Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms

Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data

(2013) Helen Senn et al.   MOLECULAR ECOLOGY

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Marked Population Structure and Recent Migration in the Critically Endangered Sumatran Orangutan (Pongo abelii)

(2012) Alexander Nater et al.   JOURNAL OF HEREDITY

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

(2012) Martin G. Elferink et al.   PLoS One

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

(2012) Hoa T. Truong et al.   PLoS One

The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis

(2012) Rudy M. Jonker et al.   PLoS One

Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans

(2012) Reeta Sharma et al.   PLoS One

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

(2012) Reeta Sharma et al.   PLoS One

Extensive X-linked adaptive evolution in central chimpanzees

(2012) C. Hvilsom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

(2012) A. Auton et al.   SCIENCE

Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

(2011) Hindrik HD Kerstens et al.   BMC GENOMICS

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)

(2011) Robert HS Kraus et al.   BMC GENOMICS

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

(2011) A Esteve-Codina et al.   HEREDITY

Sex-Biased Dispersal and Volcanic Activities Shaped Phylogeographic Patterns of Extant Orangutans (genus: Pongo)

(2011) Alexander Nater et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

959 Nematode Genomes: a semantic wiki for coordinating sequencing projects

(2011) S. Kumar et al.   NUCLEIC ACIDS RESEARCH

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

(2011) Andreia J. Amaral et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

(2010) David L Hyten et al.   BMC GENOMICS

To Pool, or Not to Pool?

(2010) David J. Cutler et al.   GENETICS

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

(2010) S. Q. Le et al.   GENOME RESEARCH

A new strategy for genome assembly using short sequence reads and reduced representation libraries

(2010) A. L. Young et al.   GENOME RESEARCH

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Application of single nucleotide polymorphisms to non-model species: a technical review

(2010) M. R. GARVIN et al.   Molecular Ecology Resources

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Effects of Pleistocene glaciations and rivers on the population structure of Bornean orangutans (Pongo pygmaeus)

(2010) N. Arora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human and Non-Human Primate Genomes Share Hotspots of Positive Selection

(2010) David Enard et al.   PLoS Genetics

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome

(2009) Andreia J Amaral et al.   BMC GENOMICS

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

(2009) Cecilia Sánchez et al.   BMC GENOMICS

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

(2009) Hindrik HD Kerstens et al.   BMC GENOMICS

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

SNP discovery in swine by reduced representation and high throughput pyrosequencing

(2008) Ralph T Wiedmann et al.   BMC GENETICS

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics