Single-molecule stretching studies of RNA chaperones. (Q34775650)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21045548 AND SRC:MED&resulttype=core&format=json

15 January 2020

title

Single-molecule stretching studies of RNA chaperones (English)

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15 January 2020

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3

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15 January 2020

author name string

Hao Wu

series ordinal

1

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15 January 2020

Ioulia Rouzina

series ordinal

2

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15 January 2020

publication date

1 November 2010

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15 January 2020

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15 January 2020

volume

7

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15 January 2020

issue

6

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15 January 2020

page(s)

712-723

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DNA stretching as a probe for nucleic acid interactions: Reply to Comments on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya, Thayaparan Paramanathan, Micah J. McCauley, Mark C. Williams

15 January 2020

cites work

1 reference

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Visualizing the formation and collapse of DNA toroids

7 July 2018

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C-terminal domain modulates the nucleic acid chaperone activity of human T-cell leukemia virus type 1 nucleocapsid protein via an electrostatic mechanism

7 July 2018

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Peeling back the mystery of DNA overstretching.

7 July 2018

1 reference

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Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging

7 July 2018

1 reference

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The structure of DNA overstretched from the 5'5' ends differs from the structure of DNA overstretched from the 3'3' ends.

7 July 2018

1 reference

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Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA.

7 July 2018

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Characterization of the behavior of functional viral genomes during the early steps of human immunodeficiency virus type 1 infection.

7 July 2018

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HIV-1 nucleocapsid protein switches the pathway of transactivation response element RNA/DNA annealing from loop-loop "kissing" to "zipper".

7 July 2018

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Human T-cell lymphotropic virus type 1 nucleocapsid protein-induced structural changes in transactivation response DNA hairpin measured by single-molecule fluorescence resonance energy transfer

7 July 2018

1 reference

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A single amino acid substitution in ORF1 dramatically decreases L1 retrotransposition and provides insight into nucleic acid chaperone activity.

7 July 2018

1 reference

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Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA

7 July 2018

1 reference

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Retroviral nucleocapsid proteins display nonequivalent levels of nucleic acid chaperone activity

7 July 2018

1 reference

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Mutations in human immunodeficiency virus type 1 nucleocapsid protein zinc fingers cause premature reverse transcription

7 July 2018

1 reference

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Isolated HIV-1 core is active for reverse transcription.

7 July 2018

1 reference

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HIV-1 protease and reverse transcriptase control the architecture of their nucleocapsid partner

7 July 2018

1 reference

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HIV-1 DNA Flap formation promotes uncoating of the pre-integration complex at the nuclear pore

7 July 2018

1 reference

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Resistance of human T cell leukemia virus type 1 to APOBEC3G restriction is mediated by elements in nucleocapsid

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

In vitro synthesis of long DNA products in reactions with HIV-RT and nucleocapsid protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Single DNA molecule stretching measures the activity of chemicals that target the HIV-1 nucleocapsid protein.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Theory of electrostatically regulated binding of T4 gene 32 protein to single- and double-stranded DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Acceptor RNA cleavage profile supports an invasion mechanism for HIV-1 minus strand transfer

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Secondary structure and secondary structure dynamics of DNA hairpins complexed with HIV-1 NC protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site

7 July 2018

1 reference

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DNA condensation by the nucleocapsid protein of HIV-1: a mechanism ensuring DNA protection

7 July 2018

1 reference

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Zinc finger-dependent HIV-1 nucleocapsid protein-TAR RNA interactions

7 July 2018

1 reference

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Human immunodeficiency virus type 1 nucleocapsid zn(2 ) fingers are required for efficient reverse transcription, initial integration processes, and protection of newly synthesized viral DNA.

7 July 2018

1 reference

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Retroviral recombination: review of genetic analyses

7 July 2018

1 reference

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Visualization of the intracellular behavior of HIV in living cells

7 July 2018

1 reference

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Force spectroscopy of single DNA and RNA molecules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Specific zinc-finger architecture required for HIV-1 nucleocapsid protein's nucleic acid chaperone function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Salt dependence of the elasticity and overstretching transition of single DNA molecules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Thermodynamics of DNA interactions from single molecule stretching experiments.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Mechanisms of retroviral recombination

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Effect of pH on the overstretching transition of double-stranded DNA: evidence of force-induced DNA melting

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Simple simulations of DNA condensation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus- and plus-strand transfer

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Human immunodeficiency virus type 1 nucleocapsid protein can prevent self-priming of minus-strand strong stop DNA by promoting the annealing of short oligonucleotides to hairpin sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Stretching of single collapsed DNA molecules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Spermine-induced aggregation of DNA, nucleosome, and chromatin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

The age and evolution of non-LTR retrotransposable elements

7 July 2018

1 reference

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Strict conservation of the retroviral nucleocapsid protein zinc finger is strongly influenced by its role in viral infection processes: characterization of HIV-1 particles containing mutant nucleocapsid zinc-coordinating sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

DNA bending by small, mobile multivalent cations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

DNA condensation by multivalent cations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Ionic effects on the elasticity of single DNA molecules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

DNA mesophases induced by spermidine: structural properties and biological implications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

DNA complexes with polycations for the delivery of genetic material into cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Kinetics of renaturation of DNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Complementary recognition in condensed DNA: accelerated DNA renaturation.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Condensation of DNA by multivalent cations: Considerations on mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

DNA probes: applications of the principles of nucleic acid hybridization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

7 July 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Mechanically manipulating the DNA threading intercalation rate

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Biophysical characterization of DNA binding from single molecule force measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Effect of Mg(2 ) and Na( ) on the nucleic acid chaperone activity of HIV-1 nucleocapsid protein: implications for reverse transcription

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Elastic response of single DNA molecules exhibits a reentrant collapsing transition

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

HIV-1 nucleocapsid protein zinc finger structures induce tRNA(Lys,3) structural changes but are not critical for primer/template annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Kinetic regulation of single DNA molecule denaturation by T4 gene 32 protein structural domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Mechanical measurement of single-molecule binding rates: kinetics of DNA helix-destabilization by T4 gene 32 protein

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: single molecule force spectroscopy measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Modulation of T4 gene 32 protein DNA binding activity by the recombination mediator protein UvsY.

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Insights into the multiple roles of pausing in HIV-1 reverse transcriptase-promoted strand transfers

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Influence of human immunodeficiency virus nucleocapsid protein on synthesis and strand transfer by the reverse transcriptase in vitro

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Specific interactions between HIV-1 nucleocapsid protein and the TAR element

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

LINE-1 retrotransposition requires the nucleic acid chaperone activity of the ORF1 protein

21 January 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Rapid kinetics of protein-nucleic acid interaction is a major component of HIV-1 nucleocapsid protein's nucleic acid chaperone function

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Properties and growth mechanism of the ordered aggregation of a model RNA by the HIV-1 nucleocapsid protein: An electron microscopy investigation

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Ordered aggregation of ribonucleic acids by the human immunodeficiency virus type 1 nucleocapsid protein.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

The mechanism of human immunodeficiency virus reverse transcriptase-catalyzed strand transfer from internal regions of heteropolymeric RNA templates.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3073330

Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

26 October 2018

1 reference

https://api.crossref.org/works/10.4161/RNA.7.6.13776

Role of Tension and Twist in Single-Molecule DNA Condensation

21 January 2018

1 reference

12 December 2020

Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution

1 reference

12 December 2020

Condensation of DNA by multivalent cations: experimental studies of condensation kinetics

1 reference

12 December 2020

Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNA

1 reference

12 December 2020

Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching

1 reference

12 December 2020

Time study of DNA condensate morphology: implications regarding the nucleation, growth, and equilibrium populations of toroids and rods

1 reference

12 December 2020

Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination

1 reference

12 December 2020

Transmission electron microscopy reveals an optimal HIV-1 nucleocapsid aggregation with single-stranded nucleic acids and the mature HIV-1 nucleocapsid protein

1 reference

12 December 2020

Mechanistic studies of mini-TAR RNA/DNA annealing in the absence and presence of HIV-1 nucleocapsid protein

1 reference

12 December 2020

Kinetics of macroion coagulation induced by multivalent counterions

1 reference

12 December 2020

DNA condensed by protamine: a "short" or "long" polycation behavior

1 reference

12 December 2020

Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis

1 reference

12 December 2020

Retroviral recombination: what drives the switch?

1 reference

12 December 2020

Recombination during reverse transcription: an evaluation of the role of the nucleocapsid protein

1 reference

12 December 2020

Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication

1 reference

12 December 2020

Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium

1 reference

12 December 2020

Destabilization of the HIV-1 complementary sequence of TAR by the nucleocapsid protein through activation of conformational fluctuations

1 reference

12 December 2020

Alteration of nucleic acid structure and stability modulates the efficiency of minus-strand transfer mediated by the HIV-1 nucleocapsid protein

1 reference

12 December 2020

DNA aggregation induced by polyamines and cobalthexamine

1 reference

12 December 2020

Identifiers

DOI

10.4161/RNA.7.6.13776

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21045548 AND SRC:MED&resulttype=core&format=json

15 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21045548 AND SRC:MED&resulttype=core&format=json

15 January 2020

PubMed publication ID

21045548

1 reference