Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

(2011) Zhangying Wang et al.   BMC GENOMICS

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

(2011) Cheng-Ying Shi et al.   BMC GENOMICS

Exploring plant transcriptomes using ultra high-throughput sequencing

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

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

(2011) R. Garg et al.   DNA RESEARCH

Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian Dugesia japonica

(2011) Yun-Fei Qin et al.   GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Transcriptomic Signatures of Ash (Fraxinus spp.) Phloem

(2011) Xiaodong Bai et al.   PLoS One

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

The First Insight into the Tissue Specific Taxus Transcriptome via Illumina Second Generation Sequencing

(2011) Da Cheng Hao et al.   PLoS One

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Digital gene expression analysis of the zebra finch genome

(2010) Robert Ekblom et al.   BMC GENOMICS

A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

(2010) Roland Schafleitner et al.   BMC GENOMICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

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

(2010) Jeffrey Martin et al.   BMC GENOMICS

De novo assembly of short sequence reads

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

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

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

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

First Report of Sweetpotato symptomless virus 1 and Sweetpotato virus A in Sweetpotatoes in Tanzania

(2010) D. R. Mbanzibwa et al.   PLANT DISEASE

Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

(2010) Maria C. Suarez Rodriguez et al.   PLANT JOURNAL

Digital Gene Expression Signatures for Maize Development

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

The Populus Class III HD ZIP, popREVOLUTA, Influences Cambium Initiation and Patterning of Woody Stems

(2010) M. Robischon et al.   PLANT PHYSIOLOGY

More genomic resources for less-studied crops

(2010) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard

(2010) Beatrix Coetzee et al.   VIROLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

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

(2009) Likun Wang et al.   BIOINFORMATICS

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

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

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

Sweetpotato viruses in China

(2009) Qingmei Wang et al.   CROP PROTECTION

Next-generation tag sequencing for cancer gene expression profiling

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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

(2009) Zoltán Hegedűs et al.   MOLECULAR IMMUNOLOGY

Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus

(2009) M. Al Rwahnih et al.   VIROLOGY

Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses

(2009) Jan F. Kreuze et al.   VIROLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome sequence and characterization of a new virus infecting Mikania micrantha H.B.K.

(2008) Rui-Long Wang et al.   ARCHIVES OF VIROLOGY

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

(2008) D. Hernandez et al.   GENOME RESEARCH

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

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

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