Exploring plant transcriptomes using ultra high-throughput sequencing

Short-Read Sequencing Technologies for Transcriptional Analyses

(2009) Stacey A. Simon et al.   Annual Review of Plant Biology

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

(2009) Jamie A O'Rourke et al.   BMC GENOMICS

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

(2009) Jingyu Zhang et al.   BMC GENOMICS

Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

(2009) Sung-Hyun Kim et al.   BMC PLANT BIOLOGY

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

(2009) Zoltán Hegedűs et al.   MOLECULAR IMMUNOLOGY

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Quantification of the yeast transcriptome by single-molecule sequencing

(2009) Doron Lipson et al.   NATURE BIOTECHNOLOGY

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

Gene expression analysis of light-modulated germination in tomato seeds

(2009) Gabriela Alejandra Auge et al.   NEW PHYTOLOGIST

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

(2009) Sika Zheng et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules

(2009) C. Lelandais-Briere et al.   PLANT CELL

Genome-wide analysis of gene expression profiles during ear development of maize

(2009) Yun Zhu et al.   PLANT MOLECULAR BIOLOGY

Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis

(2009) Xiaopeng Qi et al.   PLoS One

Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing

(2009) X. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A PCR-based platform for microRNA expression profiling studies

(2009) X. Wang   RNA

Computational and analytical framework for small RNA profiling by high-throughput sequencing

(2009) N. Fahlgren et al.   RNA

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

A Role for RNAi in the Selective Correction of DNA Methylation Defects

(2009) F. K. Teixeira et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

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

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

(2008) Thomas Wicker et al.   BMC GENOMICS

High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families

(2008) Gyorgy Szittya et al.   BMC GENOMICS

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

(2008) Ryan Lister et al.   CELL

Big impacts by small RNAs in plant development

(2008) George Chuck et al.   CURRENT OPINION IN PLANT BIOLOGY

Microarray analysis of gene expression profile induced by the biocontrol yeast Cryptococcus laurentii in cherry tomato fruit

(2008) Feng jiang et al.   GENE

Rapid whole-genome mutational profiling using next-generation sequencing technologies

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

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

(2008) X. Zhou et al.   GENOME RESEARCH

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

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

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

(2008) W. B. Barbazuk et al.   GENOME RESEARCH

A pathway-specific microarray analysis highlights the complex and co-ordinated transcriptional networks of the developing grain of field-grown barley

(2008) Michael Hansen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines

(2008) Gabriele Delp et al.   MOLECULAR GENETICS AND GENOMICS

Transcription Profiling of Soybean Nodulation byBradyrhizobium japonicum

(2008) Laurent Brechenmacher et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

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

Microarray analysis of vegetative phase change in maize

(2008) Josh Strable et al.   PLANT JOURNAL

Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant

(2008) K. Nobuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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