Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species

(2015) Jessica Stapley et al.   MOLECULAR ECOLOGY

BARLEX – the Barley Draft Genome Explorer

(2015) Christian Colmsee et al.   Molecular Plant

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

Transposons play an important role in the evolution and diversification of centromeres among closely related species

(2015) Dongying Gao et al.   Frontiers in Plant Science

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

e!DAL - a framework to store, share and publish research data

(2014) Daniel Arend et al.   BMC BIOINFORMATICS

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

Unlocking the secondary gene-pool of barley with next-generation sequencing

(2014) Neele Wendler et al.   PLANT BIOTECHNOLOGY JOURNAL

Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

(2014) Naser Poursarebani et al.   PLANT JOURNAL

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Long-read, whole-genome shotgun sequence data for five model organisms

(2014) Kristi E Kim et al.   Scientific Data

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

Kmasker - A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome SpeciesHordeum vulgare

(2013) T. Schmutzer et al.   CYTOGENETIC AND GENOME RESEARCH

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Reticulate Evolution of the Rye Genome

(2013) M. M. Martis et al.   PLANT CELL

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

(2013) R. Ariyadasa et al.   PLANT PHYSIOLOGY

Physical Mapping Integrated with Syntenic Analysis to Characterize the Gene Space of the Long Arm of Wheat Chromosome 1A

(2013) Stuart J. Lucas et al.   PLoS One

A Physical Map of the Short Arm of Wheat Chromosome 1A

(2013) James Breen et al.   PLoS One

De novo sequencing of hazelnut bacterial artificial chromosomes (BACs) using multiplex Illumina sequencing and targeted marker development for eastern filbert blight resistance

(2013) Vidyasagar R. Sathuvalli et al.   Tree Genetics & Genomes

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

(2013) Dina Raats et al.   GENOME BIOLOGY

Integrating cereal genomics to support innovation in the Triticeae

(2012) C. Feuillet et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.)

(2011) Daniela Schulte et al.   BMC GENOMICS

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

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

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

(2011) Klaus F.X. Mayer et al.   PLANT CELL

Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries

(2011) T. Matsumoto et al.   PLANT PHYSIOLOGY

Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes

(2011) Roger Barthelson et al.   PLoS One

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

(2010) Niall J Lennon et al.   GENOME BIOLOGY

Swift: primary data analysis for the Illumina Solexa sequencing platform

(2009) Nava Whiteford 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

De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

(2009) Burkhard Steuernagel et al.   BMC GENOMICS

The International Barley Sequencing Consortium--At the Threshold of Efficient Access to the Barley Genome

(2009) D. Schulte et al.   PLANT PHYSIOLOGY

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

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