(Q34558005)

3 August 2017

title

Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics (English)

1 reference

3 August 2017

1 reference

11

0 references

Ludmil B. Alexandrov

2

0 references

William S Hlavacek

10

0 references

Alan R. Bishop

5

object named as

Alan R Bishop

1 reference

3 August 2017

9

Kim Ø Rasmussen

1 reference

3 August 2017

Elizabeth Hong-Geller

8

object named as

Elizabeth Hong-Geller

1 reference

3 August 2017

Kristy Nowak-Lovato

1

1 reference

3 August 2017

Afsheen Banisadr

3

1 reference

3 August 2017

Amy L Bauer

4

1 reference

3 August 2017

Anny Usheva

6

1 reference

3 August 2017

Fangping Mu

7

1 reference

3 August 2017

publication date

17 January 2013

1 reference

PLOS Computational Biology

3 August 2017

published in

1 reference

3 August 2017

volume

9

1 reference

3 August 2017

issue

1

1 reference

3 August 2017

page(s)

e1002881

1 reference

Creative Commons CC0 License

3 August 2017

copyright license

start time

17 January 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

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7 July 2018

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7 July 2018

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The role of DNA shape in protein-DNA recognition

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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A nonlinear dynamic model of DNA with a sequence-dependent stacking term

7 July 2018

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Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

7 July 2018

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Profiling the thermodynamic softness of adenoviral promoters

7 July 2018

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Gene regulation by transcription factors and microRNAs

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

7 July 2018

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DNA sequence and structural properties as predictors of human and mouse promoters

7 July 2018

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Functional characterization of the Escherichia coli Fis-DNA binding sequence

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome.

7 July 2018

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Extensive low-affinity transcriptional interactions in the yeast genome

7 July 2018

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Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Structure and evolution of transcriptional regulatory networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

DNA dynamically directs its own transcription initiation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Computational prediction of transcription-factor binding site locations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

DNA topology-mediated control of global gene expression in Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Genome organisation and chromatin structure in Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

The physics of DNA and the annotation of the Plasmodium falciparum genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

DNA binding sites: representation and discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Information analysis of Fis binding sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Clues and consequences of DNA bending in 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=3547798

Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Transcription factor access to chromatin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

VMD: visual molecular dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Steroid hormone receptors: interaction with deoxyribonucleic acid and transcription factors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II direct basal transcription on supercoiled template 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=3547798

M.HhaI binds tightly to substrates containing mismatches at the target base

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Sequence, regulation, and functions of fis in Salmonella typhimurium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Nature of the open state in long polynucleotide double helices: possibility of soliton excitations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Host protein requirements for in vitro site-specific DNA inversion.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Structure of an alternating-B DNA helix and its relationship to A-tract 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=3547798

Energetic coupling between DNA bending and base pair opening

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

DNA conformation and protein binding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

O6-methylguanine and A.C and G.T mismatches cause asymmetric structural defects in DNA that are affected by DNA sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Crystal and molecular structure of a DNA duplex containing the carcinogenic lesion O6-methylguanine

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

High-resolution structure of a mutagenic lesion in 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=3547798

The single-stranded DNA-binding protein of Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

The Protein Data Bank: a computer-based archival file for macromolecular structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547798

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

7 July 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

DNA bubble dynamics as a quantum Coulomb problem.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Genes and the physics of the DNA double-helix.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

High DNA melting temperature predicts transcription start site location in human and mouse

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

O6-ethylguanine carcinogenic lesions in DNA: an NMR study of O6etG.C pairing in dodecanucleotide duplexes.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Sequence sensitivity of breathing dynamics in heteropolymer DNA.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Breathing dynamics in heteropolymer DNA.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Equation of State Calculations by Fast Computing Machines

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Bubble nucleation and cooperativity in DNA melting

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Probing the microscopic flexibility of DNA from melting temperatures

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

A single mode of DNA base-pair opening drives imino proton exchange

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002881

Statistical mechanics of a nonlinear model for DNA denaturation

21 January 2018

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12 December 2020

The Fis protein: it's not just for DNA inversion anymore

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12 December 2020

Structural studies of the O6meG.C interaction in the d(C-G-C-G-A-A-T-T-C-O6meG-C-G) duplex

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12 December 2020

Phase transitions in one dimension and the helix-coil transition in polyamino acids

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12 December 2020

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations

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12 December 2020

Bubble statistics and dynamics in double-stranded DNA

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12 December 2020

Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings

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12 December 2020

Entropy-driven DNA denaturation

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12 December 2020

Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

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12 December 2020

Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats

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12 December 2020

Loop dynamics in DNA denaturation

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12 December 2020

10.1371/JOURNAL.PCBI.1002881

Identifiers

DOI

1 reference

journals/ploscb/Nowak-LovatoABBBUMHRHA13

3 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 August 2017

1 reference