De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

Systematic analysis of genomic organization and structure of long non-coding RNAs in the human genome

(2013) Jie Sun et al.   FEBS LETTERS

De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids

(2013) Shaoqun Liu et al.   PLoS One

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

(2012) Douglas S Domingues et al.   BMC GENOMICS

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

(2012) Dejun Li et al.   BMC GENOMICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks

(2012) Xingli Guo et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

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

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis

(2012) Shang-Wei Li et al.   PLoS One

Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform

(2012) Mingying Liu et al.   PLoS One

Characterization of the Genetic Variability of a Sugarcane Commercial Cross Through Yield Components and Quality Parameters

(2012) M. C. Mancini et al.   Sugar Tech

Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs

(2012) R. Vicentini et al.   Tropical Plant Biology

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) R. Garg et al.   DNA RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2010) T. Lu et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

RNA-seq: from technology to biology

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

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS