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

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Invasive hybridization in a threatened species is accelerated by climate change

(2014) Clint C. Muhlfeld et al.   Nature Climate Change

Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops

(2013) Hongjian Wan et al.   BMC GENOMICS

The Landscape of Nucleotide Polymorphism among 13,500 Genes of the Conifer Picea glauca, Relationships with Functions, and Comparison with Medicago truncatula

(2013) Nathalie Pavy et al.   Genome Biology and Evolution

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal 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

OakContigDF159.1, a reference library for studying differential gene expression inQuercus roburduring controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis

(2013) Mika T. Tarkka et al.   NEW PHYTOLOGIST

Pfam: the protein families database

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

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

(2013) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings

(2012) Thomas Müller et al.   BMC GENOMICS

Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

(2012) Georges St Laurent et al.   BMC GENOMICS

Comparative mapping in the Fagaceae and beyond with EST-SSRs

(2012) Catherine Bodénès et al.   BMC PLANT BIOLOGY

High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)

(2012) R. Gaur et al.   DNA RESEARCH

Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests

(2012) Elena Mosca et al.   Evolutionary Applications

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

(2012) Pablo Cingolani et al.   FLY

Detecting the footprints of divergent selection in oaks with linked markers

(2012) P G Goicoechea et al.   HEREDITY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

(2012) Gopala K. Subbaiyan et al.   PLANT BIOTECHNOLOGY JOURNAL

MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

(2012) G. Moissiard et al.   SCIENCE

Genomics of Fagaceae

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

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Molecular and morphological support for a Florida origin of the Cuban oak

(2011) Paul F. Gugger et al.   JOURNAL OF BIOGEOGRAPHY

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

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability

(2011) Petr Šmarda et al.   NEW PHYTOLOGIST

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

(2011) J. L. Strasburg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

(2011) A. Branca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

(2010) Saneyoshi Ueno et al.   BMC GENOMICS

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

(2010) Jérôme Durand et al.   BMC GENOMICS

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

(2010) Thomas L Parchman et al.   BMC GENOMICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2010) Angela Cánovas et al.   MAMMALIAN GENOME

Rapid spread of invasive genes into a threatened native species

(2010) Benjamin M. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular, morphological, and ecological niche differentiation of sympatric sister oak species, Quercus virginiana and Q. geminata (Fagaceae)

(2009) Jeannine Cavender-Bares et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks

(2009) I. S. Pearse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution

(2008) J. J. Cai   JOURNAL OF HEREDITY

The F-Box Gene Family Is Expanded in Herbaceous Annual Plants Relative to Woody Perennial Plants

(2008) X. Yang et al.   PLANT PHYSIOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics

Natural selection of protein structural and functional properties: a SNP perspective

(2008) Jinfeng Liu et al.   GENOME BIOLOGY