Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SCARPA: scaffolding reads with practical algorithms

(2012) N. Donmez et al.   BIOINFORMATICS

Visualizing next-generation sequencing data with JBrowse

(2012) O. Westesson et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Chromosome evolution in Solanum traced by cross-species BAC-FISH

(2012) Dóra Szinay et al.   NEW PHYTOLOGIST

Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper

(2012) Sander A. Peters et al.   PLANT JOURNAL

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

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity

(2011) G. R. Rodriguez et al.   PLANT PHYSIOLOGY

Increase in Tomato Locule Number Is Controlled by Two Single-Nucleotide Polymorphisms Located Near WUSCHEL

(2011) S. Munos et al.   PLANT PHYSIOLOGY

SNP-Based Typing: A Useful Tool to Study Bordetella pertussis Populations

(2011) Marjolein van Gent et al.   PLoS One

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Structural Differences in Chromosomes Distinguish Species in the Tomato Clade

(2010) L.K. Anderson et al.   CYTOGENETIC AND GENOME RESEARCH

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

(2010) S-C Sim et al.   HEREDITY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

The 1001 Genomes Project for Arabidopsis thaliana

(2009) Detlef Weigel et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

ECOLOGICAL AND EVOLUTIONARY GENOMICS IN THE WILD TOMATOES (SOLANUM SECT. LYCOPERSICON)

(2008) Leonie C. Moyle   EVOLUTION

Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication

(2008) Bin Cong et al.   NATURE GENETICS