ANISEED 2015: a digital framework for the comparative developmental biology of ascidians (Q28334386)

22

0 references

Elijah K Lowe

Elijah K Lowe

13

0 references

Christelle Dantec

Christelle Dantec

3

0 references

Hitoyoshi Yasuo

Hitoyoshi Yasuo

27

0 references

Patrick Lemaire

Patrick Lemaire

28

0 references

Shigeki Fujiwara

Shigeki Fujiwara

11

0 references

Hiroki Nishida

Hiroki Nishida

24

0 references

Emmanuel Douzery

21

Emmanuel Douzery

0 references

author name string

Matija Brozovic

1

0 references

Cyril Martin

2

0 references

Delphine Dauga

4

0 references

Mickaël Mendez

5

0 references

Paul Simion

6

0 references

Madeline Percher

7

0 references

Baptiste Laporte

8

0 references

Céline Scornavacca

9

0 references

Anna Di Gregorio

10

0 references

Mathieu Gineste

12

0 references

Jacques Piette

14

0 references

Claudia Racioppi

15

0 references

Filomena Ristoratore

16

0 references

Yasunori Sasakura

17

0 references

Naohito Takatori

18

0 references

Titus C Brown

19

0 references

Alex McDougall

23

0 references

Hitoshi Sawada

25

0 references

Billie J Swalla

Creative Commons Attribution 4.0 International

26

0 references

language of work or name

English

0 references

publication date

4 January 2016

0 references

published in

Nucleic Acids Research

0 references

volume

44

0 references

page(s)

D808-18

0 references

issue

D1

0 references

copyright license

start time

15 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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A new heart for a new head in vertebrate cardiopharyngeal evolution

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

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Standardized description of scientific evidence using the Evidence Ontology (ECO)

20 March 2017

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The genome sequence of the colonial chordate, Botryllus schlosseri

20 March 2017

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Integrating diverse databases into an unified analysis framework: a Galaxy approach

20 March 2017

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20 March 2017

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JBrowse: a next-generation genome browser

20 March 2017

1 reference

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A Chado case study: an ontology-based modular schema for representing genome-associated biological information

20 March 2017

1 reference

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A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

20 March 2017

1 reference

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Tunicates and not cephalochordates are the closest living relatives of vertebrates

20 March 2017

1 reference

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DBTGR: a database of tunicate promoters and their regulatory elements

20 March 2017

1 reference

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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

20 March 2017

1 reference

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Identification of conserved regulatory elements by comparative genome analysis

20 March 2017

1 reference

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The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

20 March 2017

1 reference

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Web Apollo: a web-based genomic annotation editing platform

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

20 March 2017

1 reference

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Early chordate origins of the vertebrate second heart field

20 March 2017

1 reference

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

20 March 2017

1 reference

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FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Guidelines for the nomenclature of genetic elements in tunicate genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Closing the wounds: one hundred and twenty five years of regenerative biology in the ascidian Ciona intestinalis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

NK4 antagonizes Tbx1/10 to promote cardiac versus pharyngeal muscle fate in the ascidian second heart field

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Identification of a colonial chordate histocompatibility gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Transcriptional enhancers in ascidian development

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Evolutionary crossroads in developmental biology: the tunicates.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Polymorphism and divergence within the ascidian genus Ciona

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Evolution of the Sequence Ontology terms and relationships

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Use with caution: developmental systems divergence and potential pitfalls of animal models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

ChEBI: an open bioinformatics and cheminformatics resource

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

The transcription/migration interface in heart precursors of Ciona intestinalis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Developmental system drift and flexibility in evolutionary trajectories

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Evolution of alternate modes of development in ascidians

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Sequential activation of apical and basolateral contractility drives ascidian endoderm invagination.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Neurons of the ascidian larval nervous system in Ciona intestinalis: I. Central nervous system

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Isolation and characterization of a protochordate histocompatibility locus

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Regulatory blueprint for a chordate embryo.

2 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV966

Neurons of the ascidian larval nervous system in Ciona intestinalis: II. Peripheral nervous system.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV966

Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. III. Up to the tissue restricted stage

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV966

Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV966

A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV966

Germ cell mutations of the ascidian Ciona intestinalis with TALE nucleases.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

A combinatorial code of maternal GATA, Ets and beta-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Action of morpholinos in Ciona embryos.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4702943

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

27 November 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV966

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26420834

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A cDNA resource from the basal chordateCiona intestinalis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26420834

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Neural tissue in ascidian embryos is induced by FGF9/16/20, acting via a combination of maternal GATA and Ets transcription factors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26420834

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKV966

1 reference

journals/nar/BrozovicMDDMSPL16

1454834

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_ugjpglni7zdgrhebtkka25nx2e

28 January 2021

Fatcat ID

0 references

1454834

1 reference

1 reference

1 reference