Applications of next-generation sequencing in plant biology

Genomics of gene banks: A case study in rice

(2012) Susan R. McCouch et al.   AMERICAN JOURNAL OF BOTANY

Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics

(2012) Levi Yant   AMERICAN JOURNAL OF BOTANY

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum ; Fabaceae), a crop species without a reference genome

(2012) Sarwar Azam et al.   AMERICAN JOURNAL OF BOTANY

Targeted enrichment strategies for next-generation plant biology

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

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a

(2012) Alyssa A. Gulledge et al.   AMERICAN JOURNAL OF BOTANY

A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species

(2012) Daniel C. Ilut et al.   AMERICAN JOURNAL OF BOTANY

Next-generation sequencing applications for wheat crop improvement

(2012) Paul J. Berkman et al.   AMERICAN JOURNAL OF BOTANY

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

(2012) Michael R. McKain et al.   AMERICAN JOURNAL OF BOTANY

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

Next-generation sequencing and genome evolution in allopolyploids

(2012) Richard J. A. Buggs et al.   AMERICAN JOURNAL OF BOTANY

Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed, Phragmites australis (Poaceae), reveals genes involved in invasiveness and rhizome specificity

(2012) Ruifeng He et al.   AMERICAN JOURNAL OF BOTANY

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Strategies for transcriptome analysis in nonmodel plants

(2012) Judson A. Ward et al.   AMERICAN JOURNAL OF BOTANY

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

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

(2011) Zhao Lai et al.   AMERICAN JOURNAL OF BOTANY

Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences

(2011) Juan E. Zalapa et al.   AMERICAN JOURNAL OF BOTANY

True single-molecule DNA sequencing of a pleistocene horse bone

(2011) L. Orlando et al.   GENOME RESEARCH

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR

(2011) Benjamin P. Howden et al.   PLoS Pathogens

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

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

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

(2011) Kevin Ashelford et al.   GENOME BIOLOGY

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase

(2010) Kate R. Lieberman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Semiconductors Inspire New Sequencing Technologies

(2010) E. Pennisi   SCIENCE

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Editorial

(2009) A. Bateman et al.   BIOINFORMATICS

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

(2009) D. S. Horner et al.   BRIEFINGS IN BIOINFORMATICS

Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery

(2009) Stéphane Deschamps et al.   MOLECULAR BREEDING

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Virtual terminator nucleotides for next-generation DNA sequencing

(2009) Jayson Bowers et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides

(2008) J. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE