLINK is available at http://bioinfo.cs.
Victor Degruttola - One of the best experts on this subject based on the ideXlab platform.
-
short communication viral Genetic Linkage analysis among black men who have sex with men hiv prevention trials network 061
AIDS Research and Human Retroviruses, 2019Co-Authors: Julia Kobe, Octavious Talbot, Iris Chen, Susan H Eshleman, Vanessa Cummings, Darrell P Wheeler, Kenneth H Mayer, Victor DegruttolaAbstract:: Analysis of viral Genetic Linkage can reveal generalized transmission patterns within a population. The HIV Prevention Trials Network 061 study evaluated HIV incidence among black men who have sex with men. HIV genotypes from 169 men who were HIV infected at enrollment and 23 men who seroconverted during the study were analyzed for Genetic Linkage. This analysis showed some associations of viral Linkage with income, study site, and timing of infection.
Maáyan Fishelson - One of the best experts on this subject based on the ideXlab platform.
-
Optimizing exact Genetic Linkage computations.
Journal of Computational Biology, 2020Co-Authors: Maáyan Fishelson, Dan GeigerAbstract:: Genetic Linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the probability of data, which is needed for learning Linkage parameters, using exact computation procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper, we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of SUPERLINK, which is a fast Genetic Linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm and hence enlarge the class of problems that can be handled effectively by exact computations.
-
RECOMB - Optimizing exact Genetic Linkage computations
Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03, 2003Co-Authors: Maáyan Fishelson, Dan GeigerAbstract:Genetic Linkage analysis is a challenging application which requires Bayesian networks consisting of thousands of vertices. Consequently, computing the likelihood of data, which is needed for learning Linkage parameters, using exact inference procedures calls for an extremely efficient implementation that carefully optimizes the order of conditioning and summation operations. In this paper we present the use of stochastic greedy algorithms for optimizing this order. Our algorithm has been incorporated into the newest version of superlink , which is currently the fastest Genetic Linkage program for exact likelihood computations in general pedigrees. We demonstrate an order of magnitude improvement in run times of likelihood computations using our new optimization algorithm, and hence enlarge the class of problems that can be handled effectively by exact computations.
-
exact Genetic Linkage computations for general pedigrees
Intelligent Systems in Molecular Biology, 2002Co-Authors: Maáyan Fishelson, Dan GeigerAbstract:Motivation: Genetic Linkage analysis is a useful statistical tool for mapping disease genes and for associating functionality of genes with their location on the chromosome. There is a need for a program that computes multipoint likelihood on general pedigrees with many markers that also deals with two-locus disease models. Results: In this paper we present algorithms for performing exact multipoint likelihood calculations on general pedigrees with a large number of highly polymorphic markers, taking into account a variety of disease models. We have implemented these algorithms in a new computer program called SUPERLINK which outperforms leading Linkage software with regards to functionality, speed, memory requirements and extensibility. Availability: SUPERLINK is available at http://bioinfo.cs.
Julia Kobe - One of the best experts on this subject based on the ideXlab platform.
-
short communication viral Genetic Linkage analysis among black men who have sex with men hiv prevention trials network 061
AIDS Research and Human Retroviruses, 2019Co-Authors: Julia Kobe, Octavious Talbot, Iris Chen, Susan H Eshleman, Vanessa Cummings, Darrell P Wheeler, Kenneth H Mayer, Victor DegruttolaAbstract:: Analysis of viral Genetic Linkage can reveal generalized transmission patterns within a population. The HIV Prevention Trials Network 061 study evaluated HIV incidence among black men who have sex with men. HIV genotypes from 169 men who were HIV infected at enrollment and 23 men who seroconverted during the study were analyzed for Genetic Linkage. This analysis showed some associations of viral Linkage with income, study site, and timing of infection.
Iris Chen - One of the best experts on this subject based on the ideXlab platform.
-
short communication viral Genetic Linkage analysis among black men who have sex with men hiv prevention trials network 061
AIDS Research and Human Retroviruses, 2019Co-Authors: Julia Kobe, Octavious Talbot, Iris Chen, Susan H Eshleman, Vanessa Cummings, Darrell P Wheeler, Kenneth H Mayer, Victor DegruttolaAbstract:: Analysis of viral Genetic Linkage can reveal generalized transmission patterns within a population. The HIV Prevention Trials Network 061 study evaluated HIV incidence among black men who have sex with men. HIV genotypes from 169 men who were HIV infected at enrollment and 23 men who seroconverted during the study were analyzed for Genetic Linkage. This analysis showed some associations of viral Linkage with income, study site, and timing of infection.
