Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera

(2015) Lisa S. Mathew et al.   G3-Genes Genomes Genetics

Genomics: A potential panacea for the perennial problem

(2014) Kendra A. McClure et al.   AMERICAN JOURNAL OF BOTANY

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Current perspectives and the future of domestication studies

(2014) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

(2013) Filipe G. Vieira et al.   GENOME RESEARCH

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

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

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

From forest to field: Perennial fruit crop domestication

(2011) Allison J. Miller et al.   AMERICAN JOURNAL OF BOTANY

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Beginnings and early history of date palm garden cultivation in the Middle East

(2011) M. Tengberg   JOURNAL OF ARID ENVIRONMENTS

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning

(2011) F. Bourgis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genetics of genomics-based crop improvement methods

(2011) Martha T. Hamblin et al.   TRENDS IN GENETICS

Plant use at an early Islamic merchant town in the West African Sahel: the archaeobotany of Essouk-Tadmakka (Mali)

(2011) Sam Nixon et al.   VEGETATION HISTORY AND ARCHAEOBOTANY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

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

(2010) A. McKenna et al.   GENOME RESEARCH

mlRho - a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes

(2010) BERNHARD HAUBOLD et al.   MOLECULAR ECOLOGY

The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)

(2010) Meng Yang et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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

Population Genomics of the Arabidopsis thaliana Flowering Time Gene Network

(2009) J. M. Flowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification, characterisation and application of single nucleotide polymorphisms for diversity assessment in cassava (Manihot esculenta Crantz)

(2009) Robert S. Kawuki et al.   MOLECULAR BREEDING

The nature of selection during plant domestication

(2009) Michael D. Purugganan et al.   NATURE

A Systematic Approach to Mapping Recessive Disease Genes in Individuals from Outbred Populations

(2009) Friedhelm Hildebrandt et al.   PLoS Genetics

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH