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4,614 results

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Page 1
Bayesian Estimation of Population Size Changes by Sampling Tajima's Trees.
Palacios JA, Véber A, Cappello L, Wang Z, Wakeley J, Ramachandran S. Palacios JA, et al. Genetics. 2019 Nov;213(3):967-986. doi: 10.1534/genetics.119.302373. Epub 2019 Sep 11. Genetics. 2019. PMID: 31511299 Free PMC article.
The large state space of gene genealogies is a major hurdle for inference methods based on Kingman's coalescent. Here, we present a new Bayesian approach for inferring past population sizes, which relies on a lower-resolution coalescent process that we refer to as "Taji …
The large state space of gene genealogies is a major hurdle for inference methods based on Kingman's coalescent. Here, we present a n …
The population genetic test Tajima's D identifies genes encoding pathogen-associated molecular patterns and other virulence-related genes in Ralstonia solanacearum.
Eckshtain-Levi N, Weisberg AJ, Vinatzer BA. Eckshtain-Levi N, et al. Mol Plant Pathol. 2018 Sep;19(9):2187-2192. doi: 10.1111/mpp.12688. Epub 2018 May 23. Mol Plant Pathol. 2018. PMID: 29660239 Free PMC article.
Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to avoid recognition by plant PRRs. We calculated Tajima's D, a population genetic test statistic which identifies genes that do …
Therefore, we set out to identify additional R. solanacearum PAMPs based on the hypothesis that genes encoding PAMPs are under selection to …
Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation.
Thornton K. Thornton K. Genetics. 2005 Dec;171(4):2143-8. doi: 10.1534/genetics.105.043786. Epub 2005 Jul 5. Genetics. 2005. PMID: 15998723 Free PMC article.
I show that Tajima's D, a commonly used summary of the site-frequency spectrum for single-nucleotide polymorphism data, is a biased summary of the site-frequency spectrum. ...
I show that Tajima's D, a commonly used summary of the site-frequency spectrum for single-nucleotide polymorphism data, is a b …
Inferring epidemiological dynamics of infectious diseases using Tajima's D statistic on nucleotide sequences of pathogens.
Kim K, Omori R, Ito K. Kim K, et al. Epidemics. 2017 Dec;21:21-29. doi: 10.1016/j.epidem.2017.04.004. Epub 2017 May 1. Epidemics. 2017. PMID: 28552262 Free article.
Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D statistic on the nucleotide sequences of pathogens. To relate the time evolution of Tajima's D to the number of infected indivi …
Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D s …
An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties.
Zhang Q, Tyler-Smith C, Long Q. Zhang Q, et al. Stat Interface. 2015 Oct 1;8(4):447-456. doi: 10.4310/SII.2015.v8.n4.a4. Stat Interface. 2015. PMID: 26681995 Free PMC article.
In this work, we propose a modified neutrality test, Extended Tajima's D, which incorporates missing data and SNP-calling uncertainties. Because we do not specify any particular error-generating mechanism, this approach is robust and widely applicable. Simulations s …
In this work, we propose a modified neutrality test, Extended Tajima's D, which incorporates missing data and SNP-calling unce …
A non-zero variance of Tajima's estimator for two sequences even for infinitely many unlinked loci.
King L, Wakeley J, Carmi S. King L, et al. Theor Popul Biol. 2018 Jul;122:22-29. doi: 10.1016/j.tpb.2017.03.002. Epub 2017 Mar 21. Theor Popul Biol. 2018. PMID: 28341209
We show that for two sequences and n unlinked loci, the variance of Tajima's estimator (teta), which is the average number of pairwise differences, does not vanish even as n. ...
We show that for two sequences and n unlinked loci, the variance of Tajima's estimator (teta), which is the average number of …
Next-generation data filtering in the genomics era.
Hemstrom W, Grummer JA, Luikart G, Christie MR. Hemstrom W, et al. Nat Rev Genet. 2024 Nov;25(11):750-767. doi: 10.1038/s41576-024-00738-6. Epub 2024 Jun 14. Nat Rev Genet. 2024. PMID: 38877133 Review.
Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima's D value, population differentiation (F(ST)), nucleotide diversity (pi) and effective population size …
Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics stat …
Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review.
Kim K, Omori R, Ueno K, Iida S, Ito K. Kim K, et al. PLoS One. 2016 Jan 13;11(1):e0147021. doi: 10.1371/journal.pone.0147021. eCollection 2016. PLoS One. 2016. PMID: 26760775 Free PMC article. Review.
By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. ...The negative Tajima's D values in rapidly growing viral population were also observed in compu …
By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending …
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.
Korneliussen TS, Moltke I, Albrechtsen A, Nielsen R. Korneliussen TS, et al. BMC Bioinformatics. 2013 Oct 2;14:289. doi: 10.1186/1471-2105-14-289. BMC Bioinformatics. 2013. PMID: 24088262 Free PMC article.
BACKGROUND: A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Ne …
BACKGROUND: A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that a …
Distribution of long-range linkage disequilibrium and Tajima's D values in Scandinavian populations of Norway Spruce (Picea abies).
Larsson H, Källman T, Gyllenstrand N, Lascoux M. Larsson H, et al. G3 (Bethesda). 2013 May 20;3(5):795-806. doi: 10.1534/g3.112.005462. G3 (Bethesda). 2013. PMID: 23550126 Free PMC article.
As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in l …
As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that c …
4,614 results