Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

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

(2012) Pablo Cingolani et al.   FLY

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

(2012) A. Paschold et al.   GENOME RESEARCH

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

(2012) Sung-Chur Sim et al.   PLoS One

Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species

(2012) Jiaxin Xu et al.   THEORETICAL AND APPLIED GENETICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Sequencing crop genomes: approaches and applications

(2011) Scott A. Jackson et al.   NEW PHYTOLOGIST

SNP Discovery and Linkage Map Construction in Cultivated Tomato

(2010) K. Shirasawa et al.   DNA RESEARCH

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

An interspecific linkage map of SSR and intronic polymorphism markers in tomato

(2010) Kenta Shirasawa et al.   THEORETICAL AND APPLIED 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

A gene expression signature shared by human mature oocytes and embryonic stem cells

(2009) Said Assou et al.   BMC GENOMICS

A clarified position for solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae)

(2008) Nicolas Ranc et al.   BMC PLANT BIOLOGY