(Q21092408)

15 August 2022

11

Karsten Zengler

Karsten

Zengler

1 reference

15 August 2022

8

Joshua N Adkins

Joshua N

Adkins

1 reference

15 August 2022

7

Richard D Smith

Richard D

Smith

1 reference

15 August 2022

3

Vasiliy A

Portnoy

Vasiliy A Portnoy

1 reference

Alexandra C Schrimpe-Rutledge

15 August 2022

6

Alexandra C

Schrimpe-Rutledge

Alexandra C Schrimpe-Rutledge

1 reference

15 August 2022

Haythem Latif

1

Haythem

Latif

1 reference

15 August 2022

Yekaterina Tarasova

4

Yekaterina

Tarasova

1 reference

15 August 2022

Harish Nagarajan

5

Harish

Nagarajan

1 reference

15 August 2022

Dae-Hee Lee

9

Dae-Hee

Lee

1 reference

15 August 2022

Yu Qiu

10

Yu

Qiu

1 reference

Creative Commons Attribution 4.0 International

15 August 2022

language of work or name

English

0 references

publication date

April 2013

0 references

published in

PLOS Genetics

0 references

volume

9

0 references

issue

4

0 references

page(s)

e1003485

0 references

copyright license

start time

25 April 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date

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EcoCyc: a comprehensive database of Escherichia coli biology

19 March 2017

1 reference

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Rfam: Wikipedia, clans and the "decimal" release

19 March 2017

1 reference

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

19 March 2017

1 reference

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On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

19 March 2017

1 reference

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Infernal 1.0: inference of RNA alignments

19 March 2017

1 reference

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

19 March 2017

1 reference

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Regulatory RNAs in bacteria

19 March 2017

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19 March 2017

The Vienna RNA websuite

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Velvet: algorithms for de novo short read assembly using de Bruijn graphs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The RAST Server: rapid annotations using subsystems technology

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The regulatory content of intergenic DNA shapes genome architecture

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Genome Streamlining in a Cosmopolitan Oceanic Bacterium

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The transcriptional landscape of Chlamydia pneumoniae

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

WebLogo: A Sequence Logo Generator

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The primary transcriptome of the major human pathogen Helicobacter pylori

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Proteome organization in a genome-reduced bacterium

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

An antisense RNA inhibits translation by competing with standby ribosomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature 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=3636130

Systems biology: a brief overview

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Reconstruction of biochemical networks in microorganisms

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

In silico method for modelling metabolism and gene product expression at genome scale

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Comparative omics-driven genome annotation refinement: application across Yersiniae

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Quantification of mRNA and protein and integration with protein turnover in a bacterium

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Ligands of thermophilic ABC transporters encoded in a newly sequenced genomic region of Thermotoga maritima MSB8 screened by differential scanning fluorimetry

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Parallel evolution of transcriptome architecture during genome reorganization

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

A high resolution map of a cyanobacterial transcriptome.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The challenges of integrating multi-omic data sets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Comprehensive comparative analysis of strand-specific RNA sequencing methods

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Structural and operational complexity of the Geobacter sulfurreducens genome.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Searching for mesophilic Thermotogales bacteria: "mesotogas" in the wild.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

The transcription unit architecture of the Escherichia coli genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Prevalence of transcription promoters within archaeal operons and coding sequences.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Hydrothermal vents and the origin of life

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

UNAFold: software for nucleic acid folding and hybridization

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Correlation between structure and temperature in prokaryotic metabolic networks

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Annotation of bacterial and archaeal genomes: improving accuracy and consistency

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Correlation between binding rate constants and individual information of E. coli Fis binding sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Anatomy of Escherichia coli sigma70 promoters.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Detecting transcriptionally active regions using genomic tiling arrays

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

What are DNA sequence motifs?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Growth Physiology of the Hyperthermophilic Archaeon Thermococcus litoralis: Development of a Sulfur-Free Defined Medium, Characterization of an Exopolysaccharide, and Evidence of Biofilm Formation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Towards multidimensional genome annotation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Physical constraints and functional characteristics of transcription factor-DNA interaction.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

How do thermophilic proteins deal with heat?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Review: Protein function at thermal extremes: balancing stability and flexibility

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli 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=3636130

Release LTPs104 of the All-Species Living Tree

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Evidence for existence of "mesotogas," members of the order Thermotogales adapted to low-temperature environments

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Universal patterns of purifying selection at noncoding positions in bacteria

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Recombination in Thermotoga: implications for species concepts and biogeography

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Theory of molecular machines. II. Energy dissipation from molecular machines.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003485

Information content of individual genetic sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003485

Transcriptional analysis of dynamic heat-shock response by the hyperthermophilic bacterium Thermotoga maritima

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003485

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003485

Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90°C

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003485

Transcriptome Complexity in a Genome-Reduced Bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003485

The in silico prediction of promoters in bacterial genomes.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Were the original eubacteria thermophiles?

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3636130

Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations

29 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/23637642

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

1 reference

https://pubmed.ncbi.nlm.nih.gov/23637642

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1003485

0 references

PMC publication ID

3636130

0 references