(Q30661750)

9 October 2017

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation (English)

1 reference

9 October 2017

3

1 reference

9 October 2017

Filipe G Vieira

1

0 references

Matteo Fumagalli

object named as

Matteo Fumagalli

series ordinal

2

0 references

publication date

15 August 2013

1 reference

9 October 2017

1 reference

9 October 2017

23

1 reference

9 October 2017

11

1 reference

9 October 2017

1852-1861

1 reference

PMC publication ID

3814885

describes a project that uses

9 October 2017

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=3814885

cites work

Estimation of the outcrossing rate for annual Asian wild rice under field conditions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

ART: a next-generation sequencing read simulator.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Artificial selection for a green revolution gene during japonica rice domestication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Field guide to next-generation DNA sequencers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Genotype and SNP calling from next-generation sequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

A framework for variation discovery and genotyping using next-generation DNA sequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

A map of human genome variation from population-scale sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Design of association studies with pooled or un-pooled next-generation sequencing data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Exome sequencing identifies the cause of a mendelian disorder

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Genetics in geographically structured populations: defining, estimating and interpreting F(ST)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

The Sequence Alignment/Map format and SAMtools

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

SNP detection for massively parallel whole-genome resequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Population genomics of domestic and wild yeasts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Linkage disequilibrium and demographic history of wild and domestic canids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

A flexible forward simulator for populations subject to selection and demography

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Mapping short DNA sequencing reads and calling variants using mapping quality scores

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

The transcriptional landscape of the yeast genome defined by RNA sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Genetics and phylogenetics of rice domestication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Accounting for bias from sequencing error in population genetic estimates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

New insights into the history of rice domestication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Genome-wide patterns of nucleotide polymorphism in domesticated rice

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Linkage disequilibrium in a finite population that is partially selfing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Molecular signatures of natural selection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Estimation of the inbreeding coefficient through use of genomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3814885

Estimating human inbreeding coefficients: comparison of genealogical and marker heterozygosity approaches.

20 June 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

THE ESTIMATION OF GENE FREQUENCIES IN A RANDOM-MATING POPULATION

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Genetic architecture for the adaptive origin of annual wild rice, oryza nivara.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Maximum likelihood estimation of individual inbreeding coefficients and null allele frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

The dog genome: survey sequencing and comparative analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density.

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

On the Convergence Properties of the EM Algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1101%2FGR.157388.113

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23950147

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.157388.113

1 reference

9 October 2017

1 reference

PMC publication ID

3814885

9 October 2017

PubMed publication ID

23950147

1 reference

PMC publication ID

3814885