New approaches to Prunus transcriptome analysis

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

(2011) Eudald Illa et al.   BMC EVOLUTIONARY BIOLOGY

Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

(2011) Changbin Chen et al.   BMC PLANT BIOLOGY

Exploring plant transcriptomes using ultra high-throughput sequencing

(2011) L. Wang et al.   Briefings in Functional Genomics

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

(2010) Ali Bashir et al.   BMC GENOMICS

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant

(2010) Sergio Jiménez et al.   BMC PLANT BIOLOGY

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

De novo assembly of short sequence reads

(2010) K. Paszkiewicz et al.   BRIEFINGS IN BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Recent advances in DNA sequencing methods – general principles of sample preparation

(2010) Sten Linnarsson   EXPERIMENTAL CELL RESEARCH

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Identification and differential expression dynamics of peach small GTPases encoding genes during fruit development and ripening

(2010) R. Falchi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Power of Deep Sequencing and Agilent Microarray for Gene Expression Profiling Study

(2010) Lin Feng et al.   MOLECULAR BIOTECHNOLOGY

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

Simplifying complexity

(2010) Nicole Cloonan et al.   NATURE METHODS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Defining transcribed regions using RNA-seq

(2010) Brian T Wilhelm et al.   Nature Protocols

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

(2010) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

(2010) A. Bräutigam et al.   PLANT BIOLOGY

Gene expression of DAM5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break rate

(2010) S. Jiménez et al.   PLANT MOLECULAR BIOLOGY

Digital Gene Expression Signatures for Maize Development

(2010) A. L. Eveland et al.   PLANT PHYSIOLOGY

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

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing

(2010) X. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Review on The Processing and Analysis of Next-generation RNA-seq Data*

(2010) Xi WANG et al.   PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS

Whole genome transcriptome analysis

(2010) Alistair R.R. Forrest et al.   RNA Biology

Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species

(2010) Loïck Le Dantec et al.   Tree Genetics & Genomes

QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.)

(2010) Suneth S. Sooriyapathirana et al.   Tree Genetics & Genomes

Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization

(2010) C. Leida et al.   TREE PHYSIOLOGY

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Development and evaluation of RNA-seq methods

(2010) Joshua Levin et al.   GENOME BIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

Synteny of Prunus and other model plant species

(2009) Sook Jung et al.   BMC GENOMICS

A fruit quality gene map of Prunus

(2009) Ebenezer A Ogundiwin et al.   BMC GENOMICS

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

(2009) Diana Bellin et al.   BMC GENOMICS

Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

(2009) Antonio Cabrera et al.   BMC GENOMICS

Comparative EST transcript profiling of peach fruits under different post-harvest conditions reveals candidate genes associated with peach fruit quality

(2009) Paula Vizoso et al.   BMC GENOMICS

Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing

(2009) Julio C Vega-Arreguín et al.   BMC GENOMICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Selection of reliable reference genes for gene expression studies in peach using real-time PCR

(2009) Zhaoguo Tong et al.   BMC MOLECULAR BIOLOGY

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

(2009) D. S. Horner et al.   BRIEFINGS IN BIOINFORMATICS

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

The resolution of the genetics of gene expression

(2009) S. B. Montgomery et al.   HUMAN MOLECULAR GENETICS

Molecular characterization of seven genes encoding ethylene-responsive transcriptional factors during plum fruit development and ripening

(2009) I. El-Sharkawy et al.   JOURNAL OF EXPERIMENTAL BOTANY

An integrated strategy to identify key genes in almond adventitious shoot regeneration

(2009) Ana Margarida Santos et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dormancy-associated MADS genes from the EVG locus of peach [Prunus persica (L.) Batsch] have distinct seasonal and photoperiodic expression patterns

(2009) Z. Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

(2009) Iouri Chepelev et al.   NUCLEIC ACIDS RESEARCH

A simple method for directional transcriptome sequencing using Illumina technology

(2009) N. J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Quantitative resistance toPlum pox virusinPrunus davidianaP1908 linked to components of the eukaryotic translation initiation complex

(2009) G. Marandel et al.   PLANT PATHOLOGY

Differential expression levels of aroma-related genes during ripening of apricot (Prunus armeniaca L.)

(2009) Mauricio González-Agüero et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Comparative expression and transcript initiation of three peach dehydrin genes

(2009) Carole Leavel Bassett et al.   PLANTA

Molecular markers for kernel bitterness in almond

(2009) Raquel Sánchez-Pérez et al.   Tree Genetics & Genomes

Characterizing natural variation using next-generation sequencing technologies

(2009) Yoav Gilad et al.   TRENDS IN GENETICS

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

(2008) Barbara Lazzari et al.   BMC BIOINFORMATICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Transcriptome profiling of ripening nectarine (Prunus persica L. Batsch) fruit treated with 1-MCP

(2008) Fiorenza Ziliotto et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of woolliness response genes in peach fruit after post-harvest treatments

(2008) Mauricio González-Agüero et al.   JOURNAL OF EXPERIMENTAL BOTANY

Jasmonate-induced transcriptional changes suggest a negative interference with the ripening syndrome in peach fruit

(2008) Vanina Ziosi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Identification of cherry incompatibility alleles by microarray

(2008) F. Pasquer et al.   PLANT BREEDING

Development of ChillPeach genomic tools and identification of cold-responsive genes in peach fruit

(2008) Ebenezer A. Ogundiwin et al.   PLANT MOLECULAR BIOLOGY

Multiple Models for Rosaceae Genomics

(2008) V. Shulaev et al.   PLANT PHYSIOLOGY

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation

(2008) Douglas Gary Bielenberg et al.   Tree Genetics & Genomes

Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch)

(2008) A. Vecchietti et al.   Tree Genetics & Genomes

A framework physical map for peach, a model Rosaceae species

(2008) T. N. Zhebentyayeva et al.   Tree Genetics & Genomes

Leucoanthocyanidin dioxygenase gene (PpLDOX): a potential functional marker for cold storage browning in peach

(2008) E. A. Ogundiwin et al.   Tree Genetics & Genomes

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY