A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

Usefulness of Multiparental Populations of Maize ( Zea mays L.) for Genome-Based Prediction

(2014) Christina Lehermeier et al.   GENETICS

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

(2014) Shichen Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Design and Characterization of a 52K SNP Chip for Goats

(2014) Gwenola Tosser-Klopp et al.   PLoS One

Genome-based prediction of maize hybrid performance across genetic groups, testers, locations, and years

(2014) Theresa Albrecht et al.   THEORETICAL AND APPLIED GENETICS

Comparing a few SNP calling algorithms using low-coverage sequencing data

(2013) Xiaoqing Yu et al.   BMC BIOINFORMATICS

Development of a high density 600K SNP genotyping array for chicken

(2013) Andreas Kranis et al.   BMC GENOMICS

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

(2013) E. A. Thompson   GENETICS

A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

(2013) Haodong Chen et al.   Molecular Plant

Stable Carbon Isotope Discrimination Is under Genetic Control in the C4 Species Maize with Several Genomic Regions Influencing Trait Expression

(2013) S. Gresset et al.   PLANT PHYSIOLOGY

Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean

(2013) Qijian Song et al.   PLoS One

Linkage Analysis and QTL Mapping Using SNP Dosage Data in a Tetraploid Potato Mapping Population

(2013) Christine A. Hackett et al.   PLoS One

The Genomic Signature of Crop-Wild Introgression in Maize

(2013) Matthew B. Hufford et al.   PLoS Genetics

Intraspecific variation of recombination rate in maize

(2013) Eva Bauer et al.   GENOME BIOLOGY

synbreed: a framework for the analysis of genomic prediction data using R

(2012) Valentin Wimmer et al.   BIOINFORMATICS

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

(2012) John P Didion et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Maximizing the Reliability of Genomic Selection by Optimizing the Calibration Set of Reference Individuals: Comparison of Methods in Two Diverse Groups of Maize Inbreds (Zea mays L.)

(2012) R. Rincent et al.   GENETICS

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Historical genomics of North American maize

(2012) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs

(2012) Elisabetta Frascaroli et al.   THEORETICAL AND APPLIED GENETICS

The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation

(2012) Ben J. Hayes et al.   TRENDS IN GENETICS

A European perspective on maize history

(2011) Maud Irène Tenaillon et al.   COMPTES RENDUS BIOLOGIES

Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys

(2011) G. Rincon et al.   JOURNAL OF DAIRY SCIENCE

Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays

(2011) Anthony Becker et al.   PLoS One

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

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

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm

(2011) Delphine Van Inghelandt et al.   THEORETICAL AND APPLIED GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genetic signals of origin, spread, and introgression in a large sample of maize landraces

(2010) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making the most of ‘omics’ for crop breeding

(2010) Peter Langridge et al.   TRENDS IN BIOTECHNOLOGY

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genotyping Technologies for Genetic Research

(2009) Jiannis Ragoussis   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Geographical structure and differential natural selection among North European populations

(2009) B. P. McEvoy et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants

(2009) Sekar Kathiresan et al.   NATURE GENETICS

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

Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

(2009) Jianbing Yan et al.   PLoS One

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS