Advances in plant genome sequencing

Galaxy CloudMan: delivering cloud compute clusters

(2011) Enis Afgan et al.   BMC BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

(2011) Prabin Bajgain et al.   BMC GENOMICS

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

(2011) John P Délano-Frier et al.   BMC GENOMICS

An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis

(2011) Qi Tang et al.   BMC GENOMICS

Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis

(2011) Daphné Autran et al.   CELL

Transcriptome Analysis of Sarracenia, an Insectivorous Plant

(2011) A. Srivastava et al.   DNA RESEARCH

Sequence-based physical mapping of complex genomes by whole genome profiling

(2011) J. van Oeveren et al.   GENOME RESEARCH

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comparative deep transcriptional profiling of four developing oilseeds

(2011) Manuel A. Troncoso-Ponce et al.   PLANT JOURNAL

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire 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

The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

(2011) Rafał Wóycicki et al.   PLoS One

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

(2011) Rebecca M. Davidson et al.   Plant Genome

Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

(2011) Kevin Ashelford et al.   GENOME BIOLOGY

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

(2010) M. Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The case for cloud computing in genome informatics

(2010) Lincoln D Stein   GENOME BIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

A Single Molecule Scaffold for the Maize Genome

(2009) Shiguo Zhou et al.   PLoS Genetics

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Ryan Lister et al.   CELL

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

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

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

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Epigenetic Modification of Centromeric Chromatin: Hypomethylation of DNA Sequences in the CENH3-Associated Chromatin in Arabidopsis thaliana and Maize

(2008) W. Zhang et al.   PLANT CELL

A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

(2008) E. Paux et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Intergenic Locations of Rice Centromeric Chromatin

(2008) Huihuang Yan et al.   PLOS BIOLOGY