(Q21184134)

Dimensions Publication ID

Dimensions

17 August 2022

Jeffrey E Barrick

1

Jeffrey E

Barrick

1 reference

Dimensions Publication ID

Dimensions

1049360945

https://scigraph.springernature.com/pub.10.1186/gb-2007-8-11-r239

17 August 2022

language of work or name

English

0 references

publication date

2007

0 references

published in

Genome Biology

0 references

volume

8

0 references

page(s)

R239

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issue

11

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exact match

0 references

cites work

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Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor

19 March 2017

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Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure

19 March 2017

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Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria

19 March 2017

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19 March 2017

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19 March 2017

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6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

19 March 2017

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19 March 2017

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CDD: a Conserved Domain Database for protein classification

19 March 2017

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Rfam: annotating non-coding RNAs in complete genomes

19 March 2017

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Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics

19 March 2017

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Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria

19 March 2017

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New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

19 March 2017

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Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

19 March 2017

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An mRNA structure in bacteria that controls gene expression by binding lysine

19 March 2017

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The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes

19 March 2017

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19 March 2017

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Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element

19 March 2017

1 reference

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Metabolite-binding RNA domains are present in the genes of eukaryotes

19 March 2017

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The Bioperl toolkit: Perl modules for the life sciences

19 March 2017

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Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation

19 March 2017

1 reference

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Adenosylcobalamin inhibits ribosome binding to btuB RNA

19 March 2017

1 reference

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RNA sequence analysis using covariance models

19 March 2017

1 reference

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The kink-turn: a new RNA secondary structure motif

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Environmental genome shotgun sequencing of the Sargasso Sea

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Measuring covariation in RNA alignments: physical realism improves information measures

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structure of the S-adenosylmethionine riboswitch regulatory mRNA element

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Evidence for preorganization of the glmS ribozyme ligand binding pocket

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS 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=2258182

The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

A glycine-dependent riboswitch that uses cooperative binding to control gene 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=2258182

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=2258182

Adenine riboswitches and gene activation by disruption of a transcription terminator

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5'-UTR

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

An mRNA structure that controls gene expression by binding S-adenosylmethionine

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene 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=2258182

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Genetic control by a metabolite binding mRNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Comparative metagenomics of microbial communities

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Community structure and metabolism through reconstruction of microbial genomes from the environment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Regulation of bacterial gene expression by riboswitches

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Gene regulation by riboswitches

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Control of alternative RNA splicing and gene expression by eukaryotic riboswitches

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Folding of the adenine riboswitch

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

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=2258182

RNase P cleaves transient structures in some 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=2258182

Riboswitches as versatile gene control elements

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Microbial community genomics in the ocean

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Metabolic monitoring by bacterial mRNAs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Riboswitches: the oldest mechanism for the regulation of 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=2258182

Stealth regulation: biological circuits with small RNA switches

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

The non-Watson-Crick base pairs and their associated isostericity matrices

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Conserved economics of transcription termination in eubacteria

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

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=2258182

The mechanism of intrinsic transcription termination.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Expression of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Inferring consensus structure from nucleic acid sequences.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Cobalamin (vitamin B12) repression of the Cob operon in Salmonella typhimurium requires sequences within the leader and the first translated open reading frame

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Tandem riboswitch architectures exhibit complex gene control functions.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Topology of three-way junctions in folded RNAs

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Ligand requirements for glmS ribozyme self-cleavage

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

The kinetics of ligand binding by an adenine-sensing riboswitch

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

One, two, infinity: genomes filled with aptamers.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Volume changes in protein evolution.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2258182

Transcription attenuation: a highly conserved regulatory strategy used by bacteria

29 November 2018

1 reference

12 December 2020

The lonepair triloop: a new motif in RNA structure

1 reference

12 December 2020

Predicting U-turns in ribosomal RNA with comparative sequence analysis

1 reference

12 December 2020

Mechanism of intrinsic transcription termination and antitermination

1 reference

12 December 2020

10.1186/GB-2007-8-11-R239

Identifiers

DOI

1 reference

Dimensions Publication ID

4122199

1049360945

0 references

4122199

1 reference

1 reference

1 reference