Evaluating oligonucleotide properties for DNA microarray probe design (Q33922353)

30 July 2017

title

Evaluating oligonucleotide properties for DNA microarray probe design (English)

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30 July 2017

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7

Carsten Müller-Tidow

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Xiao-Qin Xia

object named as

Xiao-Qin Xia

1

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Michael McClelland

object named as

Michael McClelland

8

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author name string

Zhenyu Jia

2

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30 July 2017

Steffen Porwollik

3

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30 July 2017

Fred Long

4

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30 July 2017

Claudia Hoemme

5

1 reference

30 July 2017

Kai Ye

6

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30 July 2017

Yipeng Wang

9

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30 July 2017

language of work or name

English

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publication date

17 March 2010

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30 July 2017

published in

Nucleic Acids Research

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30 July 2017

volume

38

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30 July 2017

issue

11

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30 July 2017

page(s)

e121

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Bayesian mixture model analysis for detecting differentially expressed genes

30 July 2017

cites work

1 reference

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Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip

5 July 2018

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DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison

5 July 2018

1 reference

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An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes

5 July 2018

1 reference

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Free energy of DNA duplex formation on short oligonucleotide microarrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Comment on "Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays".

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

5 July 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

5 July 2018

1 reference

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"Promoter array" studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription factor binding in human cancer cells

5 July 2018

1 reference

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Survey of differentially methylated promoters in prostate cancer cell lines

5 July 2018

1 reference

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Use of microarrays with different probe sizes for monitoring gene expression.

5 July 2018

1 reference

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Growing applications and advancements in microarray technology and analysis tools

5 July 2018

1 reference

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OligoWiz 2.0--integrating sequence feature annotation into the design of microarray probes.

5 July 2018

1 reference

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YODA: selecting signature oligonucleotides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stress

5 July 2018

1 reference

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AutoDimer: a screening tool for primer-dimer and hairpin structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Probe selection for high-density oligonucleotide arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Thermodynamic calculations and statistical correlations for oligo-probes design.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Mfold web server for nucleic acid folding and hybridization prediction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Modeling of DNA microarray data by using physical properties of hybridization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

A model of molecular interactions on short oligonucleotide microarrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Optimization of oligonucleotide-based DNA microarrays.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

DNA chips: state-of-the art.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Probe selection for DNA microarrays using OligoWiz.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887943

Oligodb--interactive design of oligo DNA for transcription profiling of human genes

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20236987

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

ROSO: optimizing oligonucleotide probes for microarrays

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20236987

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

OligoArray: genome-scale oligonucleotide design for microarrays

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20236987

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKQ039

1 reference

30 July 2017

1 reference

30 July 2017

1 reference