Full-Length Enriched cDNA Libraries and ORFeome Analysis of Sugarcane Hybrid and Ancestor Genotypes

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Building the sugarcane genome for biotechnology and identifying evolutionary trends

(2014) Nathalia de Setta et al.   BMC GENOMICS

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

(2014) Claudio Benicio Cardoso-Silva et al.   PLoS One

Long-Read Sequencing of Chicken Transcripts and Identification of New Transcript Isoforms

(2014) Sean Thomas et al.   PLoS One

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences

(2014) Paul J. Berkman et al.   Tropical Plant Biology

Haplotype analysis of sucrose synthase gene family in three Saccharum species

(2013) Jisen Zhang et al.   BMC GENOMICS

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

(2013) Xiang Yu et al.   BMC PLANT BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Circadian Rhythms of Sense and Antisense Transcription in Sugarcane, a Highly Polyploid Crop

(2013) Carlos Takeshi Hotta et al.   PLoS One

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

(2013) Keiichi Mochida et al.   PLoS One

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

(2012) Alessandra C Palhares et al.   BMC GENETICS

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

(2012) Shikai Liu et al.   BMC GENOMICS

Sugarcane for water-limited environments. Genetic variation in cane yield and sugar content in response to water stress

(2012) J. Basnayake et al.   JOURNAL OF EXPERIMENTAL BOTANY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Epigenetic regulation of human cis -natural antisense transcripts

(2012) Andrew B. Conley et al.   NUCLEIC ACIDS RESEARCH

Identification of sense and antisense transcripts regulated by drought in sugarcane

(2012) Carolina Gimiliani Lembke et al.   PLANT MOLECULAR BIOLOGY

Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars

(2012) L. Costet et al.   THEORETICAL AND APPLIED GENETICS

Scientific challenges of bioethanol production in Brazil

(2011) Henrique V. Amorim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

(2011) M. M. Pastina et al.   THEORETICAL AND APPLIED GENETICS

Transcriptome Analysis and Functional Genomics of Sugarcane

(2011) John M. Manners et al.   Tropical Plant Biology

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

(2010) Koh Aoki et al.   BMC GENOMICS

Simultaneously accounting for population structure, genotype by environment interaction, and spatial variation in marker–trait associations in sugarcaneThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Xianming Wei et al.   GENOME

Scaffolding a Caenorhabditis nematode genome with RNA-seq

(2010) A. Mortazavi et al.   GENOME RESEARCH

Sugarcane genes associated with sucrose content

(2009) Flavia S Papini-Terzi et al.   BMC GENOMICS

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome

(2009) K. Salehi-Ashtiani et al.   GENOME RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding

(2008) Steven G Ralph et al.   BMC GENOMICS

Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

(2008) X. Zhou et al.   GENOME RESEARCH

Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

(2008) Gerben van Ooijen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol

(2008) Mariam B. Sticklen   NATURE REVIEWS GENETICS

Elevated CO2increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane

(2008) AMANDA PEREIRA DE SOUZA et al.   PLANT CELL AND ENVIRONMENT

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

(2008) A. Yilmaz et al.   PLANT PHYSIOLOGY