A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians

(2019) Alicia Madgwick et al.   DEVELOPMENTAL BIOLOGY

Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements

(2019) Magali Naville et al.   CURRENT BIOLOGY

Parallel visual circuitry in a basal chordate

(2019) Matthew J Kourakis et al.   eLife

Comprehensive single-cell transcriptome lineages of a proto-vertebrate

(2019) Chen Cao et al.   NATURE

The regulation of oocyte maturation and ovulation in the closest sister group of vertebrates

(2019) Shin Matsubara et al.   eLife

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

piRNA-like small RNAs are responsible for the maternal-specific knockdown in the ascidian Ciona intestinalis Type A

(2018) Teruki Satoh et al.   Scientific Reports

Shared evolutionary origin of vertebrate neural crest and cranial placodes

(2018) Ryoko Horie et al.   NATURE

Spatio-temporal regulation of Rx and mitotic patterns shape the eye-cup of the photoreceptor cells in Ciona

(2018) Kouhei Oonuma et al.   DEVELOPMENTAL BIOLOGY

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Differential temporal control ofFoxa.aandZic-r.bspecifies brain versus notochord fate in the ascidian embryo

(2016) Tatsuro Ikeda et al.   DEVELOPMENT

Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species

(2016) Sarah Bouchemousse et al.   MOLECULAR ECOLOGY

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

(2016) Gaik Tamazian et al.   GigaScience

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genome-wide identification and characterization of transcription start sites and promoters in the tunicateCiona intestinalis

(2015) Rui Yokomori et al.   GENOME RESEARCH

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

The pre-vertebrate origins of neurogenic placodes

(2015) Philip Barron Abitua et al.   NATURE

Migratory neuronal progenitors arise from the neural plate borders in tunicates

(2015) Alberto Stolfi et al.   NATURE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Genetic pathways for differentiation of the peripheral nervous system in ascidians

(2015) Kana Waki et al.   Nature Communications

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Sustained Heterozygosity Across a Self-Incompatibility Locus in an Inbred Ascidian

(2014) Yutaka Satou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Symmetrical Reproductive Compatibility of Two Species in theCiona intestinalis(Ascidiacea) Species Complex, a Model for Marine Genomics and Developmental Biology

(2014) Atsuko Sato et al.   ZOOLOGICAL SCIENCE

A time delay gene circuit is required for palp formation in the ascidian embryo

(2013) T. Ikeda et al.   DEVELOPMENT

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

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

A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis

(2012) Yutaka Satou et al.   BMC GENOMICS

FGF signaling establishes the anterior border of the Ciona neural tube

(2012) E. Wagner et al.   DEVELOPMENT

Field identification of ‘types’ A and B of the ascidian Ciona intestinalis in a region of sympatry

(2012) Atsuko Sato et al.   MARINE BIOLOGY

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

(2012) Philip Barron Abitua et al.   NATURE

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Reproductive protein evolution in two cryptic species of marine chordate

(2011) Marie L Nydam et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary crossroads in developmental biology: the tunicates

(2011) P. Lemaire   DEVELOPMENT

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

doublesex/mab3 related-1 (dmrt1) is essential for development of anterior neural plate derivatives in Ciona

(2010) J. Tresser et al.   DEVELOPMENT

INTROGRESSION DESPITE SUBSTANTIAL DIVERGENCE IN A BROADCAST SPAWNING MARINE INVERTEBRATE

(2010) Marie L. Nydam et al.   EVOLUTION

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

SL RNA Genes of the Ascidian TunicatesCiona intestinalisandCiona savignyi

(2010) Brendan Yeats et al.   ZOOLOGICAL SCIENCE

How and Why Chromosome Inversions Evolve

(2010) Mark Kirkpatrick   PLOS BIOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Regulatory genes in the ancestral chordate genomes

(2008) Yutaka Satou et al.   DEVELOPMENT GENES AND EVOLUTION

Trunk lateral cells are neural crest-like cells in the ascidian Ciona intestinalis: Insights into the ancestry and evolution of the neural crest

(2008) William R. Jeffery et al.   DEVELOPMENTAL BIOLOGY

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

(2008) M. M. Hill et al.   GENOME RESEARCH

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Mechanism of Self-Sterility in a Hermaphroditic Chordate

(2008) Y. Harada 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