The cavefish genome reveals candidate genes for eye loss (Q34446560)

2 August 2017

The cavefish genome reveals candidate genes for eye loss (English)

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2 August 2017

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Jean-Nicolas Volff

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Patrick Minx

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2 August 2017

Daniel Murphy

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Masato Yoshizawa

object named as

Masato Yoshizawa

20

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Clifford Tabin

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object named as

Cliff Tabin

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21

Wesley C Warren

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Steve M J Searle

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Suzanne E McGaugh

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2 August 2017

Joshua B Gross

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Maryline Blin

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Richard Borowsky

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2 August 2017

Domitille Chalopin

6

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2 August 2017

William R Jeffery

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Alex Keene

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Li Ma

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Kelly E O'Quin

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Sylvie Rétaux

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Nicolas Rohner

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2 August 2017

Bethany A Stahl

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2 August 2017

language of work or name

English

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publication date

20 October 2014

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2 August 2017

Nature Communications

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2 August 2017

5

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2 August 2017

5307

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Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

2 August 2017

start time

20 October 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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exact match

https://scigraph.springernature.com/pub.10.1038/ncomms6307

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cites work

Astyanax transgenesis and husbandry: how cavefish enters the laboratory

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Causal analysis approaches in Ingenuity Pathway Analysis

6 July 2018

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Tbx2a is required for specification of endodermal pouches during development of the pharyngeal arches

6 July 2018

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Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus

6 July 2018

1 reference

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Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms

6 July 2018

1 reference

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Bcl6a function is required during optic cup formation to prevent p53-dependent apoptosis and colobomata

6 July 2018

1 reference

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

6 July 2018

1 reference

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Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

The zebrafish reference genome sequence and its relationship to the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Albinism in phylogenetically and geographically distinct populations of Astyanax cavefish arises through the same loss-of-function Oca2 allele

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Quantitative genetic analysis of retinal degeneration in the blind cavefish Astyanax mexicanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Dact2 represses PITX2 transcriptional activation and cell proliferation through Wnt/beta-catenin signaling during odontogenesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Evolution of an adaptive behavior and its sensory receptors promotes eye regression in blind cavefish.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Taste buds as peripheral chemosensory processors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Differential analysis of gene regulation at transcript resolution with RNA-seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Transcription factors involved in lens development from the preplacodal ectoderm

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Downregulation of apoptosis-inducing factor in Harlequin mice induces progressive and severe optic atrophy which is durably prevented by AAV2-AIF1 gene therapy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Adaptation in the age of ecological genomics: insights from parallelism and convergence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Loss of Tbx2 delays optic vesicle invagination leading to small optic cups.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

The Sequence Alignment/Map format and SAMtools

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the cavefish Astyanax mexicanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

A unified classification system for eukaryotic transposable elements

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Regressive evolution in the Mexican cave tetra, Astyanax mexicanus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Tbx2b is essential for neuronal differentiation along the dorsal/ventral axis of the zebrafish retina

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Shisa promotes head formation through the inhibition of receptor protein maturation for the caudalizing factors, Wnt and FGF.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Oculofaciocardiodental and Lenz microphthalmia syndromes result from distinct classes of mutations in BCOR.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Loss of eyes in zebrafish caused by mutation of chokh/rx3.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

A greedy algorithm for aligning DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Prox1 function is crucial for mouse lens-fibre elongation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Role of the Dlx homeobox genes in proximodistal patterning of the branchial arches: mutations of Dlx-1, Dlx-2, and Dlx-1 and -2 alter morphogenesis of proximal skeletal and soft tissue structures derived from the first and second arches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

Next generation phylogeography of cave and surface Astyanax mexicanus

6 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Multi-trait evolution in a cave fish, Astyanax mexicanus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Evolutionary shift from fighting to foraging in blind cavefish through changes in the serotonin network

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Evolutionary convergence on sleep loss in cavefish populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Hedgehog signalling controls eye degeneration in blind cavefish.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Restoring sight in blind cavefish.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Developmental mechanisms for retinal degeneration in the blind cavefish Astyanax mexicanus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Lens gene expression analysis reveals downregulation of the anti-apoptotic chaperone alphaA-crystallin during cavefish eye degeneration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Zebrafish pitx3 is necessary for normal lens and retinal development

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Modulation of zebrafish pitx3 expression in the primordia of the pituitary, lens, olfactory epithelium and cranial ganglia by hedgehog and nodal signaling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Olfactomedin-2 mediates development of the anterior central nervous system and head structures in zebrafish

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Developmental expression of Shisa-2 in Xenopus laevis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Prox 1 in eye degeneration and sensory organ compensation during development and evolution of the cavefish Astyanax.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Induction of functional photoreceptor phenotype by exogenous Crx expression in mouse retinal stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Zebrafish cone-rod (crx) homeobox gene promotes retinogenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Expression of tryptophan hydroxylase in developing mouse taste papillae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

The function of wall-following behaviors in the Mexican blind cavefish and a sighted relative, the Mexican tetra (Astyanax).

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Molecular cytogenetics of blind mexican tetra and comments on the karyotypic characteristics of genus Astyanax (Teleostei, Characidae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Early and late changes in Pax6 expression accompany eye degeneration during cavefish development

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS6307

Medaka eyeless is the key factor linking retinal determination and eye growth.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4218959

27 October 2018

Identifiers

DOI

10.1038/NCOMMS6307

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Dimensions Publication ID

2 August 2017

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2 August 2017

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