(Q38114847)

English

Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information

scientific article published on 15 June 2013

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scholarly article

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Europe PubMed Central

PubMed publication ID

29 August 2017

Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information (English)

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

author name string

Georgi Muskhelishvili

1

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

Andrew Travers

2

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

publication date

15 June 2013

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

Cellular and Molecular Life Sciences

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

70

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

23

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

4555-4567

1 reference

Europe PubMed Central

PubMed publication ID

29 August 2017

https://scigraph.springernature.com/pub.10.1007/s00018-013-1394-1

0 references

Computational approaches to study transcriptional regulation

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Transcriptional regulation shapes the organization of genes on bacterial chromosomes

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Eukaryotic gene regulation in three dimensions and its impact on genome evolution

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Dissecting the logical types of network control in gene expression profiles

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Analog regulation of metabolic demand

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Chromosome architecture is a key element of bacterial cellular organization

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

General organisational principles of the transcriptional regulation system: a tree or a circle?

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

H-NS: a universal regulator for a dynamic genome

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA supercoiling - a global transcriptional regulator for enterobacterial growth?

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA information: from digital code to analogue structure

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA microloops and microdomains: a general mechanism for transcription activation by torsional transmission

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA stress and strain, in silico, in vitro and in vivo

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on tyrT promoter function

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Promoter protection by a transcription factor acting as a local topological homeostat

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA thermodynamics shape chromosome organization and topology

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA structure, nucleosome placement and chromatin remodelling: a perspective

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Dissociation and re-association of RNA polymerase with DNA during osmotic stress response in Escherichia coli

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Superhelical torsion in cellular DNA responds directly to environmental and genetic factors

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA supercoiling depends on the phosphorylation potential in Escherichia coli.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit?

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Chromatin places metabolism center stage.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Mammalian circadian clock and metabolism - the epigenetic link

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

SIRT1, metabolism and cancer

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

A genomewide oscillation in transcription gates DNA replication and cell cycle

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Multiscale analysis of biological systems.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Macrodomain organization of the Escherichia coli chromosome.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Topological domain structure of the Escherichia coli chromosome

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Organization of supercoil domains and their reorganization by transcription

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Genomic organization of evolutionarily correlated genes in bacteria: limits and strategies

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Isolation and characterization of spermidine nucleoids from Escherichia coli

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Structural and functional map of a bacterial nucleoid

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Differential regulation of Escherichia coli topoisomerase I by Fis.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

DNA supercoiling by gyrase is linked to nucleoid compaction.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Lethal overproduction of the Escherichia coli nucleoid protein H-NS: ultramicroscopic and molecular autopsy

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Spatial patterns of transcriptional activity in the chromosome of Escherichia coli

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Dynamic state of DNA topology is essential for genome condensation in bacteria.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Nucleoid remodeling by an altered HU protein: reorganization of the transcription program

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Bacterial chromatin

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Cell signaling can direct either binary or graded transcriptional responses

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

MAPK-regulated transcription: a continuously variable gene switch?

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Gene essentiality determines chromosome organisation in bacteria

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Spatial organization of the flow of genetic information in bacteria

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Gene location and DNA density determine transcription factor distributions in Escherichia coli

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Circadian rhythms of superhelical status of DNA in cyanobacteria

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Oscillations in supercoiling drive circadian gene expression in cyanobacteria

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Toward a hyperstructure taxonomy

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Chromosome organization by a nucleoid-associated protein in live bacteria

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

Pathogenicity islands and the evolution of microbes

1 reference

https://api.crossref.org/works/10.1007%2FS00018-013-1394-1

21 January 2018

H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modulation of tyrT promoter activity by template supercoiling in vivo

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA supercoiling contributes to disconnect sigmaS accumulation from sigmaS-dependent transcription in Escherichia coli

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Escherichia coli FIS protein is not required for the activation of tyrT transcription on entry into exponential growth

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleoid restructuring in stationary-state bacteria

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Bacterial DNA supercoiling and [ATP]/[ADP]. Changes associated with a transition to anaerobic growth

1 reference

https://pubmed.ncbi.nlm.nih.gov/23771629

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1007/S00018-013-1394-1

1 reference

https://api.fatcat.wiki/v0/release/x2m34gcidjeg7mpljkq4yunqa4

30 July 2022

based on heuristic

mapped directly with Wikidata item

release_x2m34gcidjeg7mpljkq4yunqa4

1 reference

https://api.fatcat.wiki/v0/release/x2m34gcidjeg7mpljkq4yunqa4

30 July 2022

based on heuristic

mapped directly with Wikidata item

PubMed publication ID

1 reference

https://api.fatcat.wiki/v0/release/x2m34gcidjeg7mpljkq4yunqa4

30 July 2022

based on heuristic

mapped directly with Wikidata item

ResearchGate publication ID

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