TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence. (Q41875083)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

title

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence (English)

1 reference

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25 February 2020

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

Connor H Fortin

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

Katharina V Schulze

series ordinal

1 reference

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25 February 2020

publication date

25 September 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json

Source Code for Biology and Medicine

25 February 2020

published in

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25 February 2020

volume

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25 February 2020

page(s)

1 reference

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Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae

25 February 2020

cites work

1 reference

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5 June 2018

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5 June 2018

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5 June 2018

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5 June 2018

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5 June 2018

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A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites.

5 June 2018

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Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions.

5 June 2018

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Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales

5 June 2018

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The ABCs of molecular dynamics simulations on B-DNA, circa 2012.

5 June 2018

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A brief review of molecular information theory.

5 June 2018

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Impact of Alu repeats on the evolution of human p53 binding sites

5 June 2018

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Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes

5 June 2018

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Origins of specificity in protein-DNA recognition.

5 June 2018

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Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro

5 June 2018

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Intrinsic flexibility of B-DNA: the experimental TRX scale

5 June 2018

1 reference

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The role of DNA shape in protein-DNA recognition

5 June 2018

1 reference

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Local DNA topography correlates with functional noncoding regions of the human genome

5 June 2018

1 reference

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A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning

5 June 2018

1 reference

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The pattern and evolution of yeast promoter bendability

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

Molecular Configuration in Sodium Thymonucleate

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids

5 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

5 June 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

Sequencing and comparison of yeast species to identify genes and regulatory elements

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

DNA helix: the importance of being GC-rich

5 June 2018

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Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

5 June 2018

1 reference

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DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

5 June 2018

1 reference

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Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study

5 June 2018

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DNA flexibility variation may dominate DNase I cleavage

5 June 2018

1 reference

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Sequence logos: a new way to display consensus sequences

5 June 2018

1 reference

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A transcriptionally active DNA-binding site for human p53 protein complexes

5 June 2018

1 reference

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Indirect readout of DNA sequence by p22 repressor: roles of DNA and protein functional groups in modulating DNA conformation

5 June 2018

1 reference

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The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

DNA sequence and structure: direct and indirect recognition in protein-DNA binding

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4583169

A Mathematical Theory of Communication

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13029-015-0040-8

Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26413153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26413153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26413153

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13029-015-0040-8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json

journals/scfbm/FortinSB15

25 February 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json

25 February 2020

PubMed publication ID

26413153

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26413153%20AND%20SRC:MED&resulttype=core&format=json