(Q33742959)

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A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

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24 February 2020

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration (English)

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24 February 2020

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24 February 2020

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24 February 2020

Konstantinos Sousounis

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24 February 2020

Richard Reinhardt

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24 February 2020

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24 February 2020

author name string

Marc Bruckskotten

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24 February 2020

Christian S Michel

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24 February 2020

Ettore Lignelli

6

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24 February 2020

Sabrina Höffner

8

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24 February 2020

Marcus Krüger

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24 February 2020

Panagiotis A Tsonis

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24 February 2020

Thilo Borchardt

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24 February 2020

publication date

20 February 2013

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24 February 2020

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24 February 2020

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24 February 2020

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24 February 2020

R16

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24 February 2020

describes a project that uses

object named as

MIRA

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

https://scigraph.springernature.com/pub.10.1186/gb-2013-14-2-r16

0 references

A microarray analysis of gene expression patterns during early phases of newt lens regeneration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Spiked-in pulsed in vivo labeling identifies a new member of the CCN family in regenerating newt hearts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

On marathons and Sprints: an integrated quantitative proteomics and transcriptomics analysis of differences between slow and fast muscle fibers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

The Pfam protein families database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

KEGG for integration and interpretation of large-scale molecular data sets

1 reference

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21 June 2018

Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

SignalP 4.0: discriminating signal peptides from transmembrane regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

The cellular basis for animal regeneration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Regenerative capacity in newts is not altered by repeated regeneration and ageing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Andromeda: a peptide search engine integrated into the MaxQuant environment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Efficient regeneration by activation of neurogenesis in homeostatically quiescent regions of the adult vertebrate brain.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Reactome: a database of reactions, pathways and biological processes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Using the Velvet de novo assembler for short-read sequencing technologies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Optimization of de novo transcriptome assembly from next-generation sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Mitosis in adult newt ventricle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

PROSITE, a protein domain database for functional characterization and annotation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Evolution of animal regeneration: re-emergence of a field

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

From fish to amphibians to mammals: in search of novel strategies to optimize cardiac regeneration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

The GOA database in 2009--an integrated Gene Ontology Annotation resource

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

An overview of the wcd EST clustering tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

On dorsal/ventral-specific genes in the iris during lens regeneration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Bridging the regeneration gap: genetic insights from diverse animal models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Appendage regeneration in adult vertebrates and implications for regenerative medicine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

NONCODE: an integrated knowledge database of non-coding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

WebLogo: A Sequence Logo Generator

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Regeneration of the lens in amphibians

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

A greedy algorithm for aligning DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

CAP3: A DNA sequence assembly program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Newt myotubes reenter the cell cycle by phosphorylation of the retinoblastoma protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Finding flexible patterns in unaligned protein sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Stimulation of lens regeneration from the newt dorsal iris when implanted into the blastema of the regenerating limb

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4054090

21 June 2018

Dopamine controls neurogenesis in the adult salamander midbrain in homeostasis and during regeneration of dopamine neurons.

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R16

21 January 2018

Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R16

21 January 2018

Evidence for the local evolution of mechanisms underlying limb regeneration in salamanders.

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R16

21 January 2018

Cardiovascular regeneration in non-mammalian model systems: what are the differences between newts and man?

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Lens regeneration from iris implants into the blastema of a regenerating newt limb

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stimulation of forelimb regeneration in the newt, Triturus viridescens, by a sensory nerve supply isolated from the central nervous system

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The histology of inhibition of limb regeneration in the newt,Triturus, by actinomycin D

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Repair and reorganization of minced cardiac muscle in the adult newt (Notophthalmus viridescens)

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effects of thyroxine on limb regeneration in the newt, Triturus viridescens

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Denervation effects on newt limb regeneration: DNA, RNA, and protein synthesis

1 reference

https://pubmed.ncbi.nlm.nih.gov/23425577

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/GB-2013-14-2-R16

1 reference

Europe PubMed Central

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24 February 2020

1 reference

Europe PubMed Central

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24 February 2020

1 reference

Europe PubMed Central

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24 February 2020

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