Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data (Q34253269)

31 July 2017

Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data (English)

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31 July 2017

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4

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15 November 2018

John S Mattick

3

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author name string

Fabian A Buske

series ordinal

1

1 reference

PubMed ID

22550012

31 July 2017

Denis C Bauer

series ordinal

2

1 reference

31 July 2017

1 May 2012

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31 July 2017

1 reference

31 July 2017

22

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31 July 2017

1372-1381

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31 July 2017

7

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A dynamic programming algorithm for identification of triplex-forming sequences

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Potential in vivo roles of nucleic acid triple-helices

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

In vitro selection of oligonucleotides that bind double-stranded DNA in the presence of triplex-stabilizing agents

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

A global view of genomic information--moving beyond the gene and the master regulator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Circular dichroism and conformational polymorphism of DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Triplex formation on DNA targets: how to choose the oligonucleotide

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

The triple helix: 50 years later, the outcome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Targeting DNA with triplex-forming oligonucleotides to modify gene sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Triplex-mediated gene modification

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

SeqAn an efficient, generic C++ library for sequence analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Extensive sugar modification improves triple helix forming oligonucleotide activity in vitro but reduces activity in vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

High-affinity triplex-forming oligonucleotide target sequences in mammalian genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

A web-based search engine for triplex-forming oligonucleotide target sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Evidence for a triplex DNA conformation at the bcl-2 major breakpoint region of the t(14;18) translocation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Triplex-forming oligonucleotide target sequences in the human genome.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Effect of divalent cations and cytosine protonation on thermodynamic properties of intermolecular DNA double and triple helices

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Chemical modification of the third strand: differential effects on purine and pyrimidine triple helix formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

A greedy algorithm for aligning DNA sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Triple helix formation by (G,A)-containing oligonucleotides: asymmetric sequence effect

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

DNA triple helix formation at oligopurine sites containing multiple contiguous pyrimidines

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Guanine-rich oligonucleotides targeted to a critical R . Y site located in the Ki-ras promoter. The effect of competing self-structures on triplex formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Electrostatic effects in DNA triple helices.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Characterization of the DNA triplex formed by d(TGGGTGGGTGGTTGGGTGGG) and a critical R.Y sequence located in the promoter of the murine Ki-ras proto-oncogene.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Stability of triple helices containing RNA and DNA strands: experimental and molecular modeling studies.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Poly(pyrimidine) . poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Specificity and stringency in DNA triplex formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Sequence specificity in triple-helix formation: experimental and theoretical studies of the effect of mismatches on triplex stability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Bias of purine stretches in sequenced chromosomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396377

Stability and Properties of Double and Triple Helices: Dramatic Effects of RNA or DNA Backbone Composition

28 October 2018

1 reference

12 December 2020

Investigations of oligodeoxyinosine for triple helix formation

1 reference

12 December 2020

Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes

1 reference

12 December 2020

A-tract DNA disfavours triplex formation

1 reference

12 December 2020

Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences

1 reference

12 December 2020

Identifiers

DOI

10.1101/GR.130237.111

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

22550012