Literature DB >> 16983372

Modern computational approaches for analysing molecular genetic variation data.

Paul Marjoram1, Simon Tavaré.   

Abstract

An explosive growth is occurring in the quantity, quality and complexity of molecular variation data that are being collected. Historically, such data have been analysed by using model-based methods. Models are useful for sharpening intuition, for explanation and for prediction: they add to our understanding of how the data were formed, and they can provide quantitative answers to questions of interest. We outline some of these model-based approaches, including the coalescent, and discuss the applicability of the computational methods that are necessary given the highly complex nature of current and future data sets.

Mesh:

Year:  2006        PMID: 16983372     DOI: 10.1038/nrg1961

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  60 in total

Review 1.  Genetic structure in African populations: implications for human demographic history.

Authors:  C A Lambert; S A Tishkoff
Journal:  Cold Spring Harb Symp Quant Biol       Date:  2010-05-07

2.  Population divergence with or without admixture: selecting models using an ABC approach.

Authors:  V C Sousa; M A Beaumont; P Fernandes; M M Coelho; L Chikhi
Journal:  Heredity (Edinb)       Date:  2011-12-07       Impact factor: 3.821

3.  A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination.

Authors:  Joshua S Paul; Yun S Song
Journal:  Genetics       Date:  2010-06-30       Impact factor: 4.562

4.  The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta.

Authors:  Ryan J Haasl; Bret A Payseur
Journal:  Mol Biol Evol       Date:  2010-07-06       Impact factor: 16.240

Review 5.  Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Authors:  Khader Shameer; Lokesh P Tripathi; Krishna R Kalari; Joel T Dudley; Ramanathan Sowdhamini
Journal:  Brief Bioinform       Date:  2015-10-22       Impact factor: 11.622

6.  Sequential Monte Carlo without likelihoods.

Authors:  S A Sisson; Y Fan; Mark M Tanaka
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-30       Impact factor: 11.205

7.  Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood.

Authors:  Daniel Wegmann; Christoph Leuenberger; Laurent Excoffier
Journal:  Genetics       Date:  2009-06-08       Impact factor: 4.562

8.  Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data.

Authors:  Kirk E Lohmueller; Carlos D Bustamante; Andrew G Clark
Journal:  Genetics       Date:  2009-03-02       Impact factor: 4.562

Review 9.  Population genetic models of duplicated genes.

Authors:  Hideki Innan
Journal:  Genetica       Date:  2009-03-06       Impact factor: 1.082

Review 10.  Post-GWAS: where next? More samples, more SNPs or more biology?

Authors:  P Marjoram; A Zubair; S V Nuzhdin
Journal:  Heredity (Edinb)       Date:  2013-06-12       Impact factor: 3.821

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