ANISEED 2015: a digital framework for the comparative developmental biology of ascidians

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Regulation and evolution of cardiopharyngeal cell identity and behavior: insights from simple chordates

(2015) Nicole Kaplan et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Evolution of the chordate regeneration blastema: Differential gene expression and conserved role of notch signaling during siphon regeneration in the ascidian Ciona

(2015) Mayuko Hamada et al.   DEVELOPMENTAL BIOLOGY

A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis

(2015) Michael J. Gilchrist et al.   DEVELOPMENTAL BIOLOGY

Neuronal map reveals the highly regionalized pattern of the juvenile central nervous system of the ascidianCiona intestinalis

(2015) Akiko Hozumi et al.   DEVELOPMENTAL DYNAMICS

Morphological evidence that the molecularly determinedCiona intestinalistype A and type B are different species:Ciona robustaandCiona intestinalis

(2015) Riccardo Brunetti et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

A new heart for a new head in vertebrate cardiopharyngeal evolution

(2015) Rui Diogo et al.   NATURE

Morphological Differences between Larvae of the Ciona intestinalis Species Complex: Hints for a Valid Taxonomic Definition of Distinct Species

(2015) Roberta Pennati et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

CRISPR/Cas9-mediated gene knockout in the ascidianCiona intestinalis

(2014) Haruka Sasaki et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Collier/OLF/EBF-Dependent Transcriptional Dynamics Control Pharyngeal Muscle Specification from Primed Cardiopharyngeal Progenitors

(2014) Florian Razy-Krajka et al.   DEVELOPMENTAL CELL

Botryllus schlosseri, an emerging model for the study of aging, stem cells, and mechanisms of regeneration

(2014) Ayelet Voskoboynik et al.   INVERTEBRATE REPRODUCTION & DEVELOPMENT

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians

(2014) Alberto Stolfi et al.   eLife

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

(2014) Ceri E Van Slyke et al.   Journal of Biomedical Semantics

The applications of single-cell genomics

(2013) M. Lovett   HUMAN MOLECULAR GENETICS

Crossing the Species Barrier: Genomic Hotspots of Introgression between Two Highly Divergent Ciona intestinalis Species

(2013) Camille Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Identification of a Colonial Chordate Histocompatibility Gene

(2013) A. Voskoboynik et al.   SCIENCE

NK4 Antagonizes Tbx1/10 to Promote Cardiac versus Pharyngeal Muscle Fate in the Ascidian Second Heart Field

(2013) Wei Wang et al.   PLOS BIOLOGY

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

Ascidians as excellent chordate models for studying the development of the nervous system during embryogenesis and metamorphosis

(2012) Yasunori Sasakura et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution

(2012) Mitsuru J. Nakamura et al.   DEVELOPMENTAL BIOLOGY

Whole-organ cell shape analysis reveals the developmental basis of ascidian notochord taper

(2012) Michael T. Veeman et al.   DEVELOPMENTAL BIOLOGY

The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis

(2012) Georgia Tsagkogeorga et al.   Genome Biology and Evolution

Identification of a rudimentary neural crest in a non-vertebrate chordate

(2012) Philip Barron Abitua et al.   NATURE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

(2011) P. L. Whetzel et al.   NUCLEIC ACIDS RESEARCH

Sequential Activation of Apical and Basolateral Contractility Drives Ascidian Endoderm Invagination

(2010) Kristin Sherrard et al.   CURRENT BIOLOGY

Ascidians: an invertebrate chordate model to study Alzheimer's disease pathogenesis

(2010) M. J. Virata et al.   Disease Models & Mechanisms

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

(2010) O. Tassy et al.   GENOME RESEARCH

Evolution of the Sequence Ontology terms and relationships

(2010) Christopher J. Mungall et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Polymorphism and divergence within the ascidian genus Ciona

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

Early Chordate Origins of the Vertebrate Second Heart Field

(2010) A. Stolfi et al.   SCIENCE

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

(2008) Eric W Deutsch et al.   NATURE BIOTECHNOLOGY

The Transcription/Migration Interface in Heart Precursors of Ciona intestinalis

(2008) L. Christiaen et al.   SCIENCE

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

(2008) Yutaka Satou et al.   GENOME BIOLOGY