A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions

(2012) Cecilia Conaco et al.   BMC GENOMICS

Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis

(2012) Q. Tu et al.   GENOME RESEARCH

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Evaluating de Bruijn Graph Assemblers on 454 Transcriptomic Data

(2012) Xianwen Ren et al.   PLoS One

A Framework for the Establishment of a Cnidarian Gene Regulatory Network for “Endomesoderm” Specification: The Inputs of ß-Catenin/TCF Signaling

(2012) Eric Röttinger et al.   PLoS Genetics

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements

(2011) Alison S Devonshire et al.   BMC GENOMICS

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

(2011) Victor Zeng et al.   BMC GENOMICS

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

(2011) Ben Ewen-Campen et al.   BMC GENOMICS

Functional roles of Notch signaling in the cnidarian Nematostella vectensis

(2011) Heather Marlow et al.   DEVELOPMENTAL BIOLOGY

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Assembling Neural Crest Regulatory Circuits into a Gene Regulatory Network

(2010) Paola Betancur et al.   Annual Review of Cell and Developmental Biology

Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica

(2010) Maja Adamska et al.   EVOLUTION & DEVELOPMENT

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction

(2009) Jon Mallatt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Properties of developmental gene regulatory networks

(2008) E. H. Davidson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA