De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

(2012) Nicole Gruenheit et al.   BMC GENOMICS

Genome wide expression profiling of two accession of G. herbaceum L. in response to drought

(2012) Alok Ranjan et al.   BMC GENOMICS

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

(2011) Bonnie A Fraser et al.   BMC GENOMICS

Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

(2011) Anna W Santure et al.   BMC GENOMICS

Establishing the baseline level of repetitive element expression in the human cortex

(2011) Svitlana Tyekucheva et al.   BMC GENOMICS

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

(2011) Barbara Feldmeyer et al.   BMC GENOMICS

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

(2011) Rob W Ness et al.   BMC GENOMICS

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

(2011) Jordi Durban et al.   BMC GENOMICS

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

(2011) R. Garg et al.   DNA RESEARCH

Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing

(2011) Todd A. Castoe et al.   Genome Biology and Evolution

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis)

(2011) Todd A. Castoe et al.   Standards in Genomic Sciences

Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

(2011) Athanasia C Tzika et al.   EvoDevo

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes

(2011) Todd A Castoe et al.   GENOME BIOLOGY

Genome Evolution in Reptilia, the Sister Group of Mammals

(2010) Daniel E. Janes et al.   Annual Review of Genomics and Human Genetics

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

(2010) Ying Huang et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

(2010) Claudia Voelckel 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

Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered european eel

(2010) Alessandro Coppe et al.   BMC GENOMICS

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

(2010) Thomas L Parchman et al.   BMC GENOMICS

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology

(2010) Jacob E. Crawford et al.   PLoS One

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

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

(2009) Daniel A Hahn et al.   BMC GENOMICS

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

(2009) Eli Meyer et al.   BMC GENOMICS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

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

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

Three tiers of genome evolution in reptiles

(2008) C. L. Organ et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

New resources inform study of genome size, content, and organization in nonavian reptiles

(2008) D. E. Janes et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

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

Analyzing the coordinated gene network underlying temperature-dependent sex determination in reptiles

(2008) Christina M. Shoemaker et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources