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

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

(2012) Phuong Dang Thai Phan et al.   BREEDING SCIENCE

Maximum likelihood estimation of individual inbreeding coefficients and null allele frequencies

(2012) NATHAN HALL et al.   Genetics Research

Domestication and geographic origin ofOryza sativain China: insights from multilocus analysis of nucleotide variation ofO. sativaandO. rufipogon

(2012) Xin Wei et al.   MOLECULAR ECOLOGY

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

(2012) PU HUANG et al.   MOLECULAR ECOLOGY

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

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

(2011) H. Li   BIOINFORMATICS

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

(2011) Su Kim et al.   BMC BIOINFORMATICS

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

(2011) I. Moltke et al.   GENOME RESEARCH

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Artificial selection for a green revolution gene during japonica rice domestication

(2011) K. Asano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

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

(2010) E. R. Martin et al.   BIOINFORMATICS

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

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

(2010) Yingrui Li et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

GENETIC ARCHITECTURE FOR THE ADAPTIVE ORIGIN OF ANNUAL WILD RICE,ORYZA NIVARA

(2009) Michael A. Grillo et al.   EVOLUTION

Linkage Disequilibrium and Demographic History of Wild and Domestic Canids

(2009) M. M. Gray et al.   GENETICS

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

(2009) Z. Tian et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)

(2009) Q. Xia et al.   SCIENCE

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

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

(2008) H. Li et al.   GENOME RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE