Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico

Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora

(2014) Thierry Leroy et al.   GENETICA

Estimating genotype error rates from high-coverage next-generation sequence data

(2014) Jeffrey D. Wall et al.   GENOME RESEARCH

The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes

(2014) James D. Stone et al.   MOLECULAR GENETICS AND GENOMICS

Molecular genetic characterization of Central European soybean breeding germplasm

(2014) Volker Hahn et al.   PLANT BREEDING

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil

(2014) Flávio de França Souza et al.   Crop Breeding and Applied Biotechnology

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

An initial assessment of linkage disequilibrium (LD) in coffee trees: LD patterns in groups of Coffea canephora Pierre using microsatellite analysis

(2013) Philippe Cubry et al.   BMC GENOMICS

Development of DArT Marker Platforms and Genetic Diversity Assessment of the U.S. Collection of the New Oilseed Crop Lesquerella and Related Species

(2013) Von Mark V. Cruz et al.   PLoS One

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

(2012) X. Zheng et al.   BIOINFORMATICS

Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects

(2012) Philippe Cubry et al.   GENETIC RESOURCES AND CROP EVOLUTION

Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal

(2012) J. I. HOFFMAN et al.   Molecular Ecology Resources

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Growing coffee: Psilanthus (Rubiaceae) subsumed on the basis of molecular and morphological data; implications for the size, morphology, distribution and evolutionary history of Coffea

(2011) AARON P. DAVIS et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)

(2011) Qingyi Yu et al.   PLANT JOURNAL

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

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

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda

(2009) P. Musoli et al.   GENOME

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

Diversity in coffee assessed with SSR markers: structure of the genus Coffea and perspectives for breeding

(2008) Philippe Cubry et al.   GENOME

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One