Domestication selected for deceleration of the circadian clock in cultivated tomato

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

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

(2014) et al.   PLANT JOURNAL

Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice

(2014) He Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single locus confers tolerance to continuous light and allows substantial yield increase in tomato

(2014) Aaron I. Velez-Ramirez et al.   Nature Communications

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

(2013) D. H. Chitwood et al.   PLANT CELL

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

Wheels within wheels: the plant circadian system

(2013) Polly Yingshan Hsu et al.   TRENDS IN PLANT SCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

(2012) Jennifer Monson-Miller et al.   BMC GENOMICS

Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs

(2012) Chiara Campoli et al.   BMC PLANT BIOLOGY

Complexity in the Wiring and Regulation of Plant Circadian Networks

(2012) Dawn H. Nagel et al.   CURRENT BIOLOGY

The Role of a Pseudo-Response Regulator Gene in Life Cycle Adaptation and Domestication of Beet

(2012) Pierre A. Pin et al.   CURRENT BIOLOGY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato

(2012) Jose Blanca et al.   PLoS One

A conserved molecular basis for photoperiod adaptation in two temperate legumes

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

Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley

(2012) S. Zakhrabekova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons

(2012) S. Faure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium

(2011) RASHID H. KAZMI et al.   PLANT CELL AND ENVIRONMENT

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

(2011) Sergei A. Filichkin et al.   PLoS One

Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum

(2011) R. L. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plants under continuous light

(2011) Aaron I. Velez-Ramirez et al.   TRENDS IN PLANT SCIENCE

Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation

(2010) R. Yang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process

(2008) Marino Expósito-Rodríguez et al.   BMC PLANT BIOLOGY