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Hidden Markov Modelling Techniques for Haplotype Analysis [chapter]

Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, Esko Ukkonen
2004 Lecture Notes in Computer Science  
A hidden Markov model is introduced for descriptive modelling the mosaic-like structures of haplotypes, due to iterated recombinations within a population.  ...  Possible applications of the models are delineated, and some preliminary analysis results on real sets of haplotypes are reported, demonstrating the potential of our methods.  ...  Introduction Hidden Markov models (HMMs) have become a standard tool in biological sequence analysis [8, 2] .  ... 
doi:10.1007/978-3-540-30215-5_4 fatcat:xitizfssebcz7j3dwma2rfonte

Constrained hidden Markov models for population-based haplotyping

Niels Landwehr, Taneli Mielikäinen, Lauri Eronen, Hannu Toivonen, Heikki Mannila
2007 BMC Bioinformatics  
We propose a novel approach for haplotype reconstruction based on constrained hidden Markov models.  ...  Conclusion: Relatively simple probabilistic approaches for haplotype reconstruction based on structured hidden Markov models are competitive with more complex, well-established techniques in this field  ...  Acknowledgements The authors would like to thank Luc De Raedt and Kristian Kersting for helpful discussions and comments. This work was supported by the European Union IST programme, contract no.  ... 
doi:10.1186/1471-2105-8-s2-s9 pmid:17493258 pmcid:PMC1892078 fatcat:tmnsxhyitjhc3nbotui7rglbjq

Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models [chapter]

Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou
2012 Lecture Notes in Computer Science  
ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations  ...  Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes.  ...  Do for helpful discussions. This material is based upon work supported by the National Science  ... 
doi:10.1007/978-3-642-29627-7_2 fatcat:xxzcpko4kfbxnellneihqmyxwq

A scalable pipeline for local ancestry inference using tens of thousands of reference haplotypes [article]

Eric Y Durand, Chuong B Do, Peter R Wilton, Joanna L Mountain, Adam Auton, G David Poznik, J Michael Macpherson
2021 bioRxiv   pre-print
In the second stage, an autoregressive pair hidden Markov model corrects phasing errors, smooths local ancestry estimates, and computes confidence scores.  ...  In this article, we describe Ancestry Composition, a modular pipeline for accurate and efficient ancestry deconvolution.  ...  Posterior probabilities for each window are estimated using the forward and backward algorithms for hidden Markov models.  ... 
doi:10.1101/2021.01.19.427308 fatcat:3osdgk66pjeg5nxe7bygr3o6aa

Whole-genome haplotyping approaches and genomic medicine

Gustavo Glusman, Hannah C Cox, Jared C Roach
2014 Genome Medicine  
These techniques can be further combined with genetic and population approaches.  ...  Haplotypes, which are more specific than less complex variants such as single nucleotide variants, also have applications in prognostics and diagnostics, in the analysis of tumors, and in typing tissue  ...  GG and JCR received support from and the National Institute of General Medical Sciences Center for Systems Biology (P50 GM076547). We thank the anonymous reviewers for their contributions.  ... 
doi:10.1186/s13073-014-0073-7 pmid:25473435 pmcid:PMC4254418 fatcat:3cwkvkr4k5bfba3cobsey4mphq

Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models

Jesse M. Rodriguez, Sivan Bercovici, Megan Elmore, Serafim Batzoglou
2013 Journal of Computational Biology  
ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations  ...  Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes.  ...  for the case of genotype-based analysis.  ... 
doi:10.1089/cmb.2012.0088 pmid:23421795 pmcid:PMC3590892 fatcat:v2zs5cl4urf6jg6hr3o6nodljq

Gene hunting with hidden Markov model knockoffs

M Sesia, C Sabatti, E J Candès
2018 Biometrika  
In this paper, we extend the methodology of knockoffs to problems where the distribution of the covariates can be described by a hidden Markov model.  ...  without relying on strong modelling assumptions.  ...  We thank Lucas Janson for inspiring discussions and for sharing his computer code.  ... 
doi:10.1093/biomet/asy033 pmid:30799875 pmcid:PMC6373422 fatcat:wicymyz7s5gofovrzfglbwc6uu

Systematic Review on Local Ancestor Inference From a Mathematical and Algorithmic Perspective

Jie Wu, Yangxiu Liu, Yiqiang Zhao
2021 Frontiers in Genetics  
HMM is combined with other statistical models and machine learning techniques for particular genetic tasks in a series of computer tools.  ...  The local ancestry inference (LAI) (also termed local ancestry deconvolution) method uses the hidden Markov model (HMM) to solve the mathematical problem of ancestry reconstruction based on genomic data  ...  MODELS BASED ON NON-HIDDEN MARKOV MODEL FAMILY Along with the HMM family models, there are also some other non-HMM family models that are based on the basic algorithm and data mining techniques.  ... 
doi:10.3389/fgene.2021.639877 pmid:34108987 pmcid:PMC8181461 fatcat:x7rtajsnxffvnnverxc4bci4oa

Robust Estimation of Local Genetic Ancestry in Admixed Populations Using a Nonparametric Bayesian Approach

K.-A. Sohn, Z. Ghahramani, E. P. Xing
2012 Genetics  
Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each  ...  We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population.  ...  This mosaic process could be modeled as a hidden Markov model in which the founders correspond to the hidden states, the individual haplotypes correspond to the observation sequences, the transition process  ... 
doi:10.1534/genetics.112.140228 pmid:22649082 pmcid:PMC3416008 fatcat:7torgl3wrrbwjmhqzeod2vxqza

Missing data imputation and haplotype phase inference for genome-wide association studies

Sharon R. Browning
2008 Human Genetics  
In this article, I review methods for haplotype inference and missing data imputation, and discuss their application to GWAS.  ...  I discuss common features of the best algorithms for haplotype phase inference and missing data imputation in largescale data sets, as well as some important differences between classes of methods, and  ...  Acknowledgments The author thanks Brian Browning for helpful discussions and the anonymous reviewers for their comments. This work was supported by NIH grant 3R01GM075091-02S1.  ... 
doi:10.1007/s00439-008-0568-7 pmid:18850115 pmcid:PMC2731769 fatcat:665vitbxszaubeu3f6mcod5zv4

Accurate construction of long range haplotype In unrelated individuals

Nicholas A Johnson, Stephanie J. London, Isabelle Romieu, Wing H. Wong, Hua Tang
2014 Statistica sinica  
In addition to inferring the most likely haplotypes, emphases produces confidence measures, allowing downstream analyses to account for the uncertainties associated with some haplotypes.  ...  Because haplotype cannot be experimentally assayed in diploid organisms in a high-throughput fashion, numerous statistical methods have been developed to reconstruct probable haplotype from genotype data  ...  Both programs employ Hidden Markov Models (HMM's), which can be computed efficiently via the EM algorithm and without lengthy MCMC runs.  ... 
doi:10.5705/ss.2012.141s fatcat:c22geyhycva2rmx553tcebexo4

A sequentially Markov conditional sampling distribution for structured populations with migration and recombination

Matthias Steinrücken, Joshua S. Paul, Yun S. Song
2013 Theoretical Population Biology  
Conditional sampling distributions (CSDs), sometimes referred to as copying models, underlie numerous practical tools in population genomic analyses.  ...  Recently, in the case of a single panmictic population, a sequentially Markov CSD has been developed as an accurate, efficient approximation to a principled CSD derived from the diffusion process dual  ...  Acknowledgments We thank John Kamm for many stimulating and fruitful discussions.  ... 
doi:10.1016/j.tpb.2012.08.004 pmid:23010245 pmcid:PMC3532580 fatcat:lkxw4ab6tzcmnmpsz2ut4iljpa

Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations

Andreas Recke, Klaus-Günther Recke, Saleh Ibrahim, Steffen Möller, Reinhard Vonthein
2015 Scientific Reports  
We developed a Bayesian hidden Markov model (HMM) approach that allows dissecting intrinsic properties and metastructures of the distribution of CNAVs within populations, in particular haplotype phases  ...  The order of events is introduced as a latent variable described by a specialized hidden Markov model (HMM) that is randomly walked according to transition probabilities, which are inferred from the data  ...  Acknowledgments We thank Miriam Freitag for performing MLPA experiments and Axel Künstner for fruitful discussions.  ... 
doi:10.1038/srep09066 pmid:25765626 pmcid:PMC4357990 fatcat:a5wxkjznbfewvficf7dpwbvequ

Haplotypes versus genotypes on pedigrees

Bonnie B Kirkpatrick
2011 Algorithms for Molecular Biology  
Two algorithms are introduced: an exponential-time hidden Markov model (HMM) for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all  ...  for certain coalescent models.  ...  I want to thank Richard Karp for reviewing a draft of the manuscript and the National Science Foundation for support through the Graduate Research Fellowship.  ... 
doi:10.1186/1748-7188-6-10 pmid:21504603 pmcid:PMC3102622 fatcat:msi5a4dpuzagjoeitptm7nnefm

Haplotypes versus Genotypes on Pedigrees [chapter]

Bonnie Kirkpatrick
2010 Lecture Notes in Computer Science  
Two algorithms are introduced: an exponential-time hidden Markov model (HMM) for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all  ...  for certain coalescent models.  ...  I want to thank Richard Karp for reviewing a draft of the manuscript and the National Science Foundation for support through the Graduate Research Fellowship.  ... 
doi:10.1007/978-3-642-15294-8_12 fatcat:3faokhlvufcfrdpya2d7nnivqa
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