(Q34768582)

4 August 2017

title

Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes (English)

1 reference

4 August 2017

1

A Maxwell Burroughs

0 references

Lakshminarayan M. Iyer

series ordinal

2

object named as

Lakshminarayan M Iyer

1 reference

4 August 2017

3

L Aravind

0 references

A Maxwell Burroughs

series ordinal

1

object named as

A Maxwell Burroughs

1 reference

4 August 2017

publication date

8 June 2013

1 reference

4 August 2017

1 reference

4 August 2017

volume

8

1 reference

4 August 2017

page(s)

13

1 reference

https://scigraph.springernature.com/pub.10.1186/1745-6150-8-13

4 August 2017

exact match

0 references

cites work

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7 July 2018

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R loops: from transcription byproducts to threats to genome stability

7 July 2018

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The N domain of Argonaute drives duplex unwinding during RISC assembly

7 July 2018

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Mechanistic insights into type III restriction enzymes

7 July 2018

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HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

7 July 2018

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Staphylococcus aureus DinG, a helicase that has evolved into a nuclease

7 July 2018

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Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

DNA elimination in ciliates: transposon domestication and genome surveillance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

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

7 July 2018

1 reference

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Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute 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=3702460

Function and regulation of the Mediator complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

A parsimonious model for gene regulation by miRNAs.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives

7 July 2018

1 reference

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Dicer-independent, Ago2-mediated microRNA biogenesis in vertebrates

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

MicroRNA targeting in mammalian genomes: genes and mechanisms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

RNA-directed epigenetic regulation of DNA rearrangements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Hidden Markov model speed heuristic and iterative HMM search procedure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute 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=3702460

Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Dali server: conservation mapping in 3D

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

SF1 and SF2 helicases: family matters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

A genome-wide RNA interference screen identifies a differential role of the mediator CDK8 module subunits for GATA/ RUNX-activated transcription in Drosophila.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Dicer-independent primal RNAs trigger RNAi and heterochromatin formation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The MED12-MED13 module of Mediator regulates the timing of embryo patterning in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The Pfam protein families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Evolution, biogenesis and function of promoter-associated RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Divergent transcription: a new feature of active promoters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator 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=3702460

Enhancement of the Seed-Target Recognition Step in RNA Silencing by a PIWI/MID Domain 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=3702460

RNA-based viral immunity initiated by the Dicer family of host immune receptors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Redox control of the DNA damage-inducible protein DinG helicase activity via its iron-sulfur cluster

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Structure of the guide-strand-containing argonaute silencing complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Mediator links epigenetic silencing of neuronal gene expression with x-linked mental retardation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The Jpred 3 secondary structure prediction server

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Pygopus activates Wingless target gene transcription through the mediator complex subunits Med12 and Med13.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Transcription and RNA interference in the formation of heterochromatin.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Structure and mechanism of helicases and nucleic acid translocases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The DNA repair helicases XPD and FancJ have essential iron-sulfur domains

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

MUSTANG: a multiple structural alignment algorithm.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on 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=3702460

Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Cleavage of the siRNA passenger strand during RISC assembly in human 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=3702460

Slicer function of Drosophila Argonautes and its involvement in RISC formation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Dynamic regulation of pol II transcription by the mammalian Mediator complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The mammalian Mediator complex and its role in transcriptional regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The many faces of the helix-turn-helix domain: transcription regulation and beyond

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi 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=3702460

Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Crystal structure of Argonaute and its implications for RISC slicer activity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

miRNAs on the move: miRNA biogenesis and the RNAi machinery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

MUSCLE: multiple sequence alignment with high accuracy and high throughput

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

TRAP230/ARC240 and TRAP240/ARC250 Mediator subunits are functionally conserved through evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Complex restriction enzymes: NTP-driven molecular motors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

TFIIH is negatively regulated by cdk8-containing mediator complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Guilt by association: contextual information in genome analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

The rde-1 gene, RNA interference, and transposon silencing in C. elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Toprim--a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR 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=3702460

Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Isolation of quelling-defective (qde) mutants impaired in posttranscriptional transgene-induced gene silencing in Neurospora crassa

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Biology of DNA restriction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Cyclin-dependent protein kinase and cyclin homologs SSN3 and SSN8 contribute to transcriptional control in yeast

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3702460

Argonaute proteins couple chromatin silencing to alternative splicing.

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-8-13

Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-8-13

The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-8-13

The DinG protein from Escherichia coli is a structure-specific helicase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-8-13

Tiny RNAs associated with transcription start sites in animals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-8-13

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-8-13

21 January 2018

Identifiers

DOI

10.1186/1745-6150-8-13

1 reference

Dimensions Publication ID

4 August 2017

0 references

1 reference

4 August 2017

1 reference