De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae)

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

(2011) Nicolas Blavet et al.   BMC GENOMICS

Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome

(2011) Yajuan Zeng et al.   BMC GENOMICS

Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

(2011) Sukhjiwan Kaur et al.   BMC GENOMICS

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

(2011) S Samuel Yang et al.   BMC GENOMICS

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

(2011) Maria D Logacheva et al.   BMC GENOMICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

(2011) José Blanca et al.   BMC GENOMICS

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

(2011) Sutapa Dutta et al.   BMC PLANT BIOLOGY

De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques

(2011) F. ANGELONI et al.   Molecular Ecology Resources

OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids

(2011) C.-H. Fu et al.   PLANT AND CELL PHYSIOLOGY

Analysis of Leaf and Root Transcriptomes of Soil-Grown Avena barbata Plants

(2011) Stéphanie M. Swarbreck et al.   PLANT AND CELL PHYSIOLOGY

Transcriptomic Signatures of Ash (Fraxinus spp.) Phloem

(2011) Xiaodong Bai et al.   PLoS One

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution

(2011) S. Fujii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome analysis and SNP/SSR marker information of red pepper variety YCM334 and Taean

(2011) Fu-Hao Lu et al.   SCIENTIA HORTICULTURAE

Use of Non-Normalized, Non-Amplified cDNA for 454-Based RNA Sequencing of Fleshy Melon Fruit

(2011) Vitaly Portnoy et al.   Plant Genome

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia

(2010) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

(2010) Tonia S Schwartz et al.   BMC GENOMICS

De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis

(2010) Chao Sun et al.   BMC GENOMICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim

(2010) Shaohua Zeng et al.   BMC GENOMICS

Paternal Leakage and Heteroplasmy of Mitochondrial Genomes in Silene vulgaris: Evidence From Experimental Crosses

(2010) K. E. Bentley et al.   GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Genomic admixture increases fitness during a biological invasion

(2010) S. R. KELLER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Characterization of duplicate gene evolution in the recent natural allopolyploidTragopogon miscellusby next-generation sequencing and Sequenom iPLEX MassARRAY genotyping

(2010) RICHARD J. A. BUGGS et al.   MOLECULAR ECOLOGY

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009

(2010) et al.   Molecular Ecology Resources

The population genomics of plant adaptation

(2010) Mathieu Siol et al.   NEW PHYTOLOGIST

Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes

(2010) Yanhui Peng et al.   PEST MANAGEMENT SCIENCE

Comparative Functional Genomic Analysis of Solanum Glandular Trichome Types

(2010) E. T. McDowell et al.   PLANT PHYSIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing

(2009) Wei Wang et al.   BMC GENOMICS

Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species

(2009) Diana Bellin et al.   BMC GENOMICS

Comparison of next generation sequencing technologies for transcriptome characterization

(2009) P Kerr Wall et al.   BMC GENOMICS

A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping

(2009) Maria Moccia et al.   BMC GENOMICS

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

(2009) Fiammetta Alagna et al.   BMC GENOMICS

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

(2009) Abdelali Barakat et al.   BMC PLANT BIOLOGY

Silene as a model system in ecology and evolution

(2009) G Bernasconi et al.   HEREDITY

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009–30 September 2009

(2009) et al.   Molecular Ecology Resources

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Adaptation and colonization history affect the evolution of clines in two introduced species

(2009) Stephen R. Keller et al.   NEW PHYTOLOGIST

Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation

(2008) Guislaine Refrégier et al.   BMC EVOLUTIONARY BIOLOGY

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

(2008) Christopher W. Wheat   GENETICA

The Effect of Breeding System on Polymorphism in Mitochondrial Genes of Silene

(2008) P. Touzet et al.   GENETICS

Maximized virulence in a sterilizing pathogen: the anther-smut fungus and its co-evolved hosts

(2008) D. B. SLOAN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

The development and impact of 454 sequencing

(2008) Jonathan M Rothberg et al.   NATURE BIOTECHNOLOGY

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources