(Q21145325)

16 August 2022

Zasha Weinberg

Zasha

Weinberg

1 reference

16 August 2022

Pascal Chartrand

Pascal

Chartrand

1 reference

16 August 2022

Gerardo Ferbeyre

Gerardo

Ferbeyre

1 reference

16 August 2022

Ronald R Breaker

Ronald R

Breaker

1 reference

16 August 2022

Adam Roth

Adam

Roth

1 reference

21573207

16 August 2022

Olivia Popescu

series ordinal

author given names

Olivia

author last names

Popescu

1 reference

21573207

PLOS Computational Biology

16 August 2022

language of work or name

English

0 references

publication date

May 2011

0 references

published in

0 references

volume

0 references

issue

0 references

page(s)

e1002031

0 references

Creative Commons Attribution 4.0 International

start time

5 May 2011

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

ImageQuant

object named as

ImageQuant

2 references

Europe PubMed Central

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3088659/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Structure-based search reveals hammerhead ribozymes in the human microbiome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

From alpaca to zebrafish: hammerhead ribozymes wherever you look

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Ubiquitous presence of the hammerhead ribozyme motif along the tree of life

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Intronic hammerhead ribozymes are ultraconserved in the human genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Widespread occurrence of self-cleaving ribozymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Infernal 1.0: inference of RNA alignments

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Rfam: updates to the RNA families database

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Functional hammerhead ribozymes naturally encoded in the genome of Arabidopsis thaliana

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Geometric nomenclature and classification of RNA base pairs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Structural diversity of self-cleaving ribozymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Schistosome satellite DNA encodes active hammerhead ribozymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

In vitro evolution suggests multiple origins for the hammerhead ribozyme

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Catalytic strategies of self-cleaving ribozymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Autolytic processing of dimeric plant virus satellite RNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Tertiary contacts distant from the active site prime a ribozyme for catalysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Control of gene expression by a natural metabolite-responsive ribozyme

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Self-cleaving transcripts of satellite DNA from the newt

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae)

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Structure and function of regulatory RNA elements: ribozymes that regulate gene expression

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

12 September 2017

Defining the mobilome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

In-line probing analysis of riboswitches

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Hammerhead redux: does the new structure fit the old biochemical data?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

RECK expression in osteosarcoma: correlation with matrix metalloproteinases activation and tumor invasiveness

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

12 September 2017

Synthetic RNA circuits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

CMfinder--a covariance model based RNA motif finding algorithm

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Sequence-based heuristics for faster annotation of non-coding RNA families.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Natural and engineered nucleic acids as tools to explore biology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

A guide to ions and RNA structure

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

In vitro selection of hammerhead ribozyme sequence variants

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

RNAMotif, an RNA secondary structure definition and search algorithm

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Numbering system for the hammerhead

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Sequence specificity of the hammerhead ribozyme revisited; the NHH rule

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Ecophysiology of Bacteriophage S5100 Infecting Halobacterium cutirubrum

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

HF1 and HF2: novel bacteriophages of halophilic archaea

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Sequence requirements of the hammerhead RNA self-cleavage reaction

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

A database search for hammerhead ribozyme motifs

19 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Solute concentrations within cells of halophilic and non-halophilic bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Extremely high mutation rate of a hammerhead viroid

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Halobacterium sodomense sp. nov., a Dead Sea Halobacterium with an Extremely High Magnesium Requirement

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Isolation and cultivation of Walsby's square archaeon

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Whole genome sequencing of a novel temperate bacteriophage of P. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

An RNA pattern matching program with enhanced performance and portability.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3088659

Self-cleaving viroid and newt RNAs may only be active as dimers

29 November 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002031

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/21573207

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

RNA-RNA and RNA-DNA ligation with the sTobRV(+) hammerhead ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/21573207

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1002031

1 reference

journals/ploscb/PerreaultWRPCFB11

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

21573207

1 reference