(Q49887022)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

title

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

Ning Jiang

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

author name string

Shujun Ou

series ordinal

1

1 reference

23 February 2018

http://europepmc.org/abstract/MED/29233850

Ning Jiang

series ordinal

2

1 reference

23 February 2018

http://europepmc.org/abstract/MED/29233850

language of work or name

English

0 references

publication date

12 December 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

volume

176

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

7 April 2020

page(s)

1410-1422

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29233850%20AND%20SRC:MED&resulttype=core&format=json

Improved maize reference genome with single-molecule technologies

7 April 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

MGEScan: a Galaxy-based system for identifying retrotransposons in genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The First Rule of Plant Transposable Element Silencing: Location, Location, Location.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

What makes up plant genomes: The vanishing line between transposable elements and genes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The pineapple genome and the evolution of CAM photosynthesis

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

A call for benchmarking transposable element annotation methods

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Transposable elements contribute to activation of maize genes in response to abiotic stress

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

GenomeTools: a comprehensive software library for efficient processing of structured genome annotations

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The Norway spruce genome sequence and conifer genome evolution

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Phytozome: a comparative platform for green plant genomics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The B73 Maize Genome: Complexity, Diversity, and Dynamics

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

DNA transposons and the evolution of eukaryotic genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

A unified classification system for eukaryotic transposable elements

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

De novo identification of LTR retrotransposons in eukaryotic genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

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

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Transposable elements and the evolution of eukaryotic genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

RetrOryza: a database of the rice LTR-retrotransposons

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The map-based sequence of the rice genome

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Rapid recent growth and divergence of rice nuclear genomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The diversity of LTR retrotransposons

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

LTR_STRUC: a novel search and identification program for LTR retrotransposons

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Repbase update: a database and an electronic journal of repetitive elements

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

26 August 2018

Plant retrotransposons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Isolation and characterization of copia-type retrotransposons in Arabidopsis thaliana

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Tandem repeats finder: a program to analyze DNA sequences

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

The paleontology of intergene retrotransposons of maize

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Nested retrotransposons in the intergenic regions of the maize genome

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Retrotransposons of rice involved in mutations induced by tissue culture

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5813529

Presidential address. Transposable elements, epigenetics, and genome evolution

26 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29233850