LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life (Q28584519)

inferred from title

author

Robert Daniel Kortschak

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

Atma M Ivancevic

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

Genome Biology and Evolution

1 June 2020

language of work or name

English

0 references

publication date

14 December 2016

0 references

published in

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

volume

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

issue

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

page(s)

3301-3322

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil

1 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Reviving the dead: history and reactivation of an extinct l1

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis)

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Turning gold into 'junk': transposable elements utilize central proteins of cellular networks

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Widespread horizontal transfer of retrotransposons

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Database resources of the National Center for Biotechnology Information

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

HMMER web server: interactive sequence similarity searching

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

LINE-1 retrotransposition activity in human genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

FastTree 2--approximately maximum-likelihood trees for large alignments

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

The Pfam protein families database

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

The impact of retrotransposons on human genome evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Databases of homologous gene families for comparative genomics

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Initial sequence and comparative analysis of the cat genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Molecular and genomic data identify the closest living relative of primates

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Evolutionary history of LINE-1 in the major clades of placental mammals

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

A higher-level MRP supertree of placental mammals

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

L1Base: from functional annotation to prediction of active LINE-1 elements

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

MUSCLE: multiple sequence alignment with high accuracy and high throughput

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Hot L1s account for the bulk of retrotransposition in the human population

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Initial sequencing and comparative analysis of the mouse genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

The human genome browser at UCSC

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Resolution of the early placental mammal radiation using Bayesian phylogenetics

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Initial sequencing and analysis of the human genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

The end of the LINE?: lack of recent L1 activity in a group of South American rodents

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Molecular evolution of two lineages of L1 (LINE-1) retrotransposons in the california mouse, Peromyscus californicus

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Basic local alignment search tool

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Search and clustering orders of magnitude faster than BLAST

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

BEDTools: a flexible suite of utilities for comparing genomic features

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Repbase Update, a database of eukaryotic repetitive elements

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

LINE-mediated retrotransposition of marked Alu sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Human LINE retrotransposons generate processed pseudogenes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

High frequency retrotransposition in cultured mammalian cells

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Primate-specific ORF0 contributes to retrotransposon-mediated diversity

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Modular organization and reticulate evolution of the ORF1 of Jockey superfamily transposable elements

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

APE-type non-LTR retrotransposons of multicellular organisms encode virus-like 2A oligopeptide sequences, which mediate translational recoding during protein synthesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Retroelements in human disease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Self-interaction, nucleic acid binding, and nucleic acid chaperone activities are unexpectedly retained in the unique ORF1p of zebrafish LINE.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Ultra-fast sequence clustering from similarity networks with SiLiX

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Loss of LINE-1 activity in the megabats

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

The genomic distribution of L1 elements: the role of insertion bias and natural selection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Mobile elements and mammalian genome evolution.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Large differences between LINE-1 amplification rates in the human and chimpanzee lineages

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Human L1 element target-primed reverse transcription in vitro

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

A physical map of the mouse genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Many human L1 elements are capable of retrotransposition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Computer simulation of transposable element evolution: random template and strict master 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=5203782

Revisiting the evolution of mouse LINE-1 in the genomic era.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

A non-LTR retroelement extinction in Spermophilus tridecemlineatus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Teleost fish genomes contain a diverse array of L1 retrotransposon lineages that exhibit a low copy number and high rate of turnover.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Different rates of LINE-1 (L1) retrotransposon amplification and evolution in New World monkeys.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Zepp, a LINE-like retrotransposon accumulated in the Chlorella telomeric region

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5203782

Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

BNR - a LINE family from Beta vulgaris - contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

The esterase and PHD domains in CR1-like non-LTR retrotransposons

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

Novel mutations and genotype-phenotype relationships in 107 families with Fukuyama-type congenital muscular dystrophy (FCMD).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW243

L1Tc non-LTR retrotransposons from Trypanosoma cruzi contain a functional viral-like self-cleaving 2A sequence in frame with the active proteins they encode

21 January 2018

1 reference

12 December 2020

Mobile elements and disease

1 reference

12 December 2020

Phylogenomic analysis of the L1 retrotransposons in Deuterostomia

1 reference

12 December 2020

L1 (LINE-1) retrotransposon evolution and amplification in recent human history

1 reference

12 December 2020

The origins of eukaryotic gene structure

1 reference

12 December 2020

Genetics. L1 retrotransposons shape the mammalian genome

1 reference

12 December 2020

Identifiers

DOI

10.1093/GBE/EVW243

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

PubMed publication ID

27702814

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27702814%20AND%20SRC:MED&resulttype=core&format=json