Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays. (Q33302865)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17939865%20AND%20SRC:MED&resulttype=core&format=json

8 January 2020

title

Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays (English)

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8 January 2020

2

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8 January 2020

Chikara Furusawa

3

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8 January 2020

author name string

Shingo Suzuki

1

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8 January 2020

Akiko Kashiwagi

4

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8 January 2020

Tetsuya Yomo

5

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8 January 2020

language of work or name

English

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publication date

16 October 2007

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8 January 2020

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8 January 2020

volume

8

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8 January 2020

page(s)

373

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Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays

8 January 2020

cites work

1 reference

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Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted

21 June 2018

1 reference

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On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes

21 June 2018

1 reference

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Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Sequence dependence of cross-hybridization on short oligo microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Specific and nonspecific hybridization of oligonucleotide probes on microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Applications of DNA tiling arrays for whole-genome analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Microarray results improve significantly as hybridization approaches equilibrium.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Dextran sulfate provides a quantitative and quick microarray hybridization reaction

21 June 2018

1 reference

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Sensitivity, specificity, and the hybridization isotherms of DNA chips.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Probe selection for high-density oligonucleotide arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

A model of molecular interactions on short oligonucleotide microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Summaries of Affymetrix GeneChip probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Gene expression analysis using oligonucleotide arrays produced by maskless photolithography

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Metal ion-catalyzed nucleic acid alkylation and fragmentation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Optimization of oligonucleotide-based DNA microarrays.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Sequence variation in genes and genomic DNA: methods for large-scale analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Gene expression microarrays and the integration of biological knowledge

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Reproducible and inexpensive probe preparation for oligonucleotide arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Resequencing and mutational analysis using oligonucleotide microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

High density synthetic oligonucleotide arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex

21 June 2018

1 reference

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Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.

21 June 2018

1 reference

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Evaluating single-base-pair discriminating capability of planar oligonucleotide microchips using a non-equilibrium dissociation approach.

31 October 2018

1 reference

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Large-scale genotyping of complex DNA.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

DNA hybridization to mismatched templates: a chip study.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2180184

Deoxynucleotide-polymerizing enzymes of calf thymus gland. II. Properties of the terminal deoxynucleotidyltransferase

31 October 2018

1 reference

12 December 2020

Biochemical properties of purified human terminal deoxynucleotidyltransferase

1 reference

12 December 2020

Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA

1 reference

12 December 2020

Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2164-8-373

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17939865%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

8 January 2020

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-8-373

9 September 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17939865%20AND%20SRC:MED&resulttype=core&format=json

8 January 2020

PubMed publication ID

17939865

1 reference