A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

(2012) Matthew Parks et al.   BMC EVOLUTIONARY BIOLOGY

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

(2012) Eleni Bachlava et al.   PLoS One

Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species

(2012) W. Walter Lorenz et al.   Tree Genetics & Genomes

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

(2011) Shiaoman Chao et al.   BMC GENOMICS

EuroPineDB: a high-coverage web database for maritime pine transcriptome

(2011) Noé Fernández-Pozo et al.   BMC GENOMICS

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

(2011) Prabin Bajgain et al.   BMC GENOMICS

Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids

(2011) Yu-Yun Hsiao et al.   BMC GENOMICS

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

(2011) John P Délano-Frier et al.   BMC GENOMICS

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

(2011) Maria D Logacheva et al.   BMC GENOMICS

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

A high-throughput apple SNP genotyping platform using the GoldenGate™ assay

(2011) M. Awais Khan et al.   GENE

The genomic evaluation system in the United States: Past, present, future

(2011) G.R. Wiggans et al.   JOURNAL OF DAIRY SCIENCE

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

(2011) M. F. R. Resende et al.   NEW PHYTOLOGIST

A comprehensive manually curated protein–protein interaction database for the Death Domain superfamily

(2011) Dongseop Kwon et al.   NUCLEIC ACIDS RESEARCH

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

Breeding without Breeding: Is a Complete Pedigree Necessary for Efficient Breeding?

(2011) Yousry A. El-Kassaby et al.   PLoS One

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

(2010) Heng Li et al.   BIOINFORMATICS

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

Genome-wide association and genomic selection in animal breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Ben Hayes et al.   GENOME

Female Reproductive Success Variation in a Pseudotsuga menziesii Seed Orchard as Revealed by Pedigree Reconstruction from a Bulk Seed Collection

(2010) Y. A. El-Kassaby et al.   JOURNAL OF HEREDITY

Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of ‘rear edge’ populations

(2010) Paul F. Gugger et al.   NEW PHYTOLOGIST

Association genetics of complex traits in plants

(2010) Pär K. Ingvarsson et al.   NEW PHYTOLOGIST

Differential responses of the promoters from nearly identical paralogs of loblolly pine (Pinus taeda L.) ACC oxidase to biotic and abiotic stresses in transgenic Arabidopsis thaliana

(2010) Shenghua Yuan et al.   PLANTA

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses

(2009) Michael S. Barker et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

(2009) Fiammetta Alagna et al.   BMC GENOMICS

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

(2009) Abdelali Barakat et al.   BMC PLANT BIOLOGY

Association Genetics of Coastal Douglas Fir ( Pseudotsuga menziesii var. menziesii , Pinaceae). I. Cold-Hardiness Related Traits

(2009) Andrew J. Eckert et al.   GENETICS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

annot8r: GO, EC and KEGG annotation of EST datasets

(2008) Ralf Schmid et al.   BMC BIOINFORMATICS

Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

(2008) Nathalie Pavy et al.   BMC GENOMICS

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

High-throughput genotyping with the GoldenGate assay in the complex genome of soybean

(2008) David L. Hyten et al.   THEORETICAL AND APPLIED GENETICS