De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program

(2012) M. Fasoli et al.   PLANT CELL

Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily

(2012) Yucheng Zhang et al.   PLoS One

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

(2012) Candice N. Hansey et al.   PLoS One

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

(2011) C. Adamidi et al.   GENOME RESEARCH

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

(2011) Thomas Sandmann et al.   GENOME BIOLOGY

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Two-Dimensional Differential in Gel Electrophoresis (2D-DIGE) Analysis of Grape Berry Proteome during Postharvest Withering

(2010) Mariasole Di Carli et al.   JOURNAL OF PROTEOME RESEARCH

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

Exploring genetic and expression differences between physiologically extreme ecotypes: comparative genomic hybridization and gene expression studies of Kas-1 and Tsu-1 accessions of Arabidopsis thaliana

(2010) THOMAS E. JUENGER et al.   PLANT CELL AND ENVIRONMENT

Identification of Putative Stage-Specific Grapevine Berry Biomarkers and Omics Data Integration into Networks

(2010) A. Zamboni et al.   PLANT PHYSIOLOGY

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

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

Rapid Genomic Characterization of the Genus Vitis

(2010) Sean Myles et al.   PLoS One

De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology

(2010) Jacob E. Crawford et al.   PLoS One

Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars

(2010) J. E. Zalapa et al.   THEORETICAL AND APPLIED GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Evidence-based gene predictions in plant genomes

(2009) C. Liang et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

(2008) José Matus et al.   BMC PLANT BIOLOGY

Molecular analysis of post-harvest withering in grape by AFLP transcriptional profiling

(2008) Anita Zamboni et al.   JOURNAL OF EXPERIMENTAL BOTANY

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Analysis of Intraspecies Diversity in Wheat and Barley Genomes Identifies Breakpoints of Ancient Haplotypes and Provides Insight into the Structure of Diploid and Hexaploid Triticeae Gene Pools

(2008) T. Wicker et al.   PLANT PHYSIOLOGY

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY