Molecular tools and analytical approaches for the characterization of farm animal genetic diversity

Population studies of 17 equine STR for forensic and phylogenetic analysis

(2011) L. H. P. van de Goor et al.   ANIMAL GENETICS

Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and structure

(2011) Tulaya Limpiti et al.   BMC BIOINFORMATICS

Evaluation of approaches for identifying population informative markers from high density SNP Chips

(2011) Samantha Wilkinson et al.   BMC GENETICS

Genomic characteristics of cattle copy number variations

(2011) Yali Hou et al.   BMC GENOMICS

The development and characterization of a 60K SNP chip for chicken

(2011) Martien AM Groenen et al.   BMC GENOMICS

Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi

(2011) Ryouka Kawahara-Miki et al.   BMC GENOMICS

Immunogenetics as a tool in anthropological studies

(2011) Alicia Sanchez-Mazas et al.   IMMUNOLOGY

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Learning about human population history from ancient and modern genomes

(2011) Mark Stoneking et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation

(2011) Ceiridwen J. Edwards et al.   PLoS One

Tracing Cattle Breeds with Principal Components Analysis Ancestry Informative SNPs

(2011) Jamey Lewis et al.   PLoS One

High-Resolution Detection of Identity by Descent in Unrelated Individuals

(2010) Sharon R. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mitochondrial genetic variation in European, African and Indian cattle populations

(2010) R T Loftus et al.   ANIMAL GENETICS

Massive parallel sequencing in animal genetics: wherefroms and wheretos

(2010) M. Pérez-Enciso et al.   ANIMAL GENETICS

Genetic diversity in farm animals - a review

(2010) L. F. Groeneveld et al.   ANIMAL GENETICS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

Linkage disequilibrium reveals different demographic history in egg laying chickens

(2010) Saber Qanbari et al.   BMC GENETICS

Copy number variation in the bovine genome

(2010) João Fadista et al.   BMC GENOMICS

Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

(2010) Ozren Polašek et al.   BMC GENOMICS

An initial comparative map of copy number variations in the goat (Capra hircus) genome

(2010) Luca Fontanesi et al.   BMC GENOMICS

An initial map of chromosomal segmental copy number variations in the chicken

(2010) Xiaofei Wang et al.   BMC GENOMICS

Demographic History of Oceania Inferred from Genome-wide Data

(2010) Andreas Wollstein et al.   CURRENT BIOLOGY

The Archaeogenetics of Europe

(2010) Pedro Soares et al.   CURRENT BIOLOGY

Quality control and quality assurance in genotypic data for genome-wide association studies

(2010) Cathy C. Laurie et al.   GENETIC EPIDEMIOLOGY

Nuclear copies of mitochondrial genes: another problem for ancient DNA

(2010) Robert-Jan den Tex et al.   GENETICA

Population Structure With Localized Haplotype Clusters

(2010) S. R. Browning et al.   GENETICS

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

(2010) A. Stella et al.   GENETICS

A two-step method for detecting selection signatures using genetic markers

(2010) DANIEL GIANOLA et al.   Genetics Research

Population genetic inference from genomic sequence variation

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

A first comparative map of copy number variations in the sheep genome

(2010) L. Fontanesi et al.   GENOMICS

An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds

(2010) S Wilkinson et al.   HEREDITY

Comparison of Genetic Distance Measures Using Human SNP Genotype Data

(2010) Ondrej Libiger et al.   HUMAN BIOLOGY

The Diverse Applications of Cladistic Analysis of Molecular Evolution, with Special Reference to Nested Clade Analysis

(2010) Alan Templeton   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

(2010) C. Flury et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes

(2010) George E. Liu et al.   MAMMALIAN GENOME

Comparisons between mitochondrial genomes of domestic goat (Capra hircus) reveal the presence of numts and multiple sequencing errors

(2010) Alexandre Hassanin et al.   Mitochondrial DNA

Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts)

(2010) Sébastien Calvignac et al.   MITOCHONDRION

Ascertainment Biases in SNP Chips Affect Measures of Population Divergence

(2010) A. Albrechtsen et al.   MOLECULAR BIOLOGY AND EVOLUTION

In defence of model-based inference in phylogeography

(2010) MARK A. BEAUMONT et al.   MOLECULAR ECOLOGY

Calculations of population differentiation based on GST and D: forget GST but not all of statistics!

(2010) GABRIELE GERLACH et al.   MOLECULAR ECOLOGY

Spatial correlations at different spatial scales are themselves highly correlated in isolation by distance processes

(2010) BRYAN K. EPPERSON   Molecular Ecology Resources

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Array-Based Whole-Genome Survey of Dog Saliva DNA Yields High Quality SNP Data

(2010) Jennifer S. Yokoyama et al.   PLoS One

Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

(2010) Mathieu Gautier et al.   PLoS One

A Bayesian Outlier Criterion to Detect SNPs under Selection in Large Data Sets

(2010) Mathieu Gautier et al.   PLoS One

Ancestral Informative Marker Selection and Population Structure Visualization Using Sparse Laplacian Eigenfunctions

(2010) Jun Zhang   PLoS One

Origin and History of Mitochondrial DNA Lineages in Domestic Horses

(2010) Michael Cieslak et al.   PLoS One

Genomic Runs of Homozygosity Record Population History and Consanguinity

(2010) Mirna Kirin et al.   PLoS One

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

Evaluating Nested Clade Phylogeographic Analysis under Models of Restricted Gene Flow

(2010) Mahesh Panchal et al.   SYSTEMATIC BIOLOGY

The population genetic effects of ancestry and admixture in a subdivided cattle breed

(2009) T. C. Bray et al.   ANIMAL GENETICS

Genetic structure of a wide-spectrum chicken gene pool

(2009) Z. Granevitze et al.   ANIMAL GENETICS

Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification

(2009) M.-H. Li et al.   ANIMAL GENETICS

Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms

(2009) C. Ginja et al.   ANIMAL GENETICS

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

(2009) Ambra Giovannini et al.   BIOINFORMATICS

Correcting for ascertainment bias in the inference of population structure

(2009) Gilles Guillot et al.   BIOINFORMATICS

Iterative pruning PCA improves resolution of highly structured populations

(2009) Apichart Intarapanich et al.   BMC BIOINFORMATICS

Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits

(2009) William Barendse et al.   BMC GENOMICS

A whole genome Bayesian scan for adaptive genetic divergence in West African cattle

(2009) Mathieu Gautier et al.   BMC GENOMICS

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

(2009) Sean MacEachern et al.   BMC GENOMICS

European admixture on the Micronesian island of Kosrae: lessons from complete genetic information

(2009) Penelope E Bonnen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Methods for Human Demographic Inference Using Haplotype Patterns From Genomewide Single-Nucleotide Polymorphism Data

(2009) K. E. Lohmueller et al.   GENETICS

mStruct: Inference of Population Structure in Light of Both Genetic Admixing and Allele Mutations

(2009) S. Shringarpure et al.   GENETICS

Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture

(2009) V. C. Sousa et al.   GENETICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Genetic markers in the playground of multivariate analysis

(2009) T Jombart et al.   HEREDITY

Detecting natural selection by empirical comparison to random regions of the genome

(2009) Fuli Yu et al.   HUMAN MOLECULAR GENETICS

ABC: A useful Bayesian tool for the analysis of population data

(2009) J.S. Lopes et al.   INFECTION GENETICS AND EVOLUTION

Population studies of 16 bovine STR loci for forensic purposes

(2009) L. H. P. van de Goor et al.   INTERNATIONAL JOURNAL OF LEGAL MEDICINE

Tracing the History of Goat Pastoralism: New Clues from Mitochondrial and Y Chromosome DNA in North Africa

(2009) F. Pereira et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Spatial patterns of variation due to natural selection in humans

(2009) John Novembre et al.   NATURE REVIEWS GENETICS

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

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

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

(2009) James W. Kijas et al.   PLoS One

The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome

(2009) Alessandro Achilli et al.   PLoS One

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

A Validated Genome Wide Association Study to Breed Cattle Adapted to an Environment Altered by Climate Change

(2009) Ben J. Hayes et al.   PLoS One

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

(2009) Antonio M. Ramos et al.   PLoS One

The Genome Response to Artificial Selection: A Case Study in Dairy Cattle

(2009) Laurence Flori et al.   PLoS One

Laplacian Eigenfunctions Learn Population Structure

(2009) Jun Zhang et al.   PLoS One

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

(2009) David López Herráez et al.   PLoS One

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

(2009) J. E. Decker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coat Color Variation at the Beginning of Horse Domestication

(2009) A. Ludwig et al.   SCIENCE

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

(2009) et al.   SCIENCE

Revealing the History of Sheep Domestication Using Retrovirus Integrations

(2009) B. Chessa et al.   SCIENCE

Characterisation and monitoring of poultry genetic resources

(2009) M. TIXIER-BOICHARD et al.   WORLDS POULTRY SCIENCE JOURNAL

Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

(2009) Sebastian H Eck et al.   GENOME BIOLOGY

Divergence between Human Populations Estimated from Linkage Disequilibrium

(2008) John A. Sved et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy

(2008) Shuhua Xu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Runs of Homozygosity in European Populations

(2008) Ruth McQuillan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The origin of selection signatures on bovine chromosome 6

(2008) B. J. Hayes et al.   ANIMAL GENETICS

Comparison of information content for microsatellites and SNPs in poultry and cattle

(2008) G. C. B. Schopen et al.   ANIMAL GENETICS

Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle

(2008) A. Prasad et al.   ANIMAL GENETICS

A genome map of divergent artificial selection betweenBos taurusdairy cattle andBos taurusbeef cattle

(2008) B. J. Hayes et al.   ANIMAL GENETICS

Re-sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes

(2008) J. R. S. Meadows et al.   ANIMAL GENETICS

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

(2008) Jean-Marie Cornuet et al.   BIOINFORMATICS

Landscape Genetics

(2008) Rolf Holderegger et al.   BIOSCIENCE

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS

Mitochondrial genomes of extinct aurochs survive in domestic cattle

(2008) Alessandro Achilli et al.   CURRENT BIOLOGY

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig

(2008) A. J. Amaral et al.   GENETICS

Linkage Disequilibrium and Persistence of Phase in Holstein-Friesian, Jersey and Angus Cattle

(2008) A. P. W. de Roos et al.   GENETICS

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Whole population, genome-wide mapping of hidden relatedness

(2008) A. Gusev et al.   GENOME RESEARCH

How accurate is the current picture of human genetic variation?

(2008) I G Romero et al.   HEREDITY

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE

Y Chromosome Haplotype Analysis in Portuguese Cattle Breeds Using SNPs and STRs

(2008) Catarina Ginja et al.   JOURNAL OF HEREDITY

Molecular characterization of breeds and its use in conservation

(2008) Miguel A. Toro et al.   Livestock Science

Nested clade analysis: an extensively validated method for strong phylogeographic inference

(2008) ALAN R. TEMPLETON   MOLECULAR ECOLOGY

Revealing the hidden complexities of mtDNA inheritance

(2008) DANIEL JAMES WHITE et al.   MOLECULAR ECOLOGY

GSTand its relatives do not measure differentiation

(2008) LOU JOST   MOLECULAR ECOLOGY

ldne: a program for estimating effective population size from data on linkage disequilibrium

(2008) ROBIN S. WAPLES et al.   Molecular Ecology Resources

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Genotype, haplotype and copy-number variation in worldwide human populations

(2008) Mattias Jakobsson et al.   NATURE

Principal component analysis of genetic data

(2008) David Reich et al.   NATURE GENETICS

Interpreting principal component analyses of spatial population genetic variation

(2008) John Novembre et al.   NATURE GENETICS

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS

A Comparison of Phylogenetic Network Methods Using Computer Simulation

(2008) Steven M. Woolley et al.   PLoS One

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds

(2008) W. M. Muir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

(2008) S. Naderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use of linked loci as individuals or haplotypes for marker-assisted breed assignment

(2007) A. Stella et al.   ANIMAL GENETICS