(Q33815667)

29 July 2017

title

Considering transposable element diversification in de novo annotation approaches (English)

1 reference

29 July 2017

3

Catherine Feuillet

0 references

Hadi Quesneville

series ordinal

4

object named as

Hadi Quesneville

0 references

Timothée Flutre

object named as

Timothée Flutre

series ordinal

1

0 references

Elodie Duprat

object named as

Elodie Duprat

series ordinal

2

0 references

language of work or name

English

0 references

publication date

31 January 2011

1 reference

29 July 2017

1 reference

29 July 2017

volume

6

1 reference

29 July 2017

issue

1

1 reference

29 July 2017

page(s)

e16526

1 reference

Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

31 January 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Genome sequence of the pea aphid Acyrthosiphon pisum

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

The B73 Maize Genome: Complexity, Diversity, and Dynamics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Transposable elements in gene regulation and in the evolution of vertebrate genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

A transposon-induced epigenetic change leads to sex determination in melon

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

A physical map of the 1-gigabase bread wheat chromosome 3B.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Identification of repeat structure in large genomes using repeat probability clouds

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Recent developments in the MAFFT multiple sequence alignment program

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Transposable elements and the evolution of regulatory networks

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Empirical comparison of ab initio repeat finding programs

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Next-generation sequencing transforms today's biology

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Evolution of genes and genomes on the Drosophila phylogeny

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

A unified classification system for eukaryotic transposable elements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Discovering and detecting transposable elements in genome sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Recent evolutions of multiple sequence alignment algorithms

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Genome sequence of Aedes aegypti, a major arbovirus vector

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Transposable elements and the epigenetic regulation of the genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

P elements and MITE relatives in the whole genome sequence of Anopheles gambiae

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Efficient q-gram filters for finding all epsilon-matches over a given length

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Chromosome evolution in eukaryotes: a multi-kingdom perspective

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Combined evidence annotation of transposable elements in genome sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Repbase Update, a database of eukaryotic repetitive elements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

An algorithm for progressive multiple alignment of sequences with insertions

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

De novo identification of repeat families in large genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

PILER: identification and classification of genomic repeats

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

The ecology of the genome - mobile DNA elements and their hosts

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

The origins of genome complexity

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Controlling elements and the gene

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Structural dynamics of eukaryotic chromosome evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

mreps: Efficient and flexible detection of tandem repeats in DNA

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Automated de novo identification of repeat sequence families in sequenced genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

BLAT—The BLAST-Like Alignment Tool

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

It takes two transposons to tango: transposable-element-mediated chromosomal rearrangements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

The genome sequence of Drosophila melanogaster

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Tandem repeats finder: a program to analyze DNA sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

CENSOR--a program for identification and elimination of repetitive elements from DNA sequences.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Selfish DNA: the ultimate parasite

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Eukaryotic transposable elements and genome evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Basic local alignment search tool

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE.

4 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016526

Transposition of hAT elements links transposable elements and V(D)J recombination.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016526

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016526

Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016526

A role for RNAi in the selective correction of DNA methylation defects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016526

TEclass--a tool for automated classification of unknown eukaryotic transposable elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016526

On global sequence alignment.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031573

Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21304975

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Biological classification: toward a synthesis of opposing methodologies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21304975

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0016526

1 reference

release_6v7yleiqpbgj5gm2cnjf5go4ia

29 July 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/6v7yleiqpbgj5gm2cnjf5go4ia

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

3031573

1 reference

29 July 2017

1 reference