A cis ‐regulatory change underlying the motor neuron‐specific loss of Ebf expression in immotile tunicate larvae

An ancient role for collier/Olf/Ebf (COE)-type transcription factors in axial motor neuron development

(2019) Catarina Catela et al.   Neural Development

Parallel visual circuitry in a basal chordate

(2019) Matthew J Kourakis et al.   eLife

Developmental system drift in motor ganglion patterning between distantly related tunicates

(2018) Elijah K. Lowe et al.   EvoDevo

Neuronal identity: the neuron types of a simple chordate sibling, the tadpole larva of Ciona intestinalis

(2018) Kerrianne Ryan et al.   CURRENT OPINION IN NEUROBIOLOGY

The peripheral nervous system of the ascidian tadpole larva: Types of neurons and their synaptic networks

(2017) Kerrianne Ryan et al.   JOURNAL OF COMPARATIVE NEUROLOGY

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Evolutionary loss of melanogenesis in the tunicate Molgula occulta

(2017) Claudia Racioppi et al.   EvoDevo

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling

(2016) Kerrianne Ryan et al.   eLife

Migratory neuronal progenitors arise from the neural plate borders in tunicates

(2015) Alberto Stolfi et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

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

Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9

(2014) A. Stolfi et al.   DEVELOPMENT

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

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

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

(2014) Alberto Stolfi et al.   eLife

Developmental mode influences diversification in ascidians

(2013) M. E. Maliska et al.   Biology Letters

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Neuronal subtype specification in the spinal cord of a protovertebrate

(2011) A. Stolfi et al.   DEVELOPMENT

Neural tube patterning by Ephrin, FGF and Notch signaling relays

(2011) A. Stolfi et al.   DEVELOPMENT

Onecut is a direct neural-specific transcriptional activator of Rx in Ciona intestinalis

(2011) Enrico D'Aniello et al.   DEVELOPMENTAL BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Coordinated regulation of cholinergic motor neuron traits through a conserved terminal selector gene

(2011) Paschalis Kratsios et al.   NATURE NEUROSCIENCE

A glycine receptor is involved in the organization of swimming movements in an invertebrate chordate

(2010) Atsuo Nishino et al.   BMC NEUROSCIENCE

Ependymal cells of chordate larvae are stem-like cells that form the adult nervous system

(2010) Takeo Horie et al.   NATURE

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

(2010) F. Denoeud et al.   SCIENCE

Neural Map of the Larval Central Nervous System in the AscidianCiona intestinalis

(2010) Katsumi Takamura et al.   ZOOLOGICAL SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system

(2008) K. S. Imai et al.   DEVELOPMENT