(Q30374731)

27 June 2018

review article

1 reference

title

Annotation and Classification of CRISPR-Cas Systems. (English)

1 reference

27 June 2018

0 references

2

Eugene V Koonin

1 reference

27 June 2018

1

Kira S Makarova

1 reference

PMC publication ID

5901762

27 June 2018

language of work or name

English

0 references

publication date

1 January 2015

1 reference

27 June 2018

Methods in Molecular Biology

published in

1 reference

27 June 2018

volume

1311

1 reference

27 June 2018

page(s)

47-75

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27 June 2018

Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.

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4 July 2018

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4 July 2018

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Classification and evolution of type II CRISPR-Cas systems

4 July 2018

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Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

4 July 2018

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Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

4 July 2018

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Fitting CRISPR-associated Cas3 into the helicase family tree

4 July 2018

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Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

4 July 2018

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The basic building blocks and evolution of CRISPR-CAS systems

4 July 2018

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Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity

4 July 2018

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Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3

4 July 2018

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Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases

4 July 2018

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Structure of an RNA silencing complex of the CRISPR-Cas immune system.

4 July 2018

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Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus

4 July 2018

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Structure of the CRISPR interference complex CSM reveals key similarities with cascade

4 July 2018

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Differential translation tunes uneven production of operon-encoded proteins

4 July 2018

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Structure of the archaeal Cascade subunit Csa5

4 July 2018

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CRISPR interference: a structural perspective

4 July 2018

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TALEN or Cas9 - rapid, efficient and specific choices for genome modifications

4 July 2018

1 reference

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Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

4 July 2018

1 reference

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Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis

4 July 2018

1 reference

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Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2.

4 July 2018

1 reference

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Two CRISPR-Cas systems in Methanosarcina mazei strain Gö1 display common processing features despite belonging to different types I and III.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Adaptation and modification of three CRISPR loci in two closely related cyanobacteria

4 July 2018

1 reference

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Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing

4 July 2018

1 reference

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CRISPR-Cas systems and RNA-guided interference

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial 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=5901762

Comparative genomics of defense systems in archaea and bacteria

4 July 2018

1 reference

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CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Structure of the Cmr2-Cmr3 Subcomplex of the Cmr RNA Silencing Complex

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Comparative analysis ofCas6b processing and CRISPR RNA stability.

4 July 2018

1 reference

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In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas System

4 July 2018

1 reference

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Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

The CRISPR associated protein Cas4 Is a 5' to 3' DNA exonuclease with an iron-sulfur cluster

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas 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=5901762

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity 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=5901762

Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR-mediated bacterial immunity

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

4 July 2018

1 reference

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Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System

4 July 2018

1 reference

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Crystal Structure of Streptococcus pyogenes Csn2 Reveals Calcium-Dependent Conformational Changes in Its Tertiary and Quaternary Structure

4 July 2018

1 reference

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Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex

4 July 2018

1 reference

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Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

4 July 2018

1 reference

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RNA-guided genetic silencing systems in bacteria and archaea

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity

4 July 2018

1 reference

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CRISPR: new horizons in phage resistance and strain identification

4 July 2018

1 reference

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Nature and intensity of selection pressure on CRISPR-associated genes

4 July 2018

1 reference

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Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference

4 July 2018

1 reference

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Structures of the RNA-guided surveillance complex from a bacterial immune system

4 July 2018

1 reference

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Defense islands in bacterial and archaeal genomes and prediction of novel defense systems

4 July 2018

1 reference

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The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli

4 July 2018

1 reference

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Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3)

4 July 2018

1 reference

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Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

4 July 2018

1 reference

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Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

4 July 2018

1 reference

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A reverse transcriptase-related protein mediates phage resistance and polymerizes untemplated DNA in vitro.

4 July 2018

1 reference

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Evolution and classification of the CRISPR-Cas systems

4 July 2018

1 reference

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RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

4 July 2018

1 reference

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Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

4 July 2018

1 reference

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CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

4 July 2018

1 reference

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RNA in defense: CRISPRs protect prokaryotes against mobile genetic 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=5901762

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas 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=5901762

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair

4 July 2018

1 reference

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The Structure of the CRISPR-Associated Protein Csa3 Provides Insight into the Regulation of the CRISPR/Cas System

4 July 2018

1 reference

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The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

4 July 2018

1 reference

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Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease

4 July 2018

1 reference

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Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains

4 July 2018

1 reference

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RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex

4 July 2018

1 reference

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CRISPR-based adaptive and heritable immunity in prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

SSO1450--a CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and 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=5901762

Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

CRISPR interference limits horizontal gene transfer in staphylococci by targeting 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=5901762

CDD: specific functional annotation with the Conserved Domain Database

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Small CRISPR RNAs guide antiviral defense in prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic 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=5901762

CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic 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=5901762

The HHpred interactive server for protein homology detection and structure prediction

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Identification of genes that are associated with DNA repeats in prokaryotes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

GGDEF domain is homologous to adenylyl cyclase

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Gapped BLAST and PSI-BLAST: a new generation of protein database search 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=5901762

Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Structure, function and evolution of the XPD family of iron-sulfur-containing 5'-->3' DNA helicases

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

BLAST QuickStart: example-driven web-based BLAST tutorial

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

Transposon Tn7 protein TnsD binding to Escherichia coli attTn7 DNA and its eukaryotic orthologs

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5901762

10.1007/978-1-4939-2687-9_4

26 November 2018

Identifiers

DOI

1 reference

27 June 2018

PMC publication ID

5901762

1 reference

27 June 2018

PubMed publication ID

25981466

1 reference

27 June 2018