Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

Galactinol synthase enzyme activity influences raffinose family oligosaccharides (RFO) accumulation in developing chickpea (Cicer arietinum L.) seeds

(2016) Manu P. Gangola et al.   PHYTOCHEMISTRY

Galactinol as marker for seed longevity

(2016) Deborah de Souza Vidigal et al.   PLANT SCIENCE

Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

(2015) Helena Sanches Marcon et al.   BMC PLANT BIOLOGY

Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses

(2015) Fabíola Carvalho Santos et al.   CHROMOSOME RESEARCH

Plant miRNAs: biogenesis, organization and origins

(2015) Hikmet Budak et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Galactinol synthase transcriptional profile in two genotypes of Coffea canephora with contrasting tolerance to drought

(2015) Tiago Benedito Dos Santos et al.   GENETICS AND MOLECULAR BIOLOGY

Impacts of Whole-Genome Triplication onMIRNAEvolution inBrassica rapa

(2015) Chao Sun et al.   Genome Biology and Evolution

Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits

(2015) Priscila Mary Yuyama et al.   MOLECULAR GENETICS AND GENOMICS

A fruit-bearing microRNA

(2015) Eytan Zlotorynski   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Greater Phenotypic Homeostasis of the AllopolyploidCoffea arabicaImproved the Transcriptional Homeostasis Over that of Both Diploid Parents

(2015) Benoît Bertrand et al.   PLANT AND CELL PHYSIOLOGY

Significance of galactinol and raffinose family oligosaccharide synthesis in plants

(2015) Sonali Sengupta et al.   Frontiers in Plant Science

Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange

(2014) Yuanlong Liu et al.   BMC GENOMICS

Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker assisted-selection

(2014) Danielle C Cardoso et al.   BMC GENOMICS

Homeologous genes involved in mannitol synthesis reveal unequal contributions in response to abiotic stress in Coffea arabica

(2014) Kenia de Carvalho et al.   MOLECULAR GENETICS AND GENOMICS

The coffee genome hub: a resource for coffee genomes

(2014) Alexis Dereeper et al.   NUCLEIC ACIDS RESEARCH

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

(2014) F. Denoeud et al.   SCIENCE

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Regulation of galactomannan biosynthesis in coffee seeds

(2013) Thierry Joët et al.   JOURNAL OF EXPERIMENTAL BOTANY

The need for transparency and good practices in the qPCR literature

(2013) Stephen A Bustin et al.   NATURE METHODS

Physiological aspects of raffinose family oligosaccharides in plants: protection against abiotic stress

(2013) A. I. ElSayed et al.   PLANT BIOLOGY

Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba

(2013) Xiao-Jiao Han et al.   PLoS One

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

(2013) Fabrício R. Lopes et al.   PLoS One

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

(2013) Michiel Van Bel et al.   GENOME BIOLOGY

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

(2012) Jorge MC Mondego et al.   BMC PLANT BIOLOGY

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Nitrogen Starvation, Salt and Heat Stress in Coffee (Coffea arabica L.): Identification and Validation of New Genes for qPCR Normalization

(2012) Kenia de Carvalho et al.   MOLECULAR BIOTECHNOLOGY

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

(2011) Isabelle Privat et al.   BMC GENOMICS

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments

(2011) Alberto Cenci et al.   PLANT MOLECULAR BIOLOGY

Expression of three galactinol synthase isoforms in Coffea arabica L. and accumulation of raffinose and stachyose in response to abiotic stresses

(2011) Tiago B. dos Santos et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Computational analysis of miRNA targets in plants: current status and challenges

(2010) X. Dai et al.   BRIEFINGS IN BIOINFORMATICS

Arabidopsis lyrataSmall RNAs: TransientMIRNAand Small Interfering RNA Loci within theArabidopsisGenus

(2010) Zhaorong Ma et al.   PLANT CELL

A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica

(2010) R. O. Vidal et al.   PLANT PHYSIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR

(2009) Fernanda Cruz et al.   MOLECULAR BREEDING

Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study

(2009) Thierry Joët et al.   NEW PHYTOLOGIST

Frost tolerance in excised leaves of the common bugle (Ajuga reptansL.) correlates positively with the concentrations of raffinose family oligosaccharides (RFOs)

(2009) SHAUN PETERS et al.   PLANT CELL AND ENVIRONMENT

Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

(2008) Fabrício Ramon Lopes et al.   MOLECULAR GENETICS AND GENOMICS

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

InterPro: the integrative protein signature database

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

Galactinol and Raffinose Constitute a Novel Function to Protect Plants from Oxidative Damage

(2008) A. Nishizawa et al.   PLANT PHYSIOLOGY

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE