Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader

Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest

(2015) Gemma B. Danks et al.   MOLECULAR BIOLOGY AND EVOLUTION

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Long-distance cell migration during larval development in the appendicularian, Oikopleura dioica

(2014) Kanae Kishi et al.   DEVELOPMENTAL BIOLOGY

Ascidian Mitogenomics: Comparison of Evolutionary Rates in Closely Related Taxa Provides Evidence of Ongoing Speciation Events

(2014) Francesca Griggio et al.   Genome Biology and Evolution

Cell Lineages and Fate Maps in Tunicates: Conservation and Modification

(2014) Hiroki Nishida et al.   ZOOLOGICAL SCIENCE

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

RNA interference in the appendicularian Oikopleura dioica reveals the function of the Brachyury gene

(2013) Tatsuya Omotezako et al.   DEVELOPMENT GENES AND EVOLUTION

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea

(2012) Bin Wu et al.   BMC GENOMICS

OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica

(2012) Gemma Danks et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Analysis of a botryllid enriched-full-length cDNA library: insight into the evolution of spliced leader trans-splicing in tunicates

(2011) Fabio Gasparini et al.   DEVELOPMENT GENES AND EVOLUTION

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Development of the appendicularian Oikopleura dioica: Culture, genome, and cell lineages

(2010) Hiroki Nishida   DEVELOPMENT GROWTH & DIFFERENTIATION

High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates

(2010) J. Matsumoto et al.   GENOME RESEARCH

Polymorphism and divergence within the ascidian genus Ciona

(2010) Marie L. Nydam et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

(2010) F. Denoeud et al.   SCIENCE

Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica

(2009) J.-M. Bouquet et al.   JOURNAL OF PLANKTON RESEARCH

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

Cleavage pattern, gastrulation, and neurulation in the appendicularian, Oikopleura dioica

(2008) Setsuko Fujii et al.   DEVELOPMENT GENES AND EVOLUTION

Embryology of a planktonic tunicate reveals traces of sessility

(2008) T. Stach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA