Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification

(2011) P. R. Steele et al.   AMERICAN JOURNAL OF BOTANY

Nuclear DNA amounts in angiosperms: targets, trends and tomorrow

(2011) M. D. Bennett et al.   ANNALS OF BOTANY

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

(2011) Kerry A Lutz et al.   BMC BIOTECHNOLOGY

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiplexed microsatellite recovery using massively parallel sequencing

(2011) T. N. JENNINGS et al.   Molecular Ecology Resources

Phylogenetic Relationships of Asclepias (Apocynaceae) Inferred from Non-coding Chloroplast DNA Sequences

(2011) Mark Fishbein et al.   SYSTEMATIC BOTANY

Evolutionary and ecological genomics of non-model plants

(2011) Bao-Hua SONG et al.   Journal of Systematics and Evolution

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods

(2010) G. Carrier et al.   AMERICAN JOURNAL OF BOTANY

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

High quality SNP calling using Illumina data at shallow coverage

(2010) N. Malhis et al.   BIOINFORMATICS

Calling SNPs without a reference sequence

(2010) Aakrosh Ratan et al.   BMC BIOINFORMATICS

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

(2010) John C Castle et al.   BMC GENOMICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Recent Trends in Molecular Phylogenetic Analysis: Where to Next?

(2010) C. Blair et al.   JOURNAL OF HEREDITY

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

(2010) M. M. Guisinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines

(2010) J. B. WHITTALL et al.   MOLECULAR ECOLOGY

Chloroplast DNA-based studies in molecular ecology may be compromised by nuclear-encoded plastid sequence

(2010) WOLFGANG ARTHOFER et al.   MOLECULAR ECOLOGY

Third-generation sequencing fireworks at Marco Island

(2010) David J Munroe et al.   NATURE BIOTECHNOLOGY

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Computational solutions to large-scale data management and analysis

(2010) Eric E. Schadt et al.   NATURE REVIEWS GENETICS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

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

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

(2010) Niall J Lennon et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Tablet--next generation sequence assembly visualization

(2009) I. Milne 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

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

A multiple-method approach reveals a declining amount of chloroplast DNA during development in Arabidopsis

(2009) Beth A Rowan et al.   BMC PLANT BIOLOGY

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Variable amounts of DNA related to the size of chloroplasts III. Biochemical determinations of DNA amounts per organelle

(2009) Uwe Rauwolf et al.   MOLECULAR GENETICS AND GENOMICS

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Large-Scale Discovery of Gene-Enriched SNPs

(2009) Michael A. Gore et al.   Plant Genome

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

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

(2008) Ray Ming et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Identification of genetic variants using bar-coded multiplexed sequencing

(2008) David W Craig et al.   NATURE METHODS

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

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

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY