Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

The rise of evo-devo: Pan-American Society for Evolutionary Developmental Biology sets the stage

(2016) C. D. Specht   AMERICAN JOURNAL OF BOTANY

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks

(2015) Shawn J. Cokus et al.   BMC GENOMICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

(2014) Jesse R. Lasky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

(2013) Kirk E. Lohmueller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

Imprints of Natural Selection Along Environmental Gradients in Phenology-Related Genes of Quercus petraea

(2013) F. J. Alberto et al.   GENETICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobataNée

(2013) Paul F. Gugger et al.   MOLECULAR ECOLOGY

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Mixed models can correct for population structure for genomic regions under selection

(2013) Jae Hoon Sul et al.   NATURE REVIEWS GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

(2013) V. L. Sork et al.   Tree Genetics & Genomes

All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs

(2013) Andrew J. Schork et al.   PLoS Genetics

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

(2012) Lucy W. Barrett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

(2012) JOAQUÍN ORTEGO et al.   MOLECULAR ECOLOGY

Characterizing genomic variation ofArabidopsis thaliana: the roles of geography and climate

(2012) JESSE R. LASKY et al.   MOLECULAR ECOLOGY

Genomics of Fagaceae

(2012) Antoine Kremer et al.   Tree Genetics & Genomes

Assessing the effects of climate change on the phenology of European temperate trees

(2011) Yann Vitasse et al.   AGRICULTURAL AND FOREST METEOROLOGY

Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity

(2011) N. A. Furlotte et al.   BIOINFORMATICS

Ecophysiological and transcriptomic responses of oak (Quercus robur) to long-term drought exposure and rewatering

(2011) Nadine Spieß et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Predicting species responses to climate change: demography and climate microrefugia in California valley oak (Quercus lobata)

(2011) BLAIR C. Mclaughlin et al.   GLOBAL CHANGE BIOLOGY

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

Spatial Genetic Structure of a Symbiotic Beetle-Fungal System: Toward Multi-Taxa Integrated Landscape Genetics

(2011) Patrick M. A. James et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

(2010) Angela Cánovas et al.   MAMMALIAN GENOME

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change

(2010) VICTORIA L. SORK et al.   MOLECULAR ECOLOGY

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)

(2010) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data

(2010) PIERRE LEGENDRE et al.   Molecular Ecology Resources

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Widespread, ecologically relevant genetic markers developed from association mapping of climate-related traits in Sitka spruce (Picea sitchensis)

(2010) Jason A. Holliday et al.   NEW PHYTOLOGIST

Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

(2009) J Derory et al.   HEREDITY

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS