(Q33566263)

28 July 2017

title

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration (English)

1 reference

28 July 2017

2

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28 July 2017

Mario Fasold

1

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28 July 2017

Hans Binder

series ordinal

3

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28 July 2017

publication date

27 April 2010

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28 July 2017

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28 July 2017

volume

11

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28 July 2017

page(s)

207

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Mismatch and G-stack modulated probe signals on SNP microarrays

28 July 2017

cites work

1 reference

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Calibration of microarray gene-expression data

21 June 2018

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Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization

21 June 2018

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Inverse Langmuir method for oligonucleotide microarray analysis

21 June 2018

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Thermodynamic scaling behavior in genechips

21 June 2018

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G-spots cause incorrect expression measurement in Affymetrix microarrays

21 June 2018

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Position dependent mismatch discrimination on DNA microarrays - experiments and model

21 June 2018

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Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.

21 June 2018

1 reference

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Background correction using dinucleotide affinities improves the performance of GCRMA.

21 June 2018

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Design and analysis of mismatch probes for long oligonucleotide microarrays

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

"Hook"-calibration of GeneChip-microarrays: theory and algorithm

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

"Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures

21 June 2018

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Modeling background intensity in DNA microarrays.

21 June 2018

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The T7-primer is a source of experimental bias and introduces variability between microarray platforms

21 June 2018

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An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.

21 June 2018

1 reference

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Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed

21 June 2018

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

21 June 2018

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Explaining differences in saturation levels for Affymetrix GeneChip arrays

21 June 2018

1 reference

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Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays

21 June 2018

1 reference

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Improving comparability between microarray probe signals by thermodynamic intensity correction

21 June 2018

1 reference

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Free energy of DNA duplex formation on short oligonucleotide microarrays

21 June 2018

1 reference

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Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

21 June 2018

1 reference

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Physical-chemistry-based analysis of affymetrix microarray 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=2884167

Non-linear analysis of GeneChip 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=2884167

Model-based analysis of tiling-arrays for ChIP-chip.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

Relationship between gene expression and observed intensities in DNA microarrays--a modeling study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

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=2884167

Specific and nonspecific hybridization of oligonucleotide probes on microarrays

21 June 2018

1 reference

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Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

21 June 2018

1 reference

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The thermodynamics of DNA structural motifs

21 June 2018

1 reference

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

21 June 2018

1 reference

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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=2884167

Solving the riddle of the bright mismatches: labeling and effective binding in 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=2884167

Thermodynamic calculations and statistical correlations for oligo-probes design.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

Modeling of DNA microarray data by using physical properties of hybridization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

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=2884167

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

Large-scale transcriptional activity in chromosomes 21 and 22

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

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=2884167

Stability of a surface-bound oligonucleotide duplex inferred from molecular dynamics: a study of single nucleotide defects using 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=2884167

Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

A benchmark for Affymetrix GeneChip expression measures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

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=2884167

Optimal design of oligonucleotide microarrays for measurement of DNA copy-number

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2884167

Statistical analysis of adsorption models for oligonucleotide microarrays

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20423484

12 December 2020

inferred from PubMed ID database lookup

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20423484

12 December 2020

inferred from PubMed ID database lookup

Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20423484

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1471-2105-11-207

1 reference

journals/bmcbi/FasoldSB10

28 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1036906198

0 references

Fatcat ID

release_qynqyj72efgr7n7wmd6vyvrhda

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/qynqyj72efgr7n7wmd6vyvrhda

24 November 2022

mapped directly with Wikidata item

PMC publication ID

2884167

1 reference

28 July 2017

1 reference