Developmental system drift in motor ganglion patterning between distantly related tunicates

A phylogenomic framework and timescale for comparative studies of tunicates

(2018) Frédéric Delsuc et al.   BMC BIOLOGY

Phylogenomics offers resolution of major tunicate relationships

(2018) Kevin M. Kocot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

(2017) Matija Brozovic et al.   NUCLEIC ACIDS RESEARCH

Nodal and FGF coordinate ascidian neural tube morphogenesis

(2016) Ignacio A. Navarrete et al.   DEVELOPMENT

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Matija Brozovic et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Determination of in vivo RNA kinetics using RATE-seq

(2014) Benjamin Neymotin et al.   RNA

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

(2014) Alberto Stolfi et al.   eLife

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Cell lineage and cis-regulation for a unique GABAergic/glycinergic neuron type in the larval nerve cord of the ascidian Ciona intestinalis

(2012) Koki Nishitsuji et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

A model of developmental evolution: selection, pleiotropy and compensation

(2012) Mihaela Pavlicev et al.   TRENDS IN ECOLOGY & EVOLUTION

Neuronal subtype specification in the spinal cord of a protovertebrate

(2011) A. Stolfi et al.   DEVELOPMENT

Divergent mechanisms specify chordate motoneurons: evidence from ascidians

(2011) C. Hudson et al.   DEVELOPMENT

Neural tube patterning by Ephrin, FGF and Notch signaling relays

(2011) A. Stolfi et al.   DEVELOPMENT

A mechanism for graded motor control encoded in the channel properties of the muscle ACh receptor

(2011) A. Nishino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Atsuo Nishino et al.   BMC NEUROSCIENCE

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

(2010) Hiroki Nishida   DEVELOPMENT GROWTH & DIFFERENTIATION

Segregation of Germ Layer Fates by Nuclear Migration-Dependent Localization of Not mRNA

(2010) Naohito Takatori et al.   DEVELOPMENTAL CELL

Spatial and temporal expression of two transcriptional isoforms of Lhx3, a LIM class homeobox gene, during embryogenesis of two phylogenetically remote ascidians, Halocynthia roretzi and Ciona intestinalis

(2010) Masaaki Kobayashi et al.   GENE EXPRESSION PATTERNS

Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates

(2010) Georgia Tsagkogeorga et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2010) F. Denoeud et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

(2009) Georgia Tsagkogeorga et al.   BMC EVOLUTIONARY BIOLOGY

Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp

(2009) Lionel Christiaen et al.   DEVELOPMENTAL BIOLOGY

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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