The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Proteomic analysis of copper-binding proteins in excess copper-stressed rice roots by immobilized metal affinity chromatography and two-dimensional electrophoresis

(2014) Yufeng Song et al.   BIOMETALS

Molecular cloning and functional characterization of a novel cotton CBL-interacting protein kinase gene (GhCIPK6) reveals its involvement in multiple abiotic stress tolerance in transgenic plants

(2013) Liangrong He et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Integrated transcriptomics and metabolomics decipher differences in the resistance of pedunculate oak to the herbivore Tortrix viridana L.

(2013) Birgit Kersten et al.   BMC GENOMICS

Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing

(2013) Saneyoshi Ueno et al.   BMC GENOMICS

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

Oak genomics takes off … and enters the ecological genomics era

(2013) Christophe Plomion et al.   NEW PHYTOLOGIST

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

De novoassembly of maritime pine transcriptome: implications for forest breeding and biotechnology

(2013) Javier Canales et al.   PLANT BIOTECHNOLOGY JOURNAL

Differential Transcriptional Profiles of Dormancy-Related Genes in Apple Buds

(2013) Vítor da Silveira Falavigna et al.   PLANT MOLECULAR BIOLOGY REPORTER

ParSOC1, a MADS-box gene closely related to Arabidopsis AGL20/SOC1, is expressed in apricot leaves in a diurnal manner and is linked with chilling requirements for dormancy break

(2013) Taly Trainin et al.   Tree Genetics & Genomes

RNA-Seq: revelation of the messengers

(2013) Marcel C. Van Verk et al.   TRENDS IN PLANT SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

Comparative mapping in the Fagaceae and beyond with EST-SSRs

(2012) Catherine Bodénès et al.   BMC PLANT BIOLOGY

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

(2012) Jérôme Salse   CURRENT OPINION IN PLANT BIOLOGY

Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense)

(2012) James V. Anderson et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Detecting the footprints of divergent selection in oaks with linked markers

(2012) P G Goicoechea et al.   HEREDITY

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

Whole-genome sequence of Schistosoma haematobium

(2012) Neil D Young et al.   NATURE GENETICS

Changes in the C/N balance caused by increasing external ammonium concentrations are driven by carbon and energy availabilities during ammonium nutrition in pea plants: the key roles of asparagine synthetase and anaplerotic enzymes

(2012) Idoia Ariz et al.   PHYSIOLOGIA PLANTARUM

Transcriptional programs regulating seed dormancy and its release by after-ripening in common wheat (Triticum aestivum L.)

(2012) Feng Gao et al.   PLANT BIOTECHNOLOGY JOURNAL

AUX/LAX Genes Encode a Family of Auxin Influx Transporters That Perform Distinct Functions during Arabidopsis Development

(2012) B. Peret et al.   PLANT CELL

Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq

(2012) A. Kakumanu et al.   PLANT PHYSIOLOGY

Genomics of Fagaceae

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

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

(2011) Patricia Faivre Rampant et al.   BMC GENOMICS

Bax inhibitor-1: a highly conserved endoplasmic reticulum-resident cell death suppressor

(2011) T Ishikawa et al.   CELL DEATH AND DIFFERENTIATION

HSG1, a grape Bcl-2-associated athanogene, promotes floral transition by activating CONSTANS expression in transgenic Arabidopsis plant

(2011) Masayuki Kobayashi et al.   MOLECULAR BIOLOGY REPORTS

Next-generation transcriptome assembly

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

Analysis of global changes in gene expression during activity-dormancy cycle in hybrid aspen apex

(2011) Anna Karlberg et al.   Plant Biotechnology

A single subunit MCM6 from pea promotes salinity stress tolerance without affecting yield

(2011) Hung Quang Dang et al.   PLANT MOLECULAR BIOLOGY

Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis

(2011) Matthieu Vignes et al.   PLoS One

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)

(2011) Caroline Pont et al.   GENOME BIOLOGY

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC 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

Nitric oxide participates in cold-responsive phosphosphingolipid formation and gene expression in Arabidopsis thaliana

(2010) Catherine Cantrel et al.   NEW PHYTOLOGIST

Low temperatures impact dormancy status, flowering competence, and transcript profiles in crown buds of leafy spurge

(2010) Münevver Doğramacı et al.   PLANT MOLECULAR BIOLOGY

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

Genomics of forest and ecosystem health in the Fagaceae: meeting report

(2010) Antoine Kremer et al.   Tree Genetics & Genomes

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

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

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

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

Nucleotide variation in Quercus crispula Blume

(2008) N D Quang et al.   HEREDITY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The DOF transcription factor OBP1 is involved in cell cycle regulation inArabidopsis thaliana

(2008) Aleksandra Skirycz et al.   PLANT JOURNAL

Transcript profiling demonstrates absence of dosage compensation in Arabidopsis following loss of a single RPL23a paralog

(2008) Rory F. Degenhardt et al.   PLANTA