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Items: 1 to 20 of 100

1.

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation.

Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R.

Genome Res. 2013 Nov;23(11):1852-61. doi: 10.1101/gr.157388.113. Epub 2013 Aug 15.

2.

SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data.

Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J.

PLoS One. 2012;7(7):e37558. doi: 10.1371/journal.pone.0037558. Epub 2012 Jul 24.

3.
4.

Estimation of allele frequency and association mapping using next-generation sequencing data.

Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, Pedersen O, Wang J, Nielsen R.

BMC Bioinformatics. 2011 Jun 11;12:231. doi: 10.1186/1471-2105-12-231.

5.

Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium.

Kuk AY, Zhang H, Yang Y.

Bioinformatics. 2009 Feb 1;25(3):379-86. doi: 10.1093/bioinformatics/btn623. Epub 2008 Dec 2.

PMID:
19050036
7.

Maximum likelihood estimation of individual inbreeding coefficients and null allele frequencies.

Hall N, Mercer L, Phillips D, Shaw J, Anderson AD.

Genet Res (Camb). 2012 Jun;94(3):151-61. doi: 10.1017/S0016672312000341. Epub 2012 Jul 18.

PMID:
22805896
8.

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping.

Gautier M, Foucaud J, Gharbi K, Cézard T, Galan M, Loiseau A, Thomson M, Pudlo P, Kerdelhué C, Estoup A.

Mol Ecol. 2013 Jul;22(14):3766-79. doi: 10.1111/mec.12360. Epub 2013 Jun 4.

PMID:
23730833
9.

Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds.

Zhang Q, Calus MP, Guldbrandtsen B, Lund MS, Sahana G.

BMC Genet. 2015 Jul 22;16:88. doi: 10.1186/s12863-015-0227-7.

11.

A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes.

Wang C, Schroeder KB, Rosenberg NA.

Genetics. 2012 Oct;192(2):651-69. doi: 10.1534/genetics.112.139519. Epub 2012 Jul 30.

12.

Fast and accurate site frequency spectrum estimation from low coverage sequence data.

Han E, Sinsheimer JS, Novembre J.

Bioinformatics. 2015 Mar 1;31(5):720-7. doi: 10.1093/bioinformatics/btu725. Epub 2014 Oct 30.

13.

A novel approach to estimating heterozygosity from low-coverage genome sequence.

Bryc K, Patterson N, Reich D.

Genetics. 2013 Oct;195(2):553-61. doi: 10.1534/genetics.113.154500. Epub 2013 Aug 9.

14.

Genotype-Frequency Estimation from High-Throughput Sequencing Data.

Maruki T, Lynch M.

Genetics. 2015 Oct;201(2):473-86. doi: 10.1534/genetics.115.179077. Epub 2015 Jul 29.

15.

Estimating individual admixture proportions from next generation sequencing data.

Skotte L, Korneliussen TS, Albrechtsen A.

Genetics. 2013 Nov;195(3):693-702. doi: 10.1534/genetics.113.154138. Epub 2013 Sep 11.

16.

Simultaneous estimation of null alleles and inbreeding coefficients.

Chybicki IJ, Burczyk J.

J Hered. 2009 Jan-Feb;100(1):106-13. doi: 10.1093/jhered/esn088. Epub 2008 Oct 20.

PMID:
18936113
17.

Estimating selfing rates from reconstructed pedigrees using multilocus genotype data.

Wang J, El-Kassaby YA, Ritland K.

Mol Ecol. 2012 Jan;21(1):100-16. doi: 10.1111/j.1365-294X.2011.05373.x. Epub 2011 Nov 22.

PMID:
22106925
18.

Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm.

Lucas-Lledó JI, Vicente-Salvador D, Aguado C, Cáceres M.

BMC Bioinformatics. 2014 May 29;15:163. doi: 10.1186/1471-2105-15-163.

19.
20.

Comparing the van Oosterhout and Chybicki-Burczyk methods of estimating null allele frequencies for inbred populations.

Campagne P, Smouse PE, Varouchas G, Silvain JF, Leru B.

Mol Ecol Resour. 2012 Nov;12(6):975-82.

PMID:
23227485

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