A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny

(2016) Davide Scaglione et al.   Scientific Reports

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation

(2015) Pablo F Cavagnaro et al.   BMC GENOMICS

Morphometrics of Daucus (Apiaceae): A counterpart to a phylogenomic study

(2014) Carlos Arbizu et al.   AMERICAN JOURNAL OF BOTANY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

New insights into domestication of carrot from root transcriptome analyses

(2014) Jun Rong et al.   BMC GENOMICS

Beyond repression of photomorphogenesis: role switching of COP/DET/FUS in light signaling

(2014) Xi Huang et al.   CURRENT OPINION IN PLANT BIOLOGY

Centromere reference models for human chromosomes X and Y satellite arrays

(2014) K. H. Miga et al.   GENOME RESEARCH

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

The 2-C-methylerythritol 4-phosphate pathway in melon is regulated by specialized isoforms for the first and last steps

(2014) Montserrat Saladié et al.   JOURNAL OF EXPERIMENTAL BOTANY

The dual role of phytoene synthase genes in carotenogenesis in carrot roots and leaves

(2014) Hui Wang et al.   MOLECULAR BREEDING

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

(2014) Y. Peng et al.   PLANT PHYSIOLOGY

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

(2014) Jeffrey C. Glaubitz et al.   PLoS One

Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae)

(2013) M. Iorizzo et al.   AMERICAN JOURNAL OF BOTANY

Biosynthesis of carotenoids in carrot: An underground story comes to light

(2013) Manuel Rodriguez-Concepcion et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool

(2013) Xinbin Dai et al.   BMC BIOINFORMATICS

TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats

(2013) Tomasz Gambin et al.   Evolutionary Bioinformatics

DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic

(2013) Alicja Macko-Podgorni et al.   GENETICA

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

(2013) Maria José Truco et al.   G3-Genes Genomes Genetics

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants

(2012) Walter Sanseverino et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Light-dependent changes in plastid differentiation influence carotenoid gene expression and accumulation in carrot roots

(2012) Paulina Fuentes et al.   PLANT MOLECULAR BIOLOGY

Epidemiology of vitamin A deficiency and xerophthalmia in at-risk populations

(2012) Justin C. Sherwin et al.   TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE

The photomorphogenic repressors COP1 and DET1: 20 years later

(2012) On Sun Lau et al.   TRENDS IN PLANT SCIENCE

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

(2011) Massimo Iorizzo et al.   BMC GENOMICS

Comparative FISH mapping of Daucus species (Apiaceae family)

(2011) Marina Iovene et al.   CHROMOSOME RESEARCH

Functional characterization of the three genes encoding 1-deoxy-D-xylulose 5-phosphate synthase in maize

(2011) E. Cordoba et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

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

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

Circoletto: visualizing sequence similarity with Circos

(2010) N. Darzentas   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Carrots of Many Colors Provide Basic Nutrition and Bioavailable Phytochemicals Acting as a Functional Food

(2010) Sara A. Arscott et al.   COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY

Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

(2010) Daniel Lang et al.   Genome Biology and Evolution

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

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals

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

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Major cytogenetic landmarks and karyotype analysis inDaucus carota and other Apiaceae

(2008) Marina Iovene et al.   AMERICAN JOURNAL OF BOTANY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Expression of carotenoid biosynthesis genes during carrot root development

(2008) J. Clotault et al.   JOURNAL OF EXPERIMENTAL BOTANY